Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. aiegot,Rpoutv rnfrain rncitm,Cl morphology Cell Transcriptome, transformation, maturation Reproductive for growth, basis tative theoretical thus in a and conchospores provide Keywords: filaments, of results release sporangial of These and of promotion filaments cells. growth extensive sporangial bipartite vegetative of the from promoted release Meanwhile, levels conchospore light inhibited high filaments. the responses under sporangial caused adaptive accumulation metabolism, free-living that energy phosphatidylinositol indicated of and analysis transformation Transcriptome endocytosis autophagy, morphological form. mainly hollow changes, struc- typical environmental autophagosome-like the of to rarely caused degradation and the vacuoles that morphology in showed cell observation tures hollow Ultrastructural the light cells. retained high bipartite light filaments by formed and stimulated sporangial density when fragments/mL), culture and (5,000–10,000 with fragments/mL) densities correlated (50–1,000 cells), closely density (bipartite all low (40–100 were form at that levels cells reproductive formed found bipartite We cells to from Bipartite cells) understood. conchospores intensity. (hollow poorly of form release are growth the filaments vegetative and sporangial from of change release morphological conchospore the and maturation of of nisms cycle life the In Abstract in filaments density sporangial culture free-living and light of by changes transcriptome and Ultrastructural for basis text theoretical Main a provide results in of These conchospores growth of vegetative cells. release promoted bipartite and levels from filaments light release sporangial high conchospore of under inhibited maturation mainly accumulation thus changes, energy and environmental of filaments, sporangial to promotion free-living sporangial extensive responses of transformation the adaptive vacuoles morphological Meanwhile, that in the indicated caused filaments. structures metabolism, analysis autophagosome-like phosphatidylinositol Transcriptome of and degradation endocytosis form. fragments/mL) autophagy, the rarely hollow (50–1,000 that and typical morphology showed density the cell observation low hollow caused Ultrastructural the at retained all cells. filaments were formed bipartite sporangial cells cells fragments/mL), formed bipartite (5,000–10,000 (40–100 Bipartite densities from levels high conchospores light At intensity. of high intensities. light release by and the stimulated and density when vegetative cells), and culture from (bipartite change with morphological form the correlated reproductive that to closely found We cells) understood. (hollow poorly form are growth filaments sporangial of release conchospore and of cycle life the In Abstract 2020 28, April 1 He Bangxiang sporangial in free-living filaments of changes transcriptome and Ultrastructural nttt fOenlg,CieeAaeyo Sciences of Academy Chinese Oceanology, of Institute ihlgt utr est,Evrnetlaatto,Ntin iiain uohg,Vege- Autophagy, limitation, Nutrient adaptation, Environmental density, Culture light, High μ o htn m photons mol yoi yezoensis Pyropia 1 ijnXie Xiujun , yoi yezoensis Pyropia yoi yezoensis Pyropia -2 prnilfiaet onc ocoei n hlu,bttemcaim fmaturation of mechanisms the but thallus, and conchocelis connect filaments sporangial , 1 s -1 n unc Wang Guangce and , ,btcnhsoerlaewsihbtda uhlgtitniis thigh At intensities. light such at inhibited was release conchospore but ), prnilfiaet onc ocoei n hlu,bttemecha- the but thallus, and conchocelis connect filaments sporangial , μ o htn m photons mol ffce ylgtadcluedensity culture and light by affected 1 .yezoensis P. .yezoensis P. -2 1 s -1 ,btcnhsoerlaewsihbtda uhlight such at inhibited was release conchospore but ), n te eae species. related other and n te eae species. related other and yoi yezoensis Pyropia affected Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. rsraino relvn prnilfilaments sporangial free-living of Preservation under filaments Methods sporangial and of Materials seeding development of the method free-living of the understanding to findings application in-depth . our for believe the and We conditions morphological increasing explored. ob- environmental light the were in different through and filaments transcriptome, helpful Further, sporangial the density be free-living filaments. of culture of will analysis sporangial of expression and free-living gene effects (TEM) and of the microscope characteristics electron release regarding transmission conchospore phenomena by and interesting servation has maturation some development observed on filament we intensity sporangial study, behind this mechanism In molecular the & Yang, However, studied. mainly Li, 2004). been environment, 2006; rarely He, Carrier, Yarish, culture & & & the He Dickson, Yang 1980; Waaland, by 1987; (Chen, 2015; affected L´opez-Vivas, density Yarish, Riosmena-Rodr´ıguez, Pacheco-Ru´ız, culture 2011; significantly & and in He, are photoperiod, generation directly light, release sporophyte to temperature, conchospore on sporophytes including ability of studies and the growth physiological vegetative have growth of Many vegetative ability cells vegetative the The conchospore bipartite released. maintain compact—massive filaments. to special not also sporangial and these when and in released paired maturity that when are of gametophytes indicated appeared— into sign which filaments develop cells the Observation cells, sporangial is bipartite round formation of of cell release. short, number propagation Bipartite large are conchospore follow. a which would to when of release related consistently filaments, features of sporangial directly typical difficultly shell-cultured are the the in filaments is that problem revealed filaments. sporangial There main has sporangial generation, The or but 2004). conchocelis sporophyte 2003). period, He, free-living Wu, shell-culture In be of & & long can Yang release (He the (He filaments, conchospore omit used 1996; costs and and sporangial widely Zheng, maturation conchocelis labor not of & controlling free-living still consisting large using Sun is seed stage, and 1980; approach to conchocelis consumption this made (Chen, the efforts shell way shell-culture some that huge free-living been present, shown have a requires At been in and has of propagated months), collection system. It vegetatively (6–7 seedling free-living development 2006). artificial time a the Yarish, large-scale the control long in & in to of a than used easier maturation takes relatively system method and is method main shell-culture growth it the this, a the remain of in nature, systems Because In release sea. conchospore the die. daytime in and would during free-living drought conchocelis with as the compared such ment which conditions, stressful in in many light stage under conchocelis high survive and to able 2013). tide divisions is al., low cell thallus et two the Yoji first because 2011; or tion, al., of first et stage (Blouin the conchocelis again during The thallus meiosis (diploid) haploid conchospores undergo a release would into then develop would Conchospores filaments and sporangial being conditions. (sporophyte, matured conchosporangium, into the suitable called conchocelis develop and studies under cycle and conchocelis) some micro shells of life (in stage a to filaments the late attach sporangial form the in would into would developed carpospores stage 1949, then The