April 21, 2020  |  

Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system.

Authors: Cai, Mingyi and Zou, Yu and Xiao, Shijun and Li, Wanbo and Han, Zhaofang and Han, Fang and Xiao, Junzhu and Liu, Fujiang and Wang, Zhiyong

Collichthys lucidus (C. lucidus) is a commercially important marine fish species distributed in coastal regions of East Asia with the X1X1X2X2/X1X2Y multiple sex chromosome system. The karyotype for female C. lucidus is 2n?=?48, while 2n?=?47 for male ones. Therefore, C. lucidus is also an excellent model to investigate teleost sex-determination and sex chromosome evolution. We reported the first chromosome genome assembly of C. lucidus using Illumina short-read, PacBio long-read sequencing and Hi-C technology. An 877?Mb genome was obtained with a contig and scaffold N50 of 1.1?Mb and 35.9?Mb, respectively. More than 97% BUSCOs genes were identified in the C. lucidus genome and 28,602 genes were annotated. We identified potential sex-determination genes along chromosomes and found that the chromosome 1 might be involved in the formation of Y specific metacentric chromosome. The first C. lucidus chromosome-level reference genome lays a solid foundation for the following population genetics study, functional gene mapping of important economic traits, sex-determination and sex chromosome evolution studies for Sciaenidae and teleosts.

Journal: Scientific data
DOI: 10.1038/s41597-019-0139-x
Year: 2019

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