DOI: 10.5061/dryad.3f08f
title: Data from: De novo assembly and characterization of four anthozoan (phylum Cnidaria) transcriptomes

description: Many nonmodel species exemplify important biological questions but lack
 the sequence resources required to study the genes and genomic regions
 underlying traits of interest. Reef-building corals are famously sensitive
 to rising seawater temperatures, motivating ongoing research into their
 stress responses and long-term prospects in a changing climate. A
 comprehensive understanding of these processes will require extending
 beyond the sequenced coral genome (Acropora digitifera) to encompass
 diverse coral species and related anthozoans. Toward that end, we have
 assembled and annotated reference transcriptomes to develop catalogs of
 gene sequences for three scleractinian corals (Fungia scutaria,
 Montastraea cavernosa, Seriatopora hystrix) and a temperate anemone
 (Anthopleura elegantissima). High-throughput sequencing of cDNA libraries
 produced ∼20-30 million reads per sample, and de novo assembly of these
 reads produced ∼75,000-110,000 transcripts from each sample with size
 distributions (mean ∼1.4 kb, N50 ∼2 kb), comparable to the distribution of
 gene models from the coral genome (mean ∼1.7 kb, N50 ∼2.2 kb). Each
 assembly includes matches for more than half the gene models from A.
 digitifera (54-67%) and many reasonably complete transcripts (∼5300-6700)
 spanning nearly the entire gene (ortholog hit ratios ≥0.75). The catalogs
 of gene sequences developed in this study made it possible to identify
 hundreds to thousands of orthologs across diverse scleractinian species
 and related taxa. We used these sequences for phylogenetic inference,
 recovering known relationships and demonstrating superior performance over
 phylogenetic trees constructed using single mitochondrial loci. The
 resources developed in this study provide gene sequences and genetic
 markers for several anthozoan species. To enhance the utility of these
 resources for the research community, we developed searchable databases
 enabling researchers to rapidly recover sequences for genes of interest.
 Our analysis of de novo assembly quality highlights metrics that we expect
 will be useful for evaluating the relative quality of other de novo
 transcriptome assemblies. The identification of orthologous sequences and
 phylogenetic reconstruction demonstrates the feasibility of these methods
 for clarifying the substantial uncertainties in the existing scleractinian
 phylogeny.
description: Anthopleura
 elegantissima de novo transcriptome assembly v1.0An annotated de novo
 transcriptome assembly produced from a nominally aposymbiotic specimen of
 Anthopleura elegantissima collected from Seal Rock, OR, USA. Sequences
 were pre-processed to exclude low quality or uninformative reads, then
 assembled using Trinity. The raw data used to produce this assembly can be
 found at NCBI's SRA, accession number SRP063463. The assembly can be
 searched by gene name or functional terms using the following database:
 http://ib.oregonstate.edu/~meyere/DB/Aele/search.php.Aele_transcriptome_v1.fasta.gzFungia scutaria de novo transcriptome assembly v1.0An annotated de novo transcriptome assembly produced from aposymbiotic planula larvae of Fungia scutaria on Coconut Island, HI, USA. Sequences were pre-processed to exclude low quality or uninformative reads, then assembled using Trinity. The raw data used to produce this assembly can be found at NCBI's SRA, accession number SRP063463. The assembly can be searched by gene name or functional terms using the following database: http://ib.oregonstate.edu/~meyere/DB/Fscu/search.php.Fscu_transcriptome_v1.fasta.gzMontastraea cavernosa de novo transcriptome assembly v1.0An annotated de novo transcriptome assembly produced from an adult specimen of Montastraea cavernosa collected from the Florida Keys, FL, USA. Sequences were pre-processed to exclude low quality or uninformative reads, then assembled using Trinity. The raw data used to produce this assembly can be found at NCBI's SRA, accession number SRP063463. The assembly can be searched by gene name or functional terms using the following database: http://ib.oregonstate.edu/~meyere/DB/Mcav/search.php.Mcav_transcriptome_v1.fasta.gzSeriatopora hystrix de novo transcriptome assembly v.10An annotated de novo transcriptome assembly produced from an adult specimen of Seriatopora hystrix collected from Nanwan Bay, Taiwan. Sequences were pre-processed to exclude low quality or uninformative reads, then assembled using Trinity. The raw data used to produce this assembly can be found at NCBI's SRA, accession number SRP063463. The assembly can be searched by gene name or functional terms using the following database: http://ib.oregonstate.edu/~meyere/DB/Shys/search.php.Shys_transcriptome_v1.fasta.gz