ArticleBMC genomics2014
The transcriptome of the NZ endemic sea urchin Kina (Evechinus chloroticus).
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 28 citations in OpenAlex.
- Article
- Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius.Genes & genomics · 2019Article
- Little evidence of adaptation potential to ocean acidification in sea urchins living in "Future Ocean" conditions at a COEcology and evolution · 2019Article
- A phylogenomic resolution of the sea urchin tree of life.BMC evolutionary biology · 2018Article
- Gene expression profiling during the embryo-to-larva transition in the giant red sea urchinEcology and evolution · 2017Article
- Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus.Scientific reports · 2016Article
- Structure and function of echinoderm telomerase RNA.RNA (New York, N.Y.) · 2016Article
- De Novo Adult Transcriptomes of Two European Brittle Stars: Spotlight on Opsin-Based Photoreception.PloS one · 2016Article
- Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes.Frontiers in genetics · 2015Review
- De Novo Assembly and Characterization of the Invasive Northern Pacific Seastar Transcriptome.PloS one · 2015Article
- A novel fatty acid-binding protein-like carotenoid-binding protein from the gonad of the New Zealand sea urchin Evechinus chloroticus.PloS one · 2014Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSea 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.
resultsIn 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.
conclusionsThis 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.
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