Posted on Authorea 3 Apr 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158592560.03447648 | This a preprint and has not been peer reviewed. Data may be preliminary. fseiesi rca oaodcmrmsn eerhadco rdcin ie hti snteasy not is it that Given production. crop and research lack compromising (2) taxonomy, avoid authentication species Therefore, to incorrect in material. crucial (1) housed old to germplasms is with due on contamination specimens mislabeled reliance (3) be our and of may increasing parameters, 2013). banks lost, morphological seed been al., diagnostic in have of et relatives seeds However, (Jia close their banks. erosion and seed genetic conserved crops of of initially forms were rounds some wild relatives several originated close undergone which their has later and wheat, and Crescent, crops bread Fertile of example, the resources loss For a Genetic in suffered ago domestication. have years crops prolonged most 8000 following however, improvement; diversity cultivar genetic for fundamental of are resources Genetic 1964). rpvreisrqie pcfi ee rmtegn olo h rpseisado t ls eaie,such relatives, close its and/or species higher-yielding crop of has the ( Creation production of rice crop pool intensification. in in gene crop gene increase the and semidwarfing rapid from unit the The together genes per as expansion. wheat, specific yields this and requires higher for varieties maize, three-fold key crop through Rice, a been largely by have 2013). achieved supported crops, Yearbook been been staple has Statistical which (FAO’s other population, some production human with crop the in in explosion expansion an global witnessed years 50 last The biodiversity. the rice clarify support to and expected germplasms, are rice results Introduction of These that use revealed mislabeled. and barcodes were identification chloroplast collections the field rice-specific in chloroplast or six aid banks a The species, seed and marker. rice rice R22), reliable from of accessions most and concept seed the (NP78 rps16- 53 was barcodes the rpoB-trnC, latter of DNA (psaJ-rpl33, The 17% nuclear barcodes barcode. genome plant DNA rice-specific conventional DNA L chloroplast two four and super trnV-ndhC), of rice-specific D genome performance and six the rufipogon. ITS), trnK-matK, evaluated O. we and rps19-rpl22, and Importantly, psbA-trnH, japonica trnQ, and extinct. minuta rbcL, was subsp. O. type (matK, sativa granulata, genome O. barcodes O. H and DNA the and indica, and meyeriana and found O. subsp. not alta, glaberrima sativa were O. O. O. types and between and grandiglumis nivara determined O. O. were longistaminata, malampuzhaensis, relationships O. O. Conspecific and identity of and glumipatula identified. species Breeding determine O. were collected to barthii, we species are genes population. O. Here, Oryza nuclear which Twenty-one world’s hypervariable misidentifications. two species, or the seeds. and issues wild genomes rice of taxonomic chloroplast in and to half complete due cultivated 58 supporting of mislabeled both phylogenomics world, are the from seeds the applied numerous resources Unfortunately, in genetic banks. crops seed on important in relies maintained most cultivars the quality of and one high-yielding is Oryza) (genus Rice Abstract 2020 28, April 3 2 1 Wu e Zhang Wen super and specific, conventional, barcodes Oryza: of barcoding DNA nttt fFrni cec,Mnsr fPbi Security Public of Ministry Science, Forensic of Institute Sciences University of Forestry Academy Northeast Chinese Botany of Institute 1 uyn Yang Xueying , nsitu in 1 uh Sun Yuzhe , nterhmlnso eryaes ihitnercaaino rbeln,mr n more and more land, arable of reclamation intense With areas. nearby or homelands their in 3 n h-in Zhou Shi-Liang and , 1 i Liu Jia , sd-1 1 and ) hoXu Chao , Rht1 1 and 1 1 ihiZou Xinhui , Rht2 nwet(ae&Mrhl,17;Jennings, 1973; Marshall, & (Gale wheat in 1 u Chen Xun , xsitu ex nse ak worldwide banks seed in 2 aliLiu Yanlei , 1 Ping , Posted on Authorea 3 Apr 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158592560.03447648 | This a preprint and has not been peer reviewed. Data may be preliminary. 