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BMC Genomics
2014 Jan 20;15:45. doi: 10.1186/1471-2164-15-45.
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The transcriptome of the NZ endemic sea urchin Kina (Evechinus chloroticus).
Gillard GB
,
Garama DJ
,
Brown CM
.
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BACKGROUND: Sea urchins are studied as model organisms for developmental and systems biology and also produce highly valued food products. Evechinus chloroticus (Kina) is a sea urchin species that is indigenous to New Zealand. It is the type member of the Evechinus genus based on its morphological characteristics. Previous research has focused on identifying physical factors affecting commercial roe quality of E. chloroticus, but there is almost no genetic information available for E. chloroticus. E. chloroticus is the only species in its genus and has yet to be subject to molecular phylogenetic analysis.
RESULTS: In this study we performed a de novo transcriptome assembly of Illumina sequencing data. A total of 123 million 100 base length paired-end reads were generated using RNA-Seq libraries from a range of E. chloroticus tissues from two individuals obtained from Fiordland, New Zealand. The assembly resulted in a set of 75,002 transcripts with an accepted read coverage and length, of which 24,655 transcripts could be functionally annotated using protein similarity. Transcripts could be further annotated with Gene Ontology, KEGG Orthology and InterPro terms. With this sequence data we could perform the first phylogenetic analysis of E. chloroticus to other species of its family using multiple genes. When sequences for the mitochondrial nitrogen dehydrogenase genes were compared, E. chloroticus remained outside of a family level clade, which indicated E. chloroticus is indeed a genetically distinct genus within its family.
CONCLUSIONS: This study has produced a large set of E. chloroticus transcripts/proteins along with functional annotations, vastly increasing the amount of genomic data available for this species. This provides a resource for current and future studies on E. chloroticus, either to increase its commercial value, or its use as a model organism. The phylogenetic results provide a basis for further analysis of relationships between E. chloroticus, its family members, and its evolutionary history.
Figure 1. Length distribution of assembled transcripts for total and reduced datasets. The sizes of the Trinity assembled transcripts are shown. The reduced set has an FPKM >0.5.
Figure 2. Protein length coverage against S. purpuratus proteins. Most matches to S. purpuratus fall into the top bin (100-91%).
Figure 3. BLASTX annotation results. (A) Proportions of transcripts with BLASTX matches and GO terms annotated. (B) Distribution of E-values for the top hit for each transcript. (C) Distribution of species for the top hit for each transcript. Analysis by Blast2GO. The data is available on the accompanying website.
Figure 4. Heatmap of most highly expressed transcripts from each tissue. Heatmap showing the log2 FPKM values of most abundant transcripts. The colour legend shows the log2 FPKM values each represents. Rows were clustered based on Euclidean distance.
Figure 5. GO annotations. Top 10 represented GO terms for each of the GO categories; Molecular Function, Biological Process and Cellular Component. GO terms annotated by protein similarity to the NCBI non-redundant database and from InterProScan results.
Figure 6. InterPro annotations. Top 10 represented InterPro terms from the InterProScan annotations.
Figure 7. KEGG pathway annotations. Top 10 represented KEGG pathways using EC (Enzyme Commission) annotations, derived from GO annotations. Shown is the number of transcripts matching to each pathway and the number of EC numbers represented in the pathways.
Figure 8. KO annotations. Top 10 represented KO terms from the KAAS annotation results.
Figure 9. Phylogenetic trees. Resulting trees for the phylogenetic analysis of Echinometridae species based on the nucleotide sequences of ND1, ND2 and combined ND1-ND2 genes. Trees were constructed using neighbour-joining (NJ), maximum-likelihood (ML), and Bayesian inference (Bayes) methods. Numbers at each internal node represent the bootstrap percentage values for the nodes support. The scale bar represents base substitutions per site. Shown are the: ND1-ND2 NJ (A), ML (B), Bayes (C) trees; ND1 NJ (D), ML (E), Bayes (F) trees; and ND2 NJ (G), ML (H), Bayes (I) trees.
Blackburn,
Telomerase: an RNP enzyme synthesizes DNA.
2011, Pubmed
Blackburn,
Telomerase: an RNP enzyme synthesizes DNA.
2011,
Pubmed
Camacho,
BLAST+: architecture and applications.
2010,
Pubmed
Cameron,
Evolution of the chordate body plan: new insights from phylogenetic analyses of deuterostome phyla.
2000,
Pubmed
Conesa,
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
2005,
Pubmed
Cox,
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.
2011,
Pubmed
Fu,
CD-HIT: accelerated for clustering the next-generation sequencing data.
2013,
Pubmed
Garama,
Extraction and analysis of carotenoids from the New Zealand sea urchin Evechinus chloroticus gonads.
2012,
Pubmed
,
Echinobase
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2012,
Pubmed
Guindon,
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
2010,
Pubmed
Hasegawa,
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.
1986,
Pubmed
Hibino,
The immune gene repertoire encoded in the purple sea urchin genome.
2007,
Pubmed
,
Echinobase
Huelsenbeck,
MRBAYES: Bayesian inference of phylogenetic trees.
2001,
Pubmed
Hunter,
InterPro in 2011: new developments in the family and domain prediction database.
2012,
Pubmed
Jurka,
Repbase Update, a database of eukaryotic repetitive elements.
2005,
Pubmed
Kinjo,
Evolutionary history of larval skeletal morphology in sea urchin Echinometridae (Echinoidea: Echinodermata) as deduced from mitochondrial DNA molecular phylogeny.
2008,
Pubmed
,
Echinobase
Langmead,
Fast gapped-read alignment with Bowtie 2.
2012,
Pubmed
Langmead,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
2009,
Pubmed
Li,
Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach.
2013,
Pubmed
,
Echinobase
Moriya,
KAAS: an automatic genome annotation and pathway reconstruction server.
2007,
Pubmed
Parra,
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
2007,
Pubmed
Pilbrow,
Carotenoid-binding proteins; accessories to carotenoid function.
2012,
Pubmed
,
Echinobase
Quevillon,
InterProScan: protein domains identifier.
2005,
Pubmed
Smith,
Diversification of innate immune genes: lessons from the purple sea urchin.
2010,
Pubmed
,
Echinobase
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Tu,
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis.
2013,
Pubmed
,
Echinobase