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Comp Biochem Physiol Part D Genomics Proteomics. 2019 May 30;31:100598. doi: 10.1016/j.cbd.2019.100598. [Epub ahead of print]

Transcriptome analysis of shell color-related genes in the hard clam Mercenaria mercenaria.

Author information

1
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China.
2
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
3
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
4
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China. Electronic address: tzhang@qdio.ac.cn.

Abstract

The shell color of marine bivalves shows great diversity and is considered as an economic trait. In China, the hard clam, Mercenaria mercenaria, commonly has three shell colors in the wild: red, white, and mottled. The genetic mechanisms controlling color segregation are not fully understood. In this study, RNA-seq was performed to exploit the related shell color genes and determine the genetic basis of the different shell colors. Nine sequence libraries with those three shell colors of hard clam were constructed; 406,377 transcripts and 248,251 unigenes were obtained with N50 values of 1365 and 1682 base pairs, respectively. Cluster analysis identified 363, 392, and 220 genes exclusively highly expressed in red, white, and mottled clams, respectively. We further classified differentially expressed genes (DEGs), the genes involved in lipid binding and transport, signal transduction, ATP synthesis, and other processes in the red vs white comparison were found, which may participate in red shell formation. DEGs related to signal transduction, particularly G protein-coupled receptor activity, were found in the red vs mottled comparison, suggesting that these genes might be important in mottled shell formation. In the white vs mottled comparison, DEGs involved in zinc ion binding were found. Our results provide new insights into shell color formation mechanisms in molluscs. This information could be used in selective breeding and marker-assisted breeding of this economically important clam species.

KEYWORDS:

Differential expression genes; Lipid binding and transport; Mercenaria mercenaria; Shell color; Transcriptome

PMID:
31202083
DOI:
10.1016/j.cbd.2019.100598

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