haploid) a which In sporophyte). conchocelis, was (gametophyte, (zygote, 2019). shells, thallus carpospores Wang, in through macroscopic & diploid) grew the Lu, which nature, Huan, “conchocelis”, He, algae In the (Ma, value that the annual economic found of The significant 1949) 2017). with (Drew, Kim, associated Drew & China, Park, Hwang, in Yarish, trend (Kim, 2011). Korea Brawley, and of & Japan, yield Xu, China, Grossman, including countries Brodie, many (Blouin, changes environmental to yezoensis Pyropia Introduction Porphyra Pyropia/Porphyra eu.Teefe,tecmlt iehsoyof history life complete the Thereafter, genus. saptnilmdlmrn pce nteitria oe a togadaptability strong a has zone, intertidal the in species marine model potential a as , .yezoensis P. .yezoensis P. a xedd1000tn nrcn er n t rdcinsosa upward an shows production its and years recent in tons 110,000 exceeded has l cu naselsbtae hc ol rvd eaieysal environ- stable relatively a provide could which substrate, shell a on occur all smr estv oevrnetlcagsta aeoht genera- gametophyte than changes environmental to sensitive more is 2 Pyropia/Porphyra .yezoensis P. .yezoensis P. a rdal elucidated. gradually was .yezoensis P. 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The experiment standard Each was conchospores. data period. released of culture which error 15-day fragments filaments the a filament and those over sporangial triplicate days of in individual 3 number performed of every the was number experiment, performed counted the was total then filaments perform 100 the and conchospore-released and to counted 80, medium well first 60, mL each we 40, 1 in release, 20, with to 10, conchospore medium plate were of PES which 48-well rate the used, a to were Using intensities added light was conchospores. observed six mg/L) of was (400 release release kanamycin conchospore the fragments/mL, in which 100 promote cultured period. reached in were culture density wells 15-day filaments culture of a When sporangial number over The the days and above. 3 antibiotics every described counted without as was system medium (˜70–150 cooling PES filament daily mL sporangial a one 1 only contained added we well density, Each low very a at release μ conchospore explore groups to all order and In moisture weekly much filaments changed as sporangial was by after conical medium release measured mL The Conchospore and 250 paper. collected in dust-free triplicate. were mg/L) measured in sterilized they (400 was analyzed using after kanamycin weight were absorbed fresh with period was The medium culture fragments/mL. possible PES 4-week 1,300 used, as mL the approximately were over was 200 intensities All density week in light filament every culture. cultured the Three 4-week were that intensities. in they so light week flasks, and the every 80 mg for system 20 and except analyzed cooling at 40, above we daily 10, as intensities, the were light same different which under the under filaments were filaments conditions sporangial sporangial other of of weight changes growth fresh the the explore to order culture In of filaments days sporangial 15 of over measurement days weight triplicate. 3 Fresh every in repeated repeated 10 (typical was was under count cells experiment fields The 30 the bipartite Japan). first field and Tokyo, with growth the (Nikon, visual in fragments of compact) microscope random filament experiments inverted and the sporangial paired initial an by round, the of short, calculated (Suppl. in number were was filaments features densities the cells cell filament counting sporangial bipartite involved the linear of of 100 which estimate a weight proportion to 50, method, created The fresh we equation 10, experiments. method, and linear 5, transcriptome this this densities and on 1, used filament Based (0.5, and medium. original between 1) densities culture calculated relationship Fig. mL fragment then this 1 the filament used and with of different finally, plate fragments prediction of and 48-well the filament a through gradient suspension, diluted in of rpm the a then fragments/mL) 12,000 number in We create 100 of the fragments to speed re-suspended. original counted suspension a the and and at fragment of China) multiple times density Beijing, 30–40 appropriate the Ltd., about an calculated cut to Co. point suspension Biotech then 70 and fragment (Tiangen a tube homogenizer through Eppendorf tissue 100 collected mL or a were and 1.5 80 filaments 60, a cells) 40, into sporangial a bipartite 20, put with moderate 10, (light) of densities, to 18 formation to culture adjusted (dark) was the different intensity 21 is light from experiments, system, which light cooling μ of In daily a characteristic photoperiod. set (light:dark) typical we 10:14 filaments, (a sporangial maturation of release explore conchospore the to and densities order weeks fragment In two filament every of setting replaced months. and was three conditions medium every Experimental The culture the streptomycin. off sporangial and cut of ampicillin were filaments mg/L clone 100 (more single long-term with a preserved medium 23 were selected in filaments number months) directly sporangial large 6 a we These than obtained filaments. filaments, eventually sporangial culture, sporangial vegetatively-propagated amplification step-by-step of free-living through and pure conchocelis from obtain filament to order In )t ahwl na4-elpaeudrdffrn ih neste 1,4,ad80 and 40, (10, intensities light different under plate 48-well a in well each to m) m photons mol -2 s -1 ° ,50 C, hog ieetdgeso clso sn ht rnigppr nodrt create to order In paper. printing white using occlusion of degrees different through μ μ o htn m photons mol o htn m photons mol -2 -2 s -1 s -1 raine(ih:ak=01) sn E Poaoi 1968) (Provasoli, PES using =10:14), (light:dark irradiance h nta rs egto prnilfiaet a set was filaments sporangial of weight fresh initial The . 3 μ o htn m photons mol × 0mgicto through magnification 10 μ -2 o htn m photons mol μ s -1 elsrie and strainer cell m ocluaethe calculate To . -2 s -1 × ). Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. ieetal-xrse eeanalysis. Orthologous gene euKaryotic Differentially-expressed of Swiss-Prot. Clusters and Pfam, (KOG), (GO), databases: proteins Ontology En- following Gene Kyoto of the (KEGG), (Nt), Groups selected Genomes on sequences was was and nucleotide based alignment non-redundant Genes gene annotated Sample NCBI of was each (Nr), cyclopedia function calculated. of sequences Gene were protein transcript unigenes non-redundant 2011). longest NCBI Dewey, and the & The transcripts (Grab- (Li Trinity of transcriptome. 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Data may be preliminary. sfrcnhsoerlae tadniyo rgetm,ams l igesoaga lmnswould filaments sporangial single all almost fragment/mL, 1 (10 in of intensity conchospores density light some 80 low a of under at release conchospores release, random release conchospore the of for release 10–20 exception conchospore As under no the density. fragments/mL virtually with low was 50 there densities, at with observation, culture group cells of the different days bipartite 15 under at whole groups of groups the the existence over in in addition, earlier and In disappeared formation and formation. 