Use Next-Generation Sequencing Data from Corals and Other Cnidaria to Illuminate the Evolution of Genes and Phenotypes by John R

Home , Acropora digitifera, Astrangia, Astrangia poculata, Stylaraea

Bioinformatics Projects Use Next-Generation Sequencing Data from Corals and other Cnidaria to Illuminate the Evolution of Genes and Phenotypes by John R. Finnerty

The Starlet Sea Anemone Nematostella vectensis

Starlet Lined Corallimorphs Cauliﬂower Northern Anemone Anemone “mushroom corals” coral star coral solitary animals, Nematostella Edwardsiella harbor photosynthetic Pocillopora Astrangia vectensis lineata algaelike corals, damicornis poculata free-living saltmarsh parasitic, marine, don’t make skeletons. tropical indo-paciﬁc temperate Atlantic & anemone anemone hard coral Caribbean coral Nematostella vectensis “Stella” the starlet sea anemone

“star-haired sword carrier” New York Times

Nematostella is an estuarine species native to saltmarsh habitats along the Atlantic coast of North America.

the holey bucket Nematostella is simple and inexpensive to culture in the laboratory.

Nematostella reproduces sexually & asexually in the lab. Nematostella develops rapidly.

Nematostella has extensive regenerative abilities. Nematostella boasts a sequenced genome (& thoroughly sequenced transcriptome) (1 of only 3 cnidarians with a sequenced genome at this time).

“The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to ﬂies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex.

Genetic & Phenotypic Polymorphism

While Nematostella’s genome has evolved relatively conservatively over deep time, the geographic isolation of estuarine habitats appears to have spawned ample genetic and phenotypic polymorphisms between populations. Temperature Adaptation Nova Scotia Boston 8 southern Cape Cod 7 New Jersey 6 South Carolina 5 4 3

(tentacles per day) 2

Tentacle Regeneration Rate Tentacle 1 0 13°C 21°C 29°C Nematostella is amenable to a wide range of organismal, molecular, and reverse-genetic protocols.

The Lined Sea Anemone Edwardsiella lineata

comb jelly

parasites

larva

Ecological Impact of the host Sea walnut in the black sea Introduced in early 1980’s in ship ballast water. By 1990, its biomass was estimated at 1 billion tons, or roughly the same as the biomass of all fish caught in the oceans. The anchovy catch fell from 500,000 tons to 100,000 tons from early ‘80s to 1990. Possible biological controls: the butterfish the lined sea anemone Edwardsiella lineata Are they specialists? Does “Ed” specialize on the sea walnut?

Mnemiopsis leidyi Pleurobrachia pileus Beroe ovata n = 1,865 n = 600 n = 181 infected: 34% infected: 0% infected: 96% parasites/host: 3.41 parasites/host: 13.88

How does Ed gain entry to its hosts?

Mnemiopsis (sea walnut) Beroe (“shark”)

20 / 50 hosts infected 0 / 16 hosts infected. Burrows through body wall. No entry even with contact. Enters through mouth. “Immune” response? How does Ed gain entry to its hosts?

In 6 of 7 trials, when Beroe ate an infected sea walnut, it became infected. (a novel finding.)

Based on this transfer rate, and knowing the average # of parasites in a sea walnut, the class was able to estimate that a particular wild-caught Beroe had eaten ~67 sea walnuts

Does its host affect Ed’s development?

70 Mnemiopsis adult 60 50 40 30 20

% develop into adult 10 Beroe 0 larva 0 10 20 30 40 50 60 parasite days after parasite is surgically excised from host Why is there an effect of host species?

Mnemiopsis adult 100

y=0.404Ln(x) + 0.0056 80 R2=0.93 p<0.0001

40 y=0.575Ln(x) - 0.223 2

% develop into adult R =0.74 20 p<0.006 Beroe

larva 5 10 15 parasite length of parasite in millimeters

Marine Invertebrates larva

comb jelly How has the parasite’s unique developmental program evolved? parasites

larva

New life cycle stage. New body plan. polyp parasite Novel developmental program. Novel developmental regulatory gene cascade. Novel gene expression pattern.

host present host absent

larva

Mushroom Corals (aka false corals; anemone corals) order Corallimopharia

Corallimorpharia (Stephenson 1937) A lineage of hexacorallian anthozoans Likely sister-group to the hard corals (Scleractinia) 50 species Solitary polyps (not colonial) Do not build skeletons. Some species form symbioses with photosynthetic zooxanthellae. Tentacles are reduced in length or absent. Can prey on macroscopic animals by enveloping them with their oral discs and long nematocysts. Marine Genomics, class of 2011

Transcriptomic sequencing of corallimorphs subjected to variable salinities (21, 31 or 41 ppt).

