First draft genome for the sand-hopper Trinorchestia longiramus

Ajit Kumar Patra, Oksung Chung, Ji Yong Yoo, Min Seop Kim, Moon Geun Yoon, Jeong Hyeon Choi, Youngik Yang

Research output: Contribution to journalArticle

Abstract

Crustacean amphipods are important trophic links between primary producers and higher consumers. Although most amphipods occur in or around aquatic environments, the family Talitridae is the only family found in terrestrial and semi-terrestrial habitats. The sand-hopper Trinorchestia longiramus is a talitrid species often found in the sandy beaches of South Korea. In this study, we present the first draft genome assembly and annotation of this species. We generated ~380.3 Gb of sequencing data assembled in a 0.89 Gb draft genome. Annotation analysis estimated 26,080 protein-coding genes, with 89.9% genome completeness. Comparison with other amphipods showed that T. longiramus has 327 unique orthologous gene clusters, many of which are expanded gene families responsible for cellular transport of toxic substances, homeostatic processes, and ionic and osmotic stress tolerance. This first talitrid genome will be useful for further understanding the mechanisms of adaptation in terrestrial environments, the effects of heavy metal toxicity, as well as for studies of comparative genomic variation across amphipods.

Original languageEnglish (US)
Article number85
JournalScientific Data
Volume7
Issue number1
DOIs
StatePublished - Dec 1 2020
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences

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    Patra, A. K., Chung, O., Yoo, J. Y., Kim, M. S., Yoon, M. G., Choi, J. H., & Yang, Y. (2020). First draft genome for the sand-hopper Trinorchestia longiramus. Scientific Data, 7(1), [85]. https://doi.org/10.1038/s41597-020-0424-8