40 formed cell of both ([?] period cells intensity From bipartite light peak fragments/mL). level, high intensity (5,000–10,000 the light density was the culture to high days According under 6–9 formed cells ( time-line, bipartite formation ana- the no of was cases intensities rate light some high and in a densities which while different in under 1A), filaments sporangial (Fig. by lyzed cells filaments bipartite of sporangial formation on The intensity light and density of Effects to performed 2 was the Results by analysis calculated curve were Melting values replicates. expression 2001). gene biological Schmittgen, related three The of specificity. product replicates confirm technical 95 three with follows: gene as set was 58 program s, The Real-Time water. 20 Multicolor (Roche, RNase-free one 10 Master iQTM5 Green for template, an DNA mix cDNA using Essential Mao, qRT-PCR Start of performed Fast 5.0 & The was with Primer qRT-PCR Liu, USA) Switzerland). using The CA, Sun, designed Basel, Hercules, 1. were Cao, (Bio-Rad, which Table. 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Data may be preliminary. ai nomto ftasrpoedata transcriptome of analysis. information transcriptome Basic performed and inhibited) was release chonchospore omdadcnhsoe ol erlae)adH lwcluedniyudrhg ih nest;less intensity; light high under density culture (low HL and 80 released) under fragments/mL 10 level, be 150 expression under could than fragments/mL gene fragments/mL 13,000 conchospores the than 150 and more at than intensity; formed filaments light less low sporangial light; under on density low density culture (high and HD light 10 under groups: of three influence up the set we explore H). to 4G, form, order (Fig. hollow In left their were retained filaments microscope vacuoles always light sporangial the density large of Finally, a low and analysis at under 4F). chloroplasts Transcriptome filaments observed reticulum, (Fig. sporangial that endoplasmic would of again like rough vacuoles cells 4E), increase only E), tip would which (Fig. 4C, the in autophagosomes form addition, (Fig. of growth In longer vegetative number 2D). become a the (Fig. almost would into large and two cells entered walls became F) a bipartite cells cells cell E, by, semicircular with or bipartite two went 4C, connections the cells time pit when (Fig. As formed no bipartite those were reappear 4D). typical but There B), (Fig. D). formed 4A, cells B, (Fig. cells 4A, circular cells semicircular (Fig. bipartite vacuole initial two the no the in density, and were starches low density. floridean autophagosomes high many at of nucleus, at filaments degradation filaments (Fig. and sporagnial sporangial degradation formation of structures In autophagosome the formation as after cell that well hollow membrane showed as of observations double F) causes These E, a main in F). 3C, with formed E, coated (Fig. vacuoles were and double-membrane D, cells and fully-formed starches G) hollow 3C, 3B), floridean 3D) of B, (Fig. some center autophagosomes and (Fig. 3A, of the 3H) formation autophagosomes in in (Fig. involved observed (Fig. composed layer being was was of vacuole fiber reticulum filaments suspected internal large sporangial endoplasmic of an A density, wall and cells. cell layer high The hollow pectin at developed. external very filaments an were F) of sporangial 3A, of (Fig. chloroplasts became cells peripheral finally hollow did and cells the cells 2D), bipartite In bipartite and the (Fig. cells If branch hollow 2G). of and characteristics elongate and (Fig. Ultrastructural would 2F) died 2E). filaments and (Fig. darkness, (Fig. color sporangial complete one again in in the by cells green placed hollow release, one were were structures and filaments as filaments they sporangial ridge move such sporangial but the the suitable, not that released, If were from sign 2H). still conditions released were the (Fig. the be conchospores was conchospores When would were that cells cells release. and released bipartite conchospore cells, the compact mature for hollow and the ready spherical from light, were approximately form low density, and would low maturity retain at F) spo- reached would cultured 2C, filaments of had When sporangial changes E). density, (Fig. morphological high 2B, cells the at (Fig. bipartite cultured release, form When conchospore hollow and 2). typical formation their (Fig. cell summarized are bipartite filaments of rangial results the and filaments by on cells sporangial inhibited Based of bipartite was conditions release of different sporangial conchospore formation under hand, on changes the other light Morphological accelerated the of light on effect while high the filaments, and hand, light. sporangial density high one of low the growth under the On formed 10–80 promote only of multifaceted. cells range was bipartite the filaments that in show increased intensity results for light These Moreover, as irreversible. increased was weight release conchospore fresh on the light μ filaments, high of sporangial effect of inhibitory growth the that meant This 1C). rget/L(i.1) vntog ih nest a usqetyrdcd(rm40 (from reduced 0 subsequently or was intensity 10 light to though Even 1B). 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Data may be preliminary. ru.Aogteu-euae Eso h LsDcmaio ru,tetperce Oaccessions GO enriched “carboxylic top process”, the metabolic group, acid comparison “organic HLvsLD process”, significantly the metabolic no “oxoacid of activity”, was DEGs “oxidoreductase There up-regulated were HLvsLD. the cat- in Among which of down-regulated group. in “regulation and and HDvsLD 2, (corrected activity”, Table in accession enriched hydrolase up-regulated complex of Suppl. were “ribonucleoprotein transduction”, “regulation activity” in activity”, signal alytic transduction”, shown factor mediated signal is exchange GTPase “intracellular “guanyl-nucleotide “small DEGs of biogenesis”, activity”, of accession GTPase accession GO of the GO “regulated group. accession, enriched GO LD 10 ribosome-related the top besides in the HLvsLD that and regarding to HDvsLD LD Information close in the was DEGs with believable. two of group were the analysis another HL RNA-Seq with enrichment of of the of group GO comparing results results expression HD When the The the the that RNA-Seq. and comparing showed 1). of when up-regulated results results DEGs, were These Table. and the eight genes as HLvsLD all (Suppl. same six in of the HLvsLD group, the up-regulated trend basically and were up/down perform and HDvsLD group, the to HDvsLD both LD showed HLvsLD in 9) in and down-regulated up-regulated HDvsLD (Fig. mapped were were of qRT-PCR reads groups DEGs DEGs million comparison per five three model the another them, exon both of Among in were kilobase experiments DEGs per qRT-PCR validation. 1,221 fragments data, from high RNA-Seq on values with based DEGs (FPKM) profiles eight expression chose of We reliability conducted. the confirm density to culture order of In those of than qRT-PCR compared cluster greater by LD heatmap were DEGs to intensity a of closer light Validation 8). make was of to samples (Fig. effects DEGs HD levels the of expression 11,185 that pattern gene all indicated expression on using which gene were After samples, which the DEGs HL that 7). 