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Related Experiment Video

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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
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A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia.

Nina Overgaard Therkildsen1, Hannes Baumann2

  • 1Department of Biology, Hopkins Marine Station, Stanford University, 120 Ocean View Blvd, CA-93950 Pacific Grove, USA.

Marine Genomics
|September 5, 2020
PubMed
Summary

Researchers developed the first Atlantic silverside (Menidia menidia) reference transcriptome. This crucial genomic resource enables molecular studies of phenotypic variation in this ecologically important fish species.

Keywords:
Atlantic silversideMenidia menidiaRNA-seqTranscriptomede novo assembly

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Area of Science:

  • Genomics
  • Marine Biology
  • Ecology

Background:

  • The Atlantic silverside (Menidia menidia) is vital for ecological and evolutionary studies.
  • Lack of genomic data has limited understanding of its phenotypic variation at the molecular level.

Purpose of the Study:

  • To create the first reference transcriptome for the Atlantic silverside (Menidia menidia).
  • To provide a foundational genomic resource for future molecular research on this species.

Main Methods:

  • RNA-sequencing data from diverse individuals, tissues, and life stages were used.
  • De novo assembly using Trinity and CLC Genomics Workbench.
  • Stringent filtering and functional annotation (Gene Ontology, InterProScan) were applied.

Main Results:

  • A final assembly of 20,998 representative contigs (53.3 Mb) was generated.
  • 91% of contigs were functionally annotated.
  • High coverage (>95%) of conserved eukaryotic core genes was achieved.

Conclusions:

  • The presented reference transcriptome is a valuable resource for Atlantic silverside research.
  • Enables investigation into the molecular basis of phenotypic diversity.
  • Facilitates future studies in evolutionary biology, ecology, and physiology.