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Gene. 2014 Dec 1;552(2):265-71. doi: 10.1016/j.gene.2014.09.053. Epub 2014 Sep 28.

Transcriptome analysis reveals positive selection on the divergent between topmouth culter and zebrafish.

Author information

1
Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
2
Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore. Electronic address: dbshyh@nus.edu.sg.
3
Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China. Electronic address: lsj@hunnu.edu.cn.

Abstract

The topmouth culter (Erythroculter ilishaeformis) is a predatory cyprinid fish that distributes widely in the East Asia. Here we report the liver transcriptome in this organism as a model of predatory fish. Sequencing of 5 Gb raw reads led to 27,741 unigenes and produced 11,131 annotatable genes. A total of 7093 (63.7%) genes were found to have putative functions by gene ontology analysis. Importantly, a blast search revealed 4033 culter genes that were orthologous to the zebrafish. Extracted from 38 candidate positive selection genes, 4 genes exhibit strong positive selection based on the ratio of nonsynonymous (Ka) to synonymous substitutions (Ks). In addition, the four genes also indicated the strong positive selection by comparing them between blunt snout bream (Megalobrama amblycephala) and zebrafish. These genes were involved in activator of gene expression, metabolic processes and development. The transcriptome variation may be reflective of natural selection in the early life history of Cyprinidae. Based on Ks ratios, date of the separation between topmouth culter and zebrafish is approximately 64 million years ago. We conclude that natural selection acts in diversifying the genomes between topmouth culter and zebrafish.

KEYWORDS:

Liver; Natural selection; Repeat sequence

PMID:
25267534
DOI:
10.1016/j.gene.2014.09.053
[Indexed for MEDLINE]

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