1,221 showed to were genes result (Fig. there up-regulated the groups that 1,438 samples, showed comparison diagram nine with two Venn DEGs The both 9,084 in 6). were found there (Fig. genes group, down-regulated comparison 7,646 HLvsLD and (p-adj) in q-value while HLvsLD) of genes, (HDvsLD, conditions groups regulated screening comparative reached the two rate analysis, with mapped comparative DEGs each > a and obtain perform transcriptome to assembled to created the order were to In mapped 2). were (Table samples 85-88% nine of reads clean The genes modification, 4). differentially-expressed “posttranslational of Fig. categories, only”, clustering the 26 (Suppl. and prediction into mechanisms” in Screening function classified transduction categories were “general “signal KOG three were and in categories chaperones”, top annotated turnover, three “translation”, unigenes the protein top which 16,639 were the The in hierarchy, metabolism” which 3). second in “carbohydrate Fig. the and (Suppl. in annotated hierarchy 12,133 degradation” categories molecular second The and nineteen and 2). into component, sorting Fig. cellular classified “folding, (Suppl. were process, unigenes respectively KEGG biological binding, 40,351 of in and the part, terms unigenes database, cell/cell top and process, least GO the function) cellular at the molecular were which in and function In among component, annotated cellular databases. terms, were process, all second-level (72.27%) (biological in 56 were terms 48,189 first-level annotated KOG) unigenes, three were and into 66,678 classified (5.19%) GO, total were PFAM, 3,465 the SwissProt, and Of KO, database NT, 3). one (NR, (Table databases annotation seven for unigenes, unigenes selected selected 66,678 66,678 were of bp these, annotation 1,966 Among For of value obtained. N50 5). were and unigenes filtering, bp (Fig. bp of 1,287 analysis After 2,090 Annotation of subsequent of length for mean value transcriptome 2). a N50 reference (Table with and the gene) sequencing as each bp transcripts of 108,936 Illumina 1,344 assembly, transcript After of through longest (the 65-66%. length obtained around mean content was GC a a reads with with obtained raw were reads 602,683,400 clean 579,432,658 of total A .I DsDcmaio ru,teewr ,2 Eswt ,3 prgltdgnsad154down- 1,584 and genes up-regulated 1,738 with DEGs 3,322 were there group, comparison HDvsLD In 1. P value > .5 mn h onrgltdDG fteHvL comparison HDvsLD the of DEGs down-regulated the among 0.05) 7 < .5and 0.05 | o2Fl change log2.Fold | Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. dpigt hne nteevrnetadtedffrne nlgtaddniycudcuecagsi the in responses changes adaptive cause environmental could associated density three and in the light roles phosphatidylinositol in Hence, basic in differences filaments. play involved the endocyto- sporangial all all and of and metabolism environment were environment the (ko04145) PtdIns metabolism growth plants, in and phagosome phosphate changes In autophagy both inositol to endocytosis, adapting included in Interestingly, (Leborgne-Castel, 4). DEGs “endocytosis” endocytosis metabolism. Table key as the (PtdIns) The described 10, Later, also always (ko04144). 2010). is (Fig. sis Bouhidel, microbes, “endocytosis” as & such and Adam, the particles, transduction”, pathways large both significantly-enriched of signal in five phagocytosis not present finally, hormone (data were enrichment, “plant HLvsLD which KEGG of DEGs “phagosome”, perform DEGs 404 to down-regulated of DEGs the total 404 (q-value and these a group Using comparison out picked HDvsLD shown). the we of analysis, DEGs pathway up-regulated above formation the cell transcriptomes. bipartite on three to the Based results related of the DEGs credibility with and high consistent pathways the basically key were supported Candidate GSEA and were of KEGG, metabolism” results in photosynthetic enrichment The “nitrogen in DEG and group. of fixation comparison “photosynthesis”, inhibition “carbon HLvsLD metabolism”, light in as on chlorophyll up-regulated such down- focusing and pathways, when be “porphyrin accumulation-related The “regulation addition, also energy organisms”, In “endocytosis”, From light. release, should high “phagosome”, system”. conchospore formation by density. signaling “ribosome”, of promoted low “phosphatidylinositol cell contained was and conditions under bipartite formation autophagy”, these cells cell of of met bipartite pathways bipartite that because regulatory of pathways group, negative main formation comparison those HLvsLD the 26 meant in to view, This and density regulated led significantly. of high up-regulated, pathways up-regulated point comparing significantly were some pathways this When were of most pathways group), down-regulation down-regulated. 47 comparison significantly that the which (HDvsLD were there in density of six low pathways, group, that, which with comparison up-regulated showed of HLvsLD 58 5) pathways, In of down-regulated comparison significantly Table. total down-regulated. two were a significantly pathways the (Suppl. was were 40 in GSEA biosynthesis) which pathways of backbone among of (terpenoid results up-regulated, level were The q-value pathways down-regulated (FDR 79 up-regulated conducted. or group, was up- comparison KEGG the HDvsLD in judge GSEA comprehensively groups, to order DEGs). In chlorophyll (up-regulated KEGG and group in “porphyrin HLvsLD GSEA the to organisms”, to of in related the related photosynthetic Results present pathways pathways both were in the in metabolism” 4), fixation and “nitrogen present “carbon and were groups, Table. as metabolism”, autophagy” DEGs) such (down-regulated of (Suppl. accumulation, HLvsLD “Regulation DEGs up-regulated energy and and of fewer “Phagosome” DEGs) energy pathways as (up-regulated to far enriched related such HDvsLD most with pathways ten catabolism, in some group, top of DEGs and comparison exception shown down-regulated the transport the HLvsLD than are with Among pathway the pathways, DEGs most every up-regulated in accumulation. in of more observed DEGs were groups down-regulated was than there comparison opposite DEGs hierarchy. HDvsLD, two second the In the the but in 3. in pathways, specific DEGs categories enriched Table. eighteen down-regulated 105 into Suppl. of and classified total in up- a be of were could there number which groups, database, The comparison KEGG HLvsLD the and in HDvsLD pathways the in in up-regulated DEGs were all Among them of signal DEGs most GTPase-mediated of to and enrichment related formation, KEGG DEGs cell HLvsLD. that bipartite in showed HLvsLD in down-regulated results bottom of and role These enriched DEGs HDvsLD important down-regulated significantly 6). an and bi- 5, most played group of the Fig. transduction comparison graph were HDvsLD (Suppl. acyclic GTPase of group directed DEGs to comparison the up-regulated related among addition, accessions terms In that GO showed process”. “oxidation-reduction processes and ological process”, metabolic acid < .5 eeotie,wihwr rglto fatpay,“nstlpopaemetabolism”, phosphate “inositol autophagy”, of “regulation were which obtained, were 0.05) < 5)adfieptwy eedw-euae,bto hs,ol n pathway one only these, of but down-regulated, were pathways five and 25%) 8 Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. eaeadmlt eyrgns,pooe bopino abndoie nteCli yl,tecr up- core the cycle, Calvin the In aminotrans- dioxide. the aspartate carbon In genes, of two fixation. absorption also carbon another promoted to was and dehydrogenase, related carboxylase fixation malate DEGs phosphoenolpyruvate and up-regulated carbon gene core ferase photosynthesis, key 22 promoted. were and the There pathway, also synthesis C4 light. was chlorophyll high 1 under of promoted protein enhancement greatly light. by binding the high promoted a/b under to were chlorophyll promoted Corresponding ATPase of be I H+-transporting would subunit complex photosynthesis