ArticleMarine biotechnology (New York, N.Y.)2014
De novo transcriptome sequencing of the snail Echinolittorina malaccana: identification of genes responsive to thermal stress and development of genetic markers for population studies.
Article in Marine biotechnology (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 38 citations in OpenAlex.
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- Sequencing of Transcriptome and Small RNA Revealed the Xenobiotic Metabolism-Related Genes and Potential Regulatory miRNA in Asian Tramp Snail.Frontiers in genetics · 2020Article
- Genetic Constraints, Transcriptome Plasticity, and the Evolutionary Response to Climate Change.Frontiers in genetics · 2020Article
- Transcriptomic Profiling Provides Insights into Inbreeding Depression in Yesso Scallop Patinopecten yessoensis.Marine biotechnology (New York, N.Y.) · 2019Article
- A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora.iScience · 2019Article
- Transcriptomic Analysis Reveals Insights on Male Infertility inFrontiers in physiology · 2018Article
- Transcriptomic response to thermal and salinity stress in introduced and native sympatric Palaemon caridean shrimps.Scientific reports · 2017Article
- Locally adapted populations of a copepod can evolve different gene expression patterns under the same environmental pressures.Ecology and evolution · 2017Article
- Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers.Molecular genetics and genomics : MGG · 2016Article
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- De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology.International journal of molecular sciences · 2016Article
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- Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing.PloS one · 2015Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Echinolittorina snails inhabit the upper intertidal rocky shore and face strong selection pressures from thermal extremes and fluctuations. Revealing the molecular processes of adaptive significance is greatly obstructed by the scarcity of genomic resource for these taxa. Here, we reported the first comprehensive transcriptome dataset for the genus Echinolittorina. Using Illumina HiSeq 2000 platform, about 52 M and 54 M paired-end clean reads were, respectively, generated for the control and heat-stressed libraries. Totally, 115,211 unique transcript fragments (unigenes) were assembled, with an average length of 453 bp and a N50 size of 492 bp. Approximately one third of the unigenes could be annotated according to their homology matches against the Nr, Swiss-Prot, COG, or KEGG databases, and they were found to represent 23,098 non-redundant genes. Gene expression comparison revealed that 1,267 and 6,663 annotated genes were, respectively, up- and downregulated with at least twofold changes upon heat stress. Gene Ontology and KEGG pathway analyses indicated that there were overrepresented amount of genes enriched in a broad spectrum of biological processes and pathways, including those associated with cytoskeleton organization, developmental regulation, signaling transduction, infection, and cardiac function. In addition, a transcriptome-wide search for polymorphic loci yielded a total of 11,228 simple sequence repeats (SSRs) from 9,938 unigenes and 138,631 single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) sites among 22,770 unigenes. The large number of transcript sequences acquired, the biological pathways identified, and the candidate microsatellite and SNP/INDEL loci discovered in the study will serve as valuable resources for further investigations of genetic differentiation and thermal adaptation among populations.
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