Novel transcriptome resources for three scleractinian coral species from the Indo-Pacific

Abstract

Transcriptomic resources for coral species can provide insight into coral evolutionary history and stress-response physiology. Goniopora columna, Galaxea astreata, and Galaxea acrhelia are scleractinian corals of the Indo-Pacific, representing a diversity of morphologies and life-history traits. G. columna and G. astreata are common and cosmopolitan, while G. acrhelia is largely restricted to the coral triangle and Great Barrier Reef. Reference transcriptomes for these species were assembled from replicate colony fragments exposed to elevated (31°C) and ambient (27°C) temperatures. Trinity was used to create de novo assemblies for each species from 92–102 million raw Illumina Hiseq 2 × 150 bp reads. Host-specific assemblies contained 65 460–72 405 contigs, representing 26 693–37 894 isogroups (∼genes) with an average N50 of 2254. Gene name and/or gene ontology annotations were possible for 58% of isogroups on average. Transcriptomes contained 93.1–94.3% of EuKaryotic Orthologous Groups comprising the core eukaryotic gene set, and 89.98–91.92% of the single-copy metazoan core gene set orthologs were complete, indicating fairly comprehensive assemblies. This work expands the complement of transcriptomic resources available for scleractinian coral species, including the first reference for a representative of Goniopora spp. as well as species with novel morphology.

Development of a Novel Reference Transcriptome for Scleractinian Coral Porites lutea Using Single-Molecule Long-Read Isoform Sequencing (Iso-Seq)

“…Mean GC content of the coral-specific assembly was 42.04%, which was comparable to the numbers reported for other anthozoan transcriptomes (Figure 1) (Shinzato et al, 2014;Anderson et al, 2016;Mansour et al, 2016;Frazier et al, 2017;Kenkel and Bay, 2017). Mean GC content of the Symbiodinium transcripts (51.77%) was also consistent with previous reports (Bayer et al, 2012;Shinzato et al, 2014;Mansour et al, 2016).…”

“…To identify the taxonomic origin of the remaining contigs, transcript sequences were queried against a custom database of publicly available Cnidarian transcriptomes and genomic sequences using BLASTN. The Cnidarian database contains transcriptome sequences from Acropora millepora (Moya et al, 2012), Acropora hyacinthus (Barshis et al, 2013), A. tenuis (Kenkel and Bay, 2017), Montastraea cavernosa (Kitchen et al, 2015), Seriatopora hystrix (Kitchen et al, 2015), Fungia scutaria (Kitchen et al, 2015), Porites astreoides (Kenkel et al, 2013), P. lobata (Kenkel and Bay, 2017), Montipora aequituberculata (Kenkel and Bay, 2017), Galaxea archelia (Kenkel and Bay, 2017), Galaxea astreata (Kenkel and Bay, 2017), Goniopora columna (Kenkel and Bay, 2017), Siderastrea siderea (Davies et al, 2016), Pocillopora damicornis (Traylor-Knowles et al, 2011), and genomic sequences from Acropora digitifera (Shinzato et al, 2011). The assembly was also screened against Symbiodinium transcriptome and genome sequences using BLASTN.…”

Development of an integrated genomic map for a threatened Caribbean coral (Orbicella faveolata)

“…For example, reefbuilding corals are severely threatened by rising ocean temperatures [9,10], and the development of genomic resources in these systems has historically lagged behind better studied systems like model or crop species. Transcriptome assemblies are now available for many corals [11][12][13][14][15][16][17], but while these collections of gene sequences are useful for many studies they offer no information on the relative positions of those genes within the genome. Draft genome assemblies are available for a smaller number of systems [18][19][20], but in most cases these assemblies have remained fragmented (thousands of scaffolds), lacking the long-range structural information provided by chromosome-scale assemblies.…”

Molecular convergence and positive selection associated with the evolution of symbiont transmission mode in stony corals

“…Remaining high quality filtered reads (37.7 million paired reads; 6.7 million unpaired reads) were assembled using Trinity v 2.0.6 (69) using the default parameters and an in silico read normalization step at the Texas Advanced Computing Center (TACC) at the University of Texas at Austin. Since corals are ‘holobionts’ comprised of host, Symbiodiniaceae and other microbial components, resulting assemblies were filtered to identify the host component following the protocol described in (70).…”

“…Transcriptomic data from 25 species of Scleractinia (stony corals) and 3 species of Actiniaria (anemones) were downloaded from the web (Table S1; (71); (72); (73); (74); (75); (42); (76); (77); (78); (79); (80); (81); (82); (83); (84); (70)).…”