F-type iron-sulfur light-harvesting that of the addition, indicates subunit protein), This In gamma pho- PsbU 1, the light. II protein and high photosystem enhancer complex, 2, oxygen-evolving b6-f protein II cytochrome (photosystem enhancer II oxygen-evolving photosystem II in tosystem genes three synthase. photosynthesis, protopor- chlorophyll In by from synthesized synthesis chlorophyll) is and of chlorophyll 8-vinyl-reductase Finally, (precursors a a phyrin. chlorophyllide chlorophyllide divinyl promote H, subunit reductase pro- chelatase protochlorophyllide up- of Magnesium core synthesis glutamate. promote these from oxidase toporphyrin of protoporphyrinogen oxygen-dependent functions 2,1-aminomutase, and glutamate-1-semialdehyde The synthase reductase, hydroxymethylbilane glutamyl-tRNA metabolism, group. chlorophyll and comparison porphyrin were In HLvsLD DEGs in the which up-regulated 8), are: Table and DEGs (Suppl. GSEA regulated accumulation in energy to metabolism”. enriched sucrose related core and DEGs “photosynthesis”, accumu- “starch regulated energy metabolism”, and core-up to metabolism” chlorophyll selected related “nitrogen and We pathways organisms”, the “porphyrin photosynthetic that in including showed fixation HLvsLD, KEGG “carbon of in analysis up-regulated GSEA were and lation DEGs HLvsLD of GO results in the the accumulation in Both energy enrichment to DEG related of 6). DEGs results 5, regulated the Fig. Core-up The in Suppl. confirmed proteins. 2, also Rab was Table. nucleotide-exchange inactivate GTPases guanine (Suppl. to and database A-inhibited related activate and brefeldin respectively, function Rab5 of by protein, DEGs, stimulated importance membrane-associated two is membrane. stromal which endosomal Another plasma (Rac1), and the 1 the oxidase. protein substrate to of toxin NADPH recycling botulinum Rab11 localization activates C3 slowing and PI3K, mediate Ras-related endosome compartment endosome, and late recycling Rab8 early the aggregation endosomal the of and the In the localization Rab5 in mediates of Rab7 roles them, localization endosome, important mediates early Among play the membrane. family) and plasma compartment vesicles. protein the recycling GTPase transport on small vesicles of the clathrin-coated localization to of as formation (belonging such initial proteins HLvsLD, the Rab of stimulates DEGs PIP5K 7). down-regulated endocytosis, Table. the In (Suppl. among ATG8 which especially and genes), HLvsLD, ATG7, (autophagy-related ATG5, or ATGs ATG4, as HDvsLD ATG3, annotated in autophagosome. DEGs present other early many gene only the were constituent were of there a DEGs, expression is in- ATG12 four membrane by these stimulates ULK1. Besides processes phosphorylating which directly autophagic kinase conjugate ATG12-ATG5-ATG16 by stimulates protein the or which AMP-activated pathway of regulator, rapamycin reticulum. of positive nucleation endoplasmic target upstream vesicle the the important initial hibiting in an the complex is stimulated PI3K protein PI3K and (AMPK) and complex ULK1) ULK or the (ATG1 through 1 protein autophagy-like autophagy, of In phosphorylation Pt- PtdIns(3,4,5)P PtdIns(4,5)P from the described mediate and PtdIns protein and of mediates PtdIns(4)P PTEN resynthesis 7 and from the VPS34) (PIP5K) mediates kinase Fig. or 5 1/2 4–phosphate protein Suppl. Phosphatidylinositol (PI3K myotubularin-related dIns(3)P. in and 3-kinase PtdIns(3)P shown form is phosphatidylinositol to pathways PtdIns three metabolism, the PtdIns in In DEGs some of in cells map hollow follows: sketch from as a formation and cell 6) bipartite of Table. pathways regulatory negative key yezoensis the as chosen finally were mn h 0 Es hr eeattlo 1DG nihdi h he ahas(Suppl. pathways three the in enriched DEGs 21 of total a were there DEGs, 404 the Among . 3 respectively. , 9 2 formation P. Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. eiee ovcoe o erdto ftxccmoet n eyln fnee uret H Klionsky, & (He nutrients needed of recycling and components and in toxic autophagosome of the described degradation as been known for vesicle vacuoles stress-induced has double-membrane to mediates a and delivered within that 2010) enclosed pathways non-selectively Levine, key are Mari˜no, & the components (Kroemer, alga of under control one limitation adaptive model nutrient is damage Among the to Autophagy 2009). and response filaments. Russinova, adaptation important sporangial & metabolic most metabolic of (Irani the of density environment series is high external a autophagy a make the change, to environmental in able to changes cell are numerous responses cells to against Through plant adapt fight 2009). systems, turnover Bunnett, to the endocytic al., & the adjustments related and Cottrell, et and cell, Hasdemir, Gonz´alez-Gait´an, exocytosis, kinases and Leborgne-Castel the Padilla, receptor-like Murphy, with 1999; cell within 2003; surface 2010; concert Brownlee, signals Guttman, the & of in & enter invagi- Lin dispersal homeostasis, Greenland, membrane to 2010; the cellular plasma James, cargoes as for (Battey, the membrane such necessary pathogens whereby plasma processes membrane process biological or plasma a most cell particles of of is the responses extracellular plethora essential Endocytosis as allowing key a selected off, three mediate 4). finally pinches them, Table were Among and 10, changes nates 5). environmental (Fig. pro- 3, to metabolic responses Table. many metabolism) important density, (Suppl. PtdIns low increases density with endocytosis, hypoxia, Compared high starvation, (autophagy, under nutrition infection. activated as microbial such were and stress, (ROS) cesses cellular species of oxygen forms reactive multiple in causes density culture High free-living in changes conditions morphological light and main high adaptation the under Environmental was cells accumulation, bipartite energy from observed of release also promotion we conchospore filaments. the addition, of sporangial In to inhibition morphological the due filaments. cyclical which, for sporangial caused growth reason free-living environments vegetative of conditions of different cells, cell-inducing promotion bipartite to obvious bipartite to adaptation cells under how hollow transcriptome inhibited from showing under on changes, severely light), (formed Based and high cells density density, growth. bipartite (low high vegetative metabolism—were in under into PtdIns stimulated and entered disappeared endocytosis significantly pathways—autophagy, cells density), response bipartite struc- environmental high key autophagosome-like conditions, when three under that environmental analysis, reappeared showed (formed to and observation cells response density) TEM hollow sensitive low light. in very and density increased a culture tures had by filaments influenced sporangial were and free-living that found also We was which hypothesis a filaments, Discussion 1D). sporangial ability fixation of (Fig. growth carbon experiments vegetative higher growth much promote in a would proven showed and accumulation light energy high to fixation. under related carbon DEGs into regulated enter core-up would promoted pro- Those anhydrase which synthetase carbonic dioxide glutamine while carbon synthesis addition, of chlorophyll In into absorption entered promoted the qRT-PCR) then formation. which by nitrite synthesis (verified intracellular glutamate reductase moted that and nitrate meant absorption and nitrate This light. transporter