Discosoma sp Cauliflower Coral Pocillopora damicornis

The Cauliﬂower Coral —Pocillopora damicornis The Cauliﬂower Coral —Pocillopora damicornis

a new lab model being developed at BU populations that can tolerate diverse & challenging habitats harbors substantial within-species variation. among the coral stocks we are growing, dramatic differences in the ability to tolerate acute exposure to low salinity. Northern Star Coral Astrangia poculata

Astrangia is facultatively symbiotic

It can survive for prolonged periods in zooxanthellate/symbiotic or azooxanthellate/ aposymbiotic states. It has an extremely large latitudinal range (Caribbean to Cape Cod). It is extremely cold- tolerant. Madracis ROBUSTA Stenocyathus caryophylliids Pocilloporidae Pocillopora damicornis Madrepora caryophylliids siderastreids siderastreids + Leptastrea Fungiidae Plocoida faviinids + meandriinids Astrangia Montastrea faveolata caryophylliids Anthemiphylliidae Pseudosiderastrea Thalamophyllia Galaxea COMPLEXA Agariciidae Astreopora Alveopora Acropora digitifera Acropora, Anacropora, Montipora Acropora millepora Guynia Acropora palmata Stephanocoenia Bathycola Siderastrea Porites asteroides Porites, Goniopora, Poritipora, Stylaraea Porites compressa Dendrophylliidae Northern Star Coral Astrangia poculata KINDS of QUESTIONS we could ask about the transcriptome.

HOW GOOD (COMPLETE) IS THIS Astrangia TRANSCRIPTOME? SEQUENCING & ASSEMBLING A TRANSCRIPTOME

SEQUENCING & ASSEMBLING A TRANSCRIPTOME SEQUENCING & ASSEMBLING A TRANSCRIPTOME

SEQUENCING & ASSEMBLING A TRANSCRIPTOME HOW GOOD (COMPLETE) IS THIS Astrangia TRANSCRIPTOME? Certain multi-gene families have been well characterized in other Cnidaria. Assume that these gene families are generally well conserved between cnidarians so all members of the gene family are likely to be present in Astrangia. APPROACH: Search the transcriptome to identify all members of the gene family (if present) and determine whether (i) the full sequences are present and (ii) the structure of the proteins are conserved. CANDIDATE GENE FAMILIES: HOX genes WNT genes GiMAP genes Cnidocyte speciﬁc genes: e.g., Minicollagens and/or toxins

HOX GENES Transcription factors involved in setting up different regions of the anterior- posterior axis in triploblastic animals. Organized in conserved genomic clusters. HOX GENES Involved in dramatic homeotic mutations.

HOX GENES Presence of conserved Hox clusters in Cnidaria and role during development is disputed. WNT GENES Secreted factors that help to control developmental decisions during embryogenesis. A “Wnt-code” may help to set up the oral-aboral axis of the cnidarian polyp.

GiMap GENES Implicated in innate immunity in mammals but absent in Drosophila, Caenorhabditis, and Nematostella.

BMC Genomics. 2013 Jun 14;14:400. doi: 10.1186/1471-2164-14-400. The acute transcriptional response of the coral Acropora millepora to immune challenge: expression of GiMAP/IAN genes links the innate immune responses of corals with those of mammals and plants. Cnidocyte-specific GENES

The possession of cnidocytes is the deﬁning characteristic of Cnidaria. The origin of this venom delivery cell-type involved the origin of new structural proteins (minicollagens) and toxin proteins.

PLoS One. 2011;6(7):e22725. doi: 10.1371/journal.pone.0022725. Epub 2011 Jul 28. Morphological and molecular analysis of the Nematostella vectensis cnidom. Zenkert C, Takahashi T, Diesner MO, Özbek S.

CAN WE IDENTIFY GENES CRITICAL TO CORAL BIOLOGY? Genes involved in CaCO3 skeletal formation.

Nature. 2011 Jul 24;476(7360):320-3. doi: 10.1038/nature10249. Using the Acropora digitifera genome to understand coral responses to environmental change. Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K, Tanaka M, Fujie M, Fujiwara M, Koyanagi R, Ikuta T, Fujiyama A, Miller DJ, Satoh N.

“A number of genes with putative roles in calcification were identified, and several of these are restricted to corals.” CAN WE IDENTIFY GENES CRITICAL TO CORAL BIOLOGY? Genes expressed by Symbiodinum.

PLoS One. 2012;7(4):e35269. doi: 10.1371/journal.pone.0035269. Epub 2012 Apr 18. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. Bayer T, Aranda M, Sunagawa S, Yum LK, Desalvo MK, Lindquist E, Coffroth MA, Voolstra CR, Medina M.

Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts.Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.

DOES ASTRANGIA POSSESS MOLECULAR NOVELTIES REPORTED IN OTHER CNIDARIA? “Complex NOD-like receptor repertoire” reported in the staghorn coral Acropora digitifera. This is a group of genes implicated in innate immunity.

Mol Biol Evol. 2013 Jan;30(1):167-76. doi: 10.1093/molbev/mss213. Epub 2012 Aug 30. The complex NOD-like receptor repertoire of the coral Acropora digitifera includes novel domain combinations. Hamada M, Shoguchi E, Shinzato C, Kawashima T, Miller DJ, Satoh N. DOES ASTRANGIA POSSESS MOLECULAR NOVELTIES REPORTED IN OTHER CNIDARIA? Absence of key genes involved in circadian rhythm regulation.

Gene. 2013 Feb 25;515(2):426-31. doi: 10.1016/j.gene.2012.12.038. Epub 2012 Dec 20. A genome-wide survey of photoreceptor and circadian genes in the coral, Acropora digitifera. Shoguchi E, Tanaka M, Shinzato C, Kawashima T, Satoh N.

“Corals exhibit circadian behaviors, but little is known about the molecular mechanisms underlying the regulation of these behaviors. We surveyed the recently decoded genome of the coral, Acropora digitifera, for photoreceptor and circadian genes, using molecular phylogenetic analyses. Our search for photoreceptor genes yielded seven opsin and three cryptochrome genes. Two genes from each family likely underwent tandem duplication in the coral lineage. We also found the following A. digitifera orthologs to Drosophila and mammalian circadian clock genes: four clock, one bmal/cycle, three pdp1-like, one creb/ atf, one sgg/zw3, two ck2alpha, one dco (csnk1d/cnsk1e), one slim/BTRC, and one grinl. No vrille, rev-ervα/nr1d1, bhlh2, vpac2, adcyap1, or adcyaplr1 orthologs were found. Intriguingly, in spite of an extensive survey, we also failed to find homologs of period and timeless, although we did find one timeout gene. In addition, the coral genes were compared to orthologous genes in the sea anemone, Nematostella vectensis. Thus, the coral and sea anemone genomes share a similar repertoire of circadian clock genes, although A. digitifera contains more clock genes and fewer photoreceptor genes than N. vectensis. This suggests that the circadian clock system was established in a common ancestor of corals and sea anemones, and was diversified by tandem gene duplications and the loss of paralogous genes in each lineage. It will be interesting to determine how the coral circadian clock functions without period.”

DOES ASTRANGIA POSSESS MOLECULAR NOVELTIES REPORTED IN OTHER CNIDARIA? An expansion in the number of ﬂuorescent proteins.

Zoolog Sci. 2012 Apr;29(4):260-4. doi: 10.2108/zsj.29.260. Fluorescent protein candidate genes in the coral Acropora digitifera genome. Shinzato C, Shoguchi E, Tanaka M, Satoh N.

“The vivid coloration of corals depends on fluorescent proteins that include cyan (CFP), green (GFP) and red (RFP) fluorescent proteins, and a non-fluorescent blue/purple chromoprotein. We examined how many genes encoding fluorescent proteins are present in the recently sequenced genome of the coral Acropora digitifera. Based on molecular phylogenetic analysis, we found one, five, one, and three candidate genes for CFP, GFP, RFP, and chromoprotein, respectively. The CFP and GFP genes are clustered in a ~80-kb-long genomic region, suggesting that they originated from an ancestral gene by tandem duplication. Since CFP and GFP possess the same chromophore, the gene clustering may provide the first genomic evidence for a common origin of the two proteins. Comparison between the fluorescent protein genes of closely related coral species suggests an expansion of chromoprotein genes in the A. digitifera genome, and of RFP genes in the A. millepora genome. The A. digitifera fluorescent protein genes are expressed during embryonic and larval developmental stages and in adults, suggesting that the genes play a variety of roles in coral physiology.” Stella Ed Mushroom Cauliﬂower Star

sequenced YES NO NO NO NO genome

sequenced YES YES YES YES YES transcriptome

stellabase.org skinnybastard.bu.edu skinnybastard.bu.edu access via edwardsiellabase.org pocilloporabase.org or NCBI (click “edbase”) (click “stellabase”)

Stella Ed Mushroom Cauliﬂower Star

sybiosis with YES YES YES NO NO Symbiodinium (constitutive?) (constitutive) (facultative)

sequenced YES YES YES YES YES transcriptome

stellabase.org skinnybastard.bu.edu skinnybastard.bu.edu access via edwardsiellabase.org pocilloporabase.org or NCBI (click “edbase”) (click “stellabase”)