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Data may be preliminary. aae otie 8clrpatgnms ersnigalrc pce 13prseis,tgte with together species), per (1~3 species rice all representing genomes, chloroplast three 58 methods. contained seed phylogenetic with 1 and using Dataset comparison, (together datasets resolution corresponding genomes delimitation, with Species chloroplast Se-Al. performed (Katoh using were 37 mafft-win manually using identification adjusted aligned with S3), and (Table combined 2013), GenBank Standley, from were & downloaded species) genomes three of chloroplast fragments chloroplast determined newly The Biosystems). calling (Applied nucleotide some preparation Analyzer correct Dataset DNA to 3730xl necessary if ABI edited an and 5.4 on Sequencher mistakes. directions using assembled both were in sequences The sequenced and 94 PEG8000 at using cycles 40 included 1 program contained mixture 5.4. reaction barcodes Sequencher PCR DNA with The rice-specific HiSeq assembled Illumina of and an sequencing references on and known together amplification using fragments sequenced PCR The and extracted fragments were primers. chloroplast Reads specific the using platform. with amplified selected Ten mixed were were X Fragments were genes sample nuclear 2008). same single-copy al., the and et variable of (Zou highly genes two candidate species, 142 polyploid from of origins the regions. determine To these sequence and amplify to all designed from 2009) Rozas, genomes & chloroplast brado all across diversity Nucleotide Lipman, & Myers, (2013). primers design Miller, barcode Zhou using and sequencing DNA Gish, Rice-specific Sanger Lin, (Altschul, by Cheng, 2.8.10 filled Xu, were blastn Dong, gaps by by (Corperation)and reported references 5.4 Sequencher closest with the assembled sorted Bioinformatics 1990), to were Novogene assembled reads mapped Beijing genome & were were Chloroplast Wang, at genomes Yu, contigs sample platform. 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DNA Oryza Leersia . matK pce sotrus aiu asmn nlsswr are u oietf n exclude and identify to out carried were analyses parsimony Maximum outgroups. as species ,dtst3( 3 dataset ), psbA-trnH h othpraibergoswr eetda ieseicbroe.Pieswere Primers barcodes. rice-specific as selected were regions hypervariable most The . rbcL ° o 0s 55 s, 30 for C eunei nerpe by interrupted is sequence ,dtst4( 4 dataset ), enovo de × a ue ihMg with buffer Taq ° sn Pds39(akvc ta. 02.Tegenerated The 2012). al., et (Bankevich 3.9 SPAdes using o 0s n 72 and s, 30 for C psbA-trnH 3 Oryza ,addtst5(T)rpeetdconventional represented (ITS) 5 dataset and ), 2+ rps19 . MdTs n 0n N.TePCR The DNA. ng 20 and dNTPs, mM 0.1 , ° o i.PRpout eecleaned were products PCR min. 2 for C pce a unie sn DnaSP using quantified was species nPaee aae ersne the represented 6 Dataset Poaceae. in (Li- Posted on Authorea 3 Apr 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158592560.03447648 | This a preprint and has not been peer reviewed. Data may be preliminary. .punctata The O. a with 1. same with species the species The Fig. of comprising with Haplotypes clade consistent The The base, species. the 2). allotetraploid at clades of (Fig. located origins clades was the monophyletic types clarified formed genes types the nuclear genome of on species a based that Phylogeny indicating clades, the monophyletic form to not belonged did parent chloroplast maternal complete their the suggesting in parent. clades maternal and species eight their The type The was 1). type genes. (Fig. genome R22 types and genome eight minuta NP78, the O. 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(46), cetfi eot,5 Reports, Scientific 11 rceig fteNtoa cdm fSciences of Academy National the of Proceedings eoeBooy 9 Biology, Genome 1,3835 https://doi.org/10.1111/1755- 348-355. (1), 47.https://doi.org/10.1038/srep14876 14876. , RIRsac ae Series Paper Research IRRI 3,R9 https://doi.org/ R49. (3), LSOE 10 ONE, PLoS urn pno in opinion Current Nature Plant . (4), Posted on Authorea 3 Apr 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158592560.03447648 | This a preprint and has not been peer reviewed. Data may be preliminary. h akr h grsbsd rnhsaebosrpvle n h eoetpsaegvni odcapital bold in given are types genome the and side. values right bootstrap the are branches on in beside letters species figures barcode. all DNA The chloroplast of marker. rice-specific sequences the the on regions) based hypervariable tree six consensus strict (concatenated parsimony barcode maximum DNA The nuclear S6. 