extracellular high nitrate/nitrite starch. by metabolism, promoted from amylose nitrogen both In from 1-phosphate were starch D-Glucose starch of of of formation consumption formation and the promoted synthesis synthesis promoted phosphorylase starch enzyme starch branching the while 1,4-alpha-glucan into intermediate metabolism, enter fixation starch then carbon In would the which made isomerase phosphate, triosephosphate glycerone sporangial pathway. addition, of form ability In 3-phosphate fixation glyceraldehyde carbon light. the high promoted under qRT-PCR) by filaments sedoheptulose- (verified 3-epimerase, ki- transketolase ribulose-phosphate A, phosphoglycerate and isomerase dehydrogenase, bisphosphatase 5-phosphate 3-phosphate ribose qRT-PCR), glyceraldehyde by aldolase-class (verified II, nase fructose-bisphosphate class qRT-PCR), aldolase, by fructose-bisphosphate (verified I, I fructose-1,6-bisphosphatase DEGs, regulated hayooa reinhardtii Chlamydomonas Pe e-´ rz&Cep,21) uigatpay cytoplasmic autophagy, During 2010). (P´erez-P´erez Crespo, & 10 Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. iatt el,adte epn iatt el nalwvgttv rwhevrnet uha o light low as such environment, growth steps of vegetative important formation low the promote a Hence, to in pressure cells growth. environmental bipartite vegetative the keeping with reducing conchospore then (10–20 competition first, subsequent and the in cells, are: was and stage stage bipartite release environments cell a stress conchospore bipartite was the low promoting the that in cells in and seen cells appeared 2) bipartite be process bipartite which (Fig. could of When stage the It process release short-term cyclical in skipped. 4). and a of morphology, be was special would (Fig. reappearance From filaments a release vacuoles with sporangial conchospore small elongate of of 8). and change would stage 5, morphological autophagosomes the cells growth, structure, 3, bipartite vegetative connection into growth, entered Table. pit vegetative fixation, wall, into carbon cell enter (Suppl. the cells photosynthesis, synthesis light bipartite synthesis, starch high which chlorophyll that and via showed included nitrogen also which of intensities pathways, absorption light accumulation different energy under changes of 1). expression gene Table. and C, (80 1D) (Fig.1B, filaments (86 (Fig. weight light sporangial was high release free-living 2015; Li appropriate conchospore of al., by above, under (40–100 L´opez-Vivas intensities et mentioned study pathways light 2011; light a the al., high those inhibiting In et by although by 1A) Li study, inhibited 2006; (Fig. significantly this Yarish, cells lower In bipartite & relatively of conchospore 1987). He a and formation 1980; maturation al., that the showed (Chen, et for studies filaments Waaland needed Many were sporangial mystery. seed photoperiod of a shorter the release and been of are intensity always light They thallus has lower gametophyte. of filaments temperature, and sporangial culture sporophyte from between artificial release intermediate large-scale the of as sources seen study. be PI3K, in-depth could as further Conchospores worth such are study, release 6) this conchospore Table. the and in (Suppl. growth of selected Rac1 Vegetative studies DEGs and subsequent Rab7, For candidate Rab5, morph stress. important ATG12, adaptive high ATG1, the the and PIP5K, are filaments, deficiency cells sporangial energy hollow deficiency, contrast, of environment in nutritional development an and of in stress environment morph low adaptive of an and the conditions in different energy are under sufficient cells rate Table. nutrition, bipartite formation that adequate (Suppl. cell indicate with groups bipartite could the which three intensity, of light the results and the among density with consistent HL as are in (such results the lowest these autophagy among All and to group HD related HL in DEGs the of highest 2012). in Hawley, expression lowest also and the & was 6). group AMPK, Ross, PI3K) HD of (Hardie, and the expression limited ATG12, in the ATG, is highest to cells was Correlated in AMPK of groups. energy of factor three Kundu, expression when stimulating (Kim, the stimulated a that 2012), AMPK is is found Xing, is which 6). also We & 2011), factor ROS Table. Zhou, Guan, and autophagy-inducing high Suppl. & 2019), (Liu, Another under 4, Mattevi, Viollet, process 2012). (P´erez-P´erez (formed 3, & activation al., algae (Magnani cells oxidase (Fig. structu- et in produced NADAPH hollow density starch autophagy be the low of of would in under that ROS number role which down-regulated than the important through was greater study, an morphology, PI3K played was this cell also of density) In PI3K altered low expression 2018). growth, under the al., cell (formed while et density), decreased cells (Ramanan the significantly bipartite contents catalyze to in starch which res led and Ptd- PIP5K PI3K lipid to and related higher of PI3K genes knockdown and genes autophagy, PtdIns(4,5)P and key and and inhibition two PtdIns system the the from endocytic severe especially PtdIns(3)P the by of roles, of formation caused important transport were played the density metabolism and high Ins formation to under vesicle related cells both DEGs hollow and In to TEM by change observed the structures that autophagosome-like autophagy. showed of pathway results autophagy the 2012). P´erez-P´erez,the Crespo, both 2011; & Ohsumi, research, Lemaire, & this Yoshimori, Mizushima, In 2012; Bassham, & Liu 2009; μ o htn m photons mol μ o htn m photons mol tal. et -2 s -1 -2 L ta. 01,tefe-iigsoaga lmnsof filaments sporangial free-living the 2011), al., et (Li rmtdtegot fsoaga lmnsbcueo h rmto faseries a of promotion the of because filaments sporangial of growth the promoted ) s -1 ,t rmt ocopr release. conchospore promote to ), μ o htn m photons mol -2 s 11 -1 Pyropia/Porphyra .I u td,terslso nlsso ohfresh both of analysis of results the study, our In ). 2 rmPdn().In PtdIns(4)P. from μ o htn m photons mol h ehns fconchospore of mechanism The . hayooa reinhardtii Chlamydomonas .yezoensis P. -2 s -1 rmtdthe promoted ) rwfastest grew , Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. i,J . aih . wn,E . ak . i,Y 21) ewe qautr:cliaintech- cultivation aquaculture: Seaweed (2017). Y. Kim, & M., services. Park, ecosystem K., its direct E. and through Hwang, challenges autophagy C., nologies, regulate Yarish, mTOR K., and J. AMPK Kim, (2011). K. Guan, & Ulk1. B., of Viollet, phosphorylation M., Kundu, plants. J., in for signaling Kim, conchocelis and free-living endocytosis Receptor of (2009). cultures 12 E. Russinova, biology, mass & of G., N. regulation resistance Irani, developmental temperature The high of (2006). seeding with C. net HB Yarish, commercial line & cell P., of He, cultivation autophagy. and of Establishment in pathways growth (2003). fast signaling W. and Wu, and maintains & that mechanisms P., sensor Regulation He, energy (2009). and 43 J. nutrient genetics, D. a of Klionsky, AMPK: review & (2012). C., A. S. He, Hawley, & A., F. homeostasis. energy Ross, G., D. Hardie, pathway. 