The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum)

Genome Biology and Evolution
Seyoung MunKyudong Han

Abstract

The manila clam, Ruditapes philippinarum, is an important bivalve species in worldwide aquaculture including Korea. The aquaculture production of R. philippinarum is under threat from diverse environmental factors including viruses, microorganisms, parasites, and water conditions with subsequently declining production. In spite of its importance as a marine resource, the reference genome of R. philippinarum for comprehensive genetic studies is largely unexplored. Here, we report the de novo whole-genome and transcriptome assembly of R. philippinarum across three different tissues (foot, gill, and adductor muscle), and provide the basic data for advanced studies in selective breeding and disease control in order to obtain successful aquaculture systems. An approximately 2.56 Gb high quality whole-genome was assembled with various library construction methods. A total of 108,034 protein coding gene models were predicted and repetitive elements including simple sequence repeats and noncoding RNAs were identified to further understanding of the genetic background of R. philippinarum for genomics-assisted breeding. Comparative analysis with the bivalve marine invertebrates uncover that the gene family related to complement C1q was e...Continue Reading

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Feb 20, 2019·Scientific Data·Huimin CaiJian Wang
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Methods Mentioned

BETA
environmental stress
RNA-Seq
GTPase
PCR

Software Mentioned

RepeatModeler
INFERNAL
AUGUTUS
TGICL
FigTree
LongRead
HaploMerger
ET
perl
R

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