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Oryza Oryza Oryza Oryza Oryza eosrtn h eouino h akr h grsbsd branches beside figures The marker. the of resolution the demonstrating , branches beside figures The marker. the of resolution the demonstrating , Oryza eosrtn h eouino h akr h grsbsd branches beside figures The marker. the of resolution the demonstrating , ape nti td with study this in sampled Oryza h grsbsd rnhsaebosrpvle fbt maximum both of values bootstrap are branches beside figures The . eosrtn h eouino h akr h grsbeside figures The marker. the of resolution the demonstrating , and Oryza Oryza Leersia ihcrmsm ubr eoetp n distribution and type genome number, chromosome with eosrtn h eouino h akr h figures The marker. the of resolution the demonstrating , 12 pce onoddfo GenBank. from downloaded species Leersia Oryza Oryza pce soutgroups. as species eosrtn h eouinof resolution the demonstrating , pce n 6vral regions variable 36 and species psbA- matK rbcL Posted on Authorea 3 Apr 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158592560.03447648 | This a preprint and has not been peer reviewed. Data may be preliminary. * 0.0005 substitutions/site * 2 1 100/100/1 95/96 90/93 * 100/82/1 * * 100/98/1 96/99/1 * * * O. meyerianaKF359921.1 O. granulataKF359920.1 100/98/0.99 O. coarctata O. granulataBOP204877 O. schlechteriBOP022683 * * O. coarctataBOP022690 61/70/1 * O. neocaledonica O. neocaledonica * * * * * 1 * * O. longiglumisBOP022664 O. ridleyi O. ridleyi 98/99/1 * 98/98/1 O. altaBOP022645 O. grandiglumisKF359914.1 * O. grandiglumisBOP022694 O. altaKF359913.1 O. schweinfurthianaBOP022678 O. longiglumisKF359918.1 O. latifoliaBOP204878 O. eichingeriMF401450.1 O. eichingeriBOP204879 O. latifolia O. officinalisBOP022672 O. officinalisKM881643.1 * O. rhizomatisMF401452.1 O. rhizomatisBOP204880 * 87/94/1 O. australiensisKF359916.1 O. australiensisBOP022647 13 * 2 BOP022680 KF359919.1 * * * O. malampuzhaensisBOP204667 O. minutaBOP022670 O. minutaKF359909.1 * * * O. punctataKF359908.1 O. punctataKM103375.1 * * * * * * * * * BOP022671 O. malampuzhaensis KF359915.1 * O. glumipatulaKM881640.1 O. longistaminataKM088024.1 O. glumipatulaW2201KR364803.1 O. longistaminataKF359907.1 O. sativasubsp.indica O. sativasubsp.indica O. sativasubsp.indica O. barthiiKM103371.1 O. sativasubsp.indica O. rufipogonKF359902.1 O. nivaraKM088022.1 O. meridionalisKF359906.1 O. sativasubsp.japonica O. barthiiKF359904.1 O. meridionalisKM103373.1 O. rufipogonDongXiangKF562709.1 O. glaberrimaKJ513090 O. brachyanthaKF359917.1 O. brachyanthaBOP022653 O. nivaraAP006728.1 Leersia japonica Leersia perrieri O. glaberrimaKF359903.1 Leersia perrieri O. sativajaponicaX15901.1 BOP022686 KF359922 KY347906 AY522329.1 RPBio-226KU705873.1 JN861110.1 RPBio-226KY780370.1

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FF GG AA BB/BBCC CC/CCBB/CCDD EE HHKK HHJJ Posted on Authorea 3 Apr 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158592560.03447648 | This a preprint and has not been peer reviewed. Data may be preliminary. of-oryza-conventional-specific-and-super-barcodes Primer.docx 2. Table file Hosted of-oryza-conventional-specific-and-super-barcodes Materials.docx 1. Table file Hosted 100/83/1 10 changes 64/-/0.67 vial at available 100/83/1 vial at available 97/52/1 98/95/1 92/-/1 100/91/1 O.neocalidonia BOP022671 O.granulata 106469 O.granulata EF578073+EF578236.1 O.granulata BOP022661 100/91/1 https://authorea.com/users/308394/articles/439407-dna-barcoding- 100/96/1 100/82/1 https://authorea.com/users/308394/articles/439407-dna-barcoding- Leersia perrieriBOP022686 100/99/1 Leersia tisserantii105610 O.longiglumis BOP022664 O.longiglumis BOP022665 O.ridleyi BOP022680 78/-/1 100/98/1 O.schlechteri BOP022683 O.brachyantha EF578235.1 O.brachyantha EF578072 O.brachyantha 105151 O.longiglumis BOP022664 O.brachyantha BOP022654 O.longiglumis BOP022665 O.coarctata BOP022690 O.ridleyi BOP022680 82/100/1 81/58/1 96/93/0.96 O.schlechteri BOP022683 100/100/1 83/100/1 82/-/1 14 O.coarctata BOP022690 100/100/1 60/-/- 71/-/- 61/-/- 62/-/- 94/94/1 50/79/1 71/76/1 100/100/1 77/-/1 71/-/- 56/-/- O.latifolia BOP204878C 75/83/1 O.rhizomatis EU503439.1 O.officinalis EF578070.1+EF578233.1 O.officinalis 104972 O.officinalis BOP022700 O.eichingeri BOP022656 O.eichingeri EU503440.1 O.eichingeri BOP022646 O.latifolia BOP022669 100/100/1 O.schweinfurthiana BOP022678 O.alta BOP022645 O.minuta BOP022670 O.grandiglumis BOP022694 O.rhizomatis BOP204880 O.minuta BOP022670 O.rufipogon 105480 O.rufipogon EF578068.1+EF578231.1 O.sativa subsp.japonicaAP014967.1 O.sativa subsp.japonicaAC119671.4 O.sativa subsp.indicaCP012619.1 O.sativa subsp.indicaCP018167.1+CP018157.1 O.sativa subsp.indicaCP012609.1 O.nivara BOP022699 O.alta BOP022645 O.malampuzhaensis BOP204667 O.meridionalis BOP022667 O.glumipatula BOP022657 O.barthii BOP022652 O.grandiglumis BOP022694 O.barthii EU503438.1 O.barthii BOP022651 O.latifolia BOP022669 O.punctata EF578069.1+EF578232.1 O.punctata 103903 O.schweinfurthiana BOP022678 O.latifolia BOP204878 O.punctata BOP022676 O.rufipogon BOP022682 O.malampuzhaensis BOP204667 O.australiensis BOP022647 O.australiensis EF578071.1+EF578234.1 O.australiensis 105263 K C B H J G E F A