4 endocytic biology, the cell through Molecular transduction views and of dispersal life-history Signal Gonz´alez-Gait´an, the (2003). in in M. seeding Conchocelis-phase and 748. (1949). (4174), culture crop M. marine filament K. a conchocelis Drew, Porphyra: free 4 the Aquac., (2011). on H. Fish. S. J. Studies Brawley, Chin. & (1980). P., G. Xu, endocytosis. C., Chen, and A. Exocytosis Grossman, A., stress. (1999). by J. C. shaped Brodie, Brownlee, A., & N. J., Blouin, A. Greenland, 11 C., Cell, N. Plant James, H., N. Battey, interest. References of conflict no declare authors The China of (CARS- Interest China Biology Program of of Marine R&D Republic Conflict People’s Key for the of National Laboratory (Qing- Affairs Technology (41876160), Rural of and and China 50). grant Agriculture Science of of the Ministry Foundations Marine and by for Science (2018YFD0901500) support Natural Laboratory National National financial Pilot dao), the (OF2019NO07), acknowledge Biotechnology production to and and wish research authors fundamental The to beneficial be will Acknowledgments results These sporangial light. in of change low application demonstrated morphological as of we such bases analysis, environment, the transcriptome were Through environments of bipartite different filaments detected. phenomena, under important were responses two release, adaptive The sporan- that conchospore free-living visualization. of and microscope intensity formation optical light and and cell density TEM culture through by filaments caused changes gial morphological the all observed We Conclusion 6,653-659. (6), .yezoensis P. .yezoensis P. 4,643-659. (4), rnsi ln cec,16 science, plant in Trends opyayezoensis Porphyra auervesMlclrcl ilg,13 biology, cell Molecular reviews Nature 67-93. , ute,cnhsoe eesdfo iatt el edalwvgttv growth vegetative low a need cells bipartite from released conchospores Further, . auecl ilg,13 biology, cell Nature 1,19-29. (1), opyaleucosticta Porphyra . 3,213-224. (3), . h a hn uxebo 36 bao, xue wu sheng yan Shi 1,29-37. (1), rmNrhatAmerica. Northeast from la,32 Algae, 2,132-141. (2), 12 1,1-13. (1), opyaumbilicalis Porphyra 4,251-262. (4), 3,191-196. (3), qautr,257 Aquaculture, urn pno nplant in opinion Current L)K (L.) opyahaitanensis Porphyra utz. ¨ 14,373-381. (1-4), aue 164 Nature, auere- Nature Annual The . Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. rvsl,L 16)Mdaadpopcsfrtecliaino aieage n aaaeA atr A September. 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NADPH Orthology Wei, by KEGG & the G., generation J. using ROS Olyarchuk, cation of T., mechanisms Cai, X., and Mao, Structure 59 biology, strain structural (2019). mutant in high-growth-rate A. opinion a Mattevi, Current of & Characterization (2019). F., G. Magnani, Wang, & X., Lu, L., Huan, of RNA-seq L., for He, dispersion and Y., change Ma, fold of estimation Moderated (2014). DESeq2. S. with Anders, data & W., Huber, I., M. Love, 27 phycology, applied of of quanti- Journal phase real-time conchocelis using the data of reproductive and expression responses Growth gene (2015). C. relative Yarish, Pacheco-Ru´ız, of Riosmena-Rodr´ıguez, & L´opez-Vivas, R., M., I., Analysis J. cells. 2- (2001). plant the D. and in T. PCR self-eating Schmittgen, tative for & rice pathways J., of K. regulation Autophagy: Livak, in (2012). role C. vital 63 D. a biology, Bassham, plays plant 3-kinase & Phosphatidylinositol Y., activity. Liu, oxidase (2012). NADPH D. altering Xing, via pathogens. & vigor microbial J., seed by Zhou, machinery J., endocytic the Liu, Hijacking (2010). A. J. 244 Guttman, plasma, & intensity. E.-J., of light A. conchosporangia and Lin, free-living of temperature growth photoperiod, and Formation of (2011). effects P. He, : without & or L., Yang, with X., data Li, RNA-Seq from quantification transcript accurate genome. RSEM: reference (2011). interactions. a N. C. plant–microbe Dewey, & in B., Endocytosis Li, (2010). K. Bouhidel, & 247 plasma, T., Adam, N., expression response. Leborgne-Castel, gene stress integrated for the genes and Autophagy reference (2010). of 40 B. Levine, Selection & Mari˜no, (2015). G., G., Kroemer, Y. Mao, & W., Liu, 1003-1010. P., Sun, in M., normalization Cao, F., Kong, yoi yezoensis Pyropia 2,280-293. (2), ln hsooy 160 Physiology, Plant 14,75-90. (1-4), 177-193. (3-4), 4,562-563. (4), yoi yezoensis Pyropia 215-237. , eoebooy 15 biology, Genome M iifrais 12 bioinformatics, BMC sn hsooymaueetadtasrpoeanalysis. transcriptome and measurement physiology using ΔΔ Tmethod. CT 4,1561-1570. (4), 1,156-164. (1), sn uniaiera-iePCR. real-time quantitative using yoi hollenbergii Pyropia ehd,25 methods, 1) 550. (12), 91-97. , 1,323. (1), rceig fteNtoa cdm fSine,106 Sciences, of Academy National the of Proceedings lsOe 7 One, Plos 4,402-408. (4), 13 107-132. , Bnils hdpya olgtadtemperature. and light to Rhodophyta) (Bangiales, qautr eerh 42 Research, Aquaculture (3). iifrais 21 Bioinformatics, ora fapidpyooy 27 phycology, applied of Journal hayooa reinhardtii Chlamydomonas ora fphycology of Journal 8,1079-1086. (8), opyayezoensis Porphyra 1) 3787-3793. (19), nulrve of review Annual oeua cell, Molecular Proto- Proto- . (42), (2), . Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. D 676325,8,1 .900 67 25 61 48,113,220 73,591,006 66.10 66,394,968 65.12 73,023,174 92.55 49,338,392 66.02 92.22 66.68 96.76 63,689,860 65.45 92.47 51,715,118 96.58 91.79 66.08 0.03 92.77 96.66 65.88 33.33 0.03 96.35 92.41 8.19 96.92 83.33 0.03 92.44 97.91 54,589,112 12.93 0.03 16/48 96.73 56,786,392 86,216,082 0.03 11.34 96.74 40/48 89,235,100 75,623,196 47/48 12.49 0.03 LD1 79,386,504 16/48 83,286,642 8.4 0.03 HL3 86,950,532 40/48 55,980,466 47/48 10.84 HL2 58,084,156 72,275,946 5/48 8.81 HL1 74,995,026 37/48 58,727,046 47/48 HD3 60,828,832 HD2 1/48 Reads Raw 12/48 HD1 43/48 Sample 0/48 samples 0/48 nine of summary analysis 0/48 Sequence 2 Table 80 40 10 m ( Intensities Light filament sporangial single of release RNA-seq: Conchospores for 1 analysis Table ontology Gene (2010). A. Oshlack, Tables & The K., bias. (2013). G. selection Smyth, T. for J., Atsumi, accounting M. . Wakefield, D., . M. ( Young, . Susabi-nori S., Alga, Yuya, con- Red Y., on Marine Motoshige, e57122. density of O., (3), conchosporangium Sequence Nobuhiko, and Genome K., Symbiont-Free intensity Masahiro, First S., light Naobumi, temperature, N., of of Yoji, control Effect photoperiodic (2004). and in P. growth releasing Conchocelis He, chospores & (1987). L., E. Yang, J. of Carrier, clon & in of G., release L. culture aquaculture. conchospore Dickson, laver suspension R., purple on J. Waaland, for report conchospores Preliminary The of 27 (2018). production Sinica, (1996). S.-J. the Limnologia Lee, C. in filaments . Zheng, conchosporangial & . A., . metabolism carbon S.-Y., Sun, and Shin, energy of B.-H., regulator Kim, master algae. a J.-E., is in Jung, system signaling D.-H., 3-kinase Cho, phosphatidylinositol ancient Q.-G., Tran, R., Ramanan, μ -2 o photons mol s -1 ) ln hsooy 177 Physiology, Plant 3 oa holes total / holes Released rd a 6 day opyatorta Porphyra opyayezoensis Porphyra 6,667-668. (6), eoebooy 11 biology, Genome Reads Clean 3,1050-1065. (3), oa holes total / holes Released th (rhodophyta). a 9 day . ae G)Err()Q0()Q0(%) Q30 (%) Q20 (%) Error (Gb) Bases Clean aieTieheries Marine 2,R14. (2), 14 ora fpyooy 23 phycology, of Journal oa holes total / holes Released th a 12 day . oa holes total / holes Released th yoi yezoensis Pyropia a 15 day 3,399-406. (3), opyayezoensis Porphyra oa holes total / holes Released th ). caooi et Oceanologia day lsOe 8 One, Plos (%) Content GC (%) Percentages Final Mapped Total (88.14%) (85.36%) (87.80%) (87.68%) (88.14%) (88.12%) (88.06%) Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. :Rlae ocoprsudrcmlt akescniin :Nra eesn ocoprs :Thallus cells; I: bipartite conchospores; of releasing form Normal growth H: Vegetative condition; D: darkness filaments; complete of sporangial under conchospores of Released cells G: bipartite Typical CF: filaments; yezoensis 2 Figure (mean fragments/mL (mean changes 100 weight of (mean fresh density fragments/mL at 100 release of conchospore (mean density cells at bipartite release of formation on light 1 Figure legends Figure in up-regulated a. selection: group. DEG comparison for HLvsLD 35,528,640 Basis in down-regulated DEGs. b. 404 group; selected comparison of pathways HDvsLD enriched 45,862,774 Significantly 4 Table 66.64 65.89 92.06 92.56 96.55 96.75 0.03 databases 0.03 seven in annotated unigenes 86.91 of value Number 6.06 Phred 3 Table a 579,432,658 with bases of Percentage 602,683,400 40,409,780 Q20: 7.85 42,032,086 52,324,388 Total 54,384,772 LD3 Reads Raw LD2 Sample .yezoensis P. ht ro hwdasoaga lmn ncnhcls E yia olwfr fsporangial of form hollow Typical BE: conchocelis; in filament sporangial a showed arrow white , opooia hnecceo prnilfiaet ne ieetcniin.A ocoei of Conchocelis A: conditions. different under filaments sporangial of cycle change Morphological noyoi o44 .118 7 0.0121 0.0016 ko04144 7 4 ko04145 7 Number DEGs P-Value Corrected 0.0001 ID KEGG 0.0121 0.0010 ko04140 ko04075 ko00562 Endocytosis transduction signal hormone Plant Phagosome metabolism phosphate Inositol autophagy of Regulation Terms Pathway ffcso utr est n ih nest nsoaga lmns :Eet fdniyand density of Effects A: filaments. sporangial on intensity light and density culture of Effects oa ngns6,7 100 24.95 60.51 5.19 66,678 60.51 72.27 16.00 18.19 42.52 41.55 16,639 40,351 3,465 40,351 (%) Percentage 48,189 Unigenes Database Unigenes 10,672 of one Total 12,133 Number 28,356 least at in 27,706 Annotated Databases all in Annotated KOG in Annotated GO in Annotated PFAM in Annotated SwissProt in Annotated KEGG in Annotated NT in Annotated NR in Annotated Databases a nalfiue ee20 were figures all in Bar ; ± Reads Clean ..o he repetitions). three of s.d. μ ± ae G)Err()Q0()Q0(%) Q30 (%) Q20 (%) Error (Gb) Bases Clean m. > ..o he eeiin) :Eet flgto conchospores on light of Effects B: repetitions); three of s.d. 0 3:Pretg fbsswt he value Phred a with bases of Percentage Q30: 20; ± ..o v eeiin) :Eet flgtrdcinon reduction light of Effects C: repetitions); five of s.d. 15 ± ..o i eeiin) :Eet flgton light of Effects D: repetitions); six of s.d. > 30. (%) Content GC P. Mapped Total (87.92%) (87.65%) Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. up.Fg 2 Fig. Suppl. 1 Fig. Suppl. group. rison 8 Table Suppl. 7 Table. Suppl. 6 Table. Suppl. 5 Table. Suppl. 4 Table. Suppl. 3 Table. Suppl. 2 Table. Suppl. 1 Table. Suppl. information group. Supporting comparison HLvsLD in down-regulated b. group; 10 Figure repetitions). three of s.d. down-regulation. represents 9 color Figure blue and up-regulation represents color red 8 Figure 7 Figure (p-adj egh ftecnis n o hc h olcino l otg fta egho hre otisa least the at of contains total shorter the or length of that (90%) contigs. (p-adj of DEGs the 50% contigs of least all lengths at 6 the of contains Figure of collection longer total the or the which of length for Pit (90%) that and 50% E: contigs, of in the contigs of Arrowhead all lengths of wall; collection Cell the Arrow: which density; P: connection; Vacuole; low 5 Pit V: under Figure Pc: filaments reticulum; Nucleus; endoplasmic sporangial 1 N: Rough of Bar: starch; RER: cells connection; connection; Floridean structure; Tip pit FS: Autophagosome-like with GH: cell Pyrenoid; Elongated As: cell; E: chloroplast; elongated connection; pit in and Ch: wall autophagosomes cell Increased with cells F: bipartite Late D: 1 cells; (D), bipartite nm Fibrous 4 200 FL: (BE), layer; Figure nm Pectin 500 PL: arrowhead: Bar: Black wall; structure; structure; Cell autophagosome-like autophagosome-like figures). CW: of of degradation Nucleus; structure by membrane N: formed chloroplast; vacuole Double starch; Small Ch: Floridean filaments; arrow: FS: Black reticulum; sporangial layer; endoplasmic Pyrenoid; of Smooth wall P: SER: cell reticulum; Vacuole; endoplasmic Details of V: rough G: Details RER: membrane; H: structure; double autophagosome-like reticulum; by after endoplasmic As: separated membrane vacuoles rough Formed double many and with D: with nucleus vacuole cell cell; A of hollow hollow E: A Late C); F: C: of degradation; enlargement A); autophagosome (local of autophagosome enlargement coated (local membrane reticulum double endoplasmic in autophagosome Forming 3 Figure < .5and 0.05 ocn aso Es bv h otdln,tedt ntelf gen ersn down-regulated represent (green) left the on dots the line, dotted the Above DEGs. of maps Volcano etmpcutro oa 115DG fnn ape.TeYai ersnsrltv expression, relative represents axis Y The samples. nine of DEGs 11,185 total of cluster map Heat endarmo DEGs. of diagram Venn eut fqTPRo ih Esi he rus Dgopwssta h oto (mean control the as set was group LD groups. three in DEGs eight of qRT-PCR of Results eghdsrbto ftasrpsaduiee.N0(0 eghwsdfie stelnt for length the as defined was length (90) N50 unigenes. and transcripts of distribution Length lrsrcua hrceitc fhlo el fsoaga lmns :Eryhlo el B: cell; hollow Early A: filaments. sporangial of cells hollow of characteristics Ultrastructural lrsrcua hne fbpriecls B al iatt el;C nta lnainof elongation Initial C: cells; bipartite Early AB: cells. bipartite of changes Ultrastructural ahaserce f44DG.BssfrDGslcin .u-euae nHvL comparison HDvsLD in up-regulated a. selection: DEG for Basis DEGs. 404 of enriched Pathways < eefnto lsicto fuiee noae yGO. by annotated unigenes weight. of fresh classification and function fragments Gene filaments of number between prediction Linear .5and 0.05 nomto fcr-prgltdDG eae oeeg cuuaini LsDcompa- HLvsLD in accumulation energy to related DEGs regulated core-up of Information nomto fttlDG nihdi uohg pathway. autophagy in formation. enriched cells DEGs bipartite total to of related Information DEGs regulatory negative key of Information eeStErcmn nlssi KEGG. in Analysis Enrichment DEGs. Set of Gene KEGG in pathway. pathways enriched enriched every ten in Top DEGs down-regulated or up of DEGs. Number of accessions enrichment GO ten qRT-PCR. Top of primers and DEGs of Information | o2Fl change log2.Fold μ nalfigures. all in m | o2Fl change log2.Fold | > 1). | > ) h oso h ih rd ersn h prgltdDEGs up-regulated the represent (red) right the on dots the 1); 16 μ (other m ± Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. up.Fg 7 Fig. Suppl. group. comparison 6 Fig. Suppl. group. parison 5 Fig. Suppl. 4 Fig. Suppl. 3 Fig. Suppl. kthmpo motn Esi h he ai niomna dpieresponses. adaptive environmental basic three the in DEGs important of map Sketch KOG. by annotated unigenes all of classification KEGG. functional by Gene annotated unigenes of classification function Gene ietdaylcgaho ilgclpoesi Oo prgltdDG nHvL com- HDvsLD in DEGs up-regulated of GO in process biological of graph acyclic Directed ietdaylcgaho ilgclpoesi Oo onrgltdDG nHLvsLD in DEGs down-regulated of GO in process biological of graph acyclic Directed 17 Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. 18 Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. 19 Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. 20 Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. 21 Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. 22 Posted on Authorea 4 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158602473.36139405 — This a preprint and has not been peer reviewed. Data may be preliminary. 23