The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth

Honglin Luo; Yongde Zhang; Fuyan Liu; Yongzhen Zhao; Jinxia Peng; Yuhui Xu; Xiuli Chen; Yin Huang; Changmian Ji; Qingyun Liu; Pingping He; Pengfei Feng; Chunling Yang; Pinyuan Wei; Zhenhua Ma; Jianguang Qin; Shengjie Zhou; Shiming Dai; Yaoyao Zhang; Zhongquan Zhao; Hongling Liu; Hongkun Zheng; Jisen Zhang; Yong Lin; Xiaohan Chen

Journal of Advanced Research (Nov 2024)

The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth

Honglin Luo,
Yongde Zhang,
Fuyan Liu,
Yongzhen Zhao,
Jinxia Peng,
Yuhui Xu,
Xiuli Chen,
Yin Huang,
Changmian Ji,
Qingyun Liu,
Pingping He,
Pengfei Feng,
Chunling Yang,
Pinyuan Wei,
Zhenhua Ma,
Jianguang Qin,
Shengjie Zhou,
Shiming Dai,
Yaoyao Zhang,
Zhongquan Zhao,
Hongling Liu,
Hongkun Zheng,
Jisen Zhang,
Yong Lin,
Xiaohan Chen

Affiliations

Honglin Luo: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; Institute of Oncology, Guangxi Academy of Medical Sciences, Nanning, Guangxi 530021, China
Yongde Zhang: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Fuyan Liu: Biomarker Technologies, Beijing 101300, China; BGI-Beijing, Beijing 102601, China
Yongzhen Zhao: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Jinxia Peng: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Yuhui Xu: Biomarker Technologies, Beijing 101300, China
Xiuli Chen: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Yin Huang: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Changmian Ji: Biomarker Technologies, Beijing 101300, China
Qingyun Liu: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Pingping He: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Pengfei Feng: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Chunling Yang: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Pinyuan Wei: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
Zhenhua Ma: South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
Jianguang Qin: College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
Shengjie Zhou: Sanya Tropical Fisheries Research Institute, Sanya 572018, China
Shiming Dai: Sanya Tropical Fisheries Research Institute, Sanya 572018, China
Yaoyao Zhang: The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
Zhongquan Zhao: College of Animal Science and Technology, Southwest University, Beibei, Chongqing 400715, China
Hongling Liu: Biomarker Technologies, Beijing 101300, China
Hongkun Zheng: Biomarker Technologies, Beijing 101300, China; Corresponding authors at: Biomarker Technologies, Beijing 101300, China (H. Zheng). Center for Genomics and Biotechnology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China (J. Zhang).
Jisen Zhang: Center for Genomics and Biotechnology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China; Corresponding authors at: Biomarker Technologies, Beijing 101300, China (H. Zheng). Center for Genomics and Biotechnology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China (J. Zhang).
Yong Lin: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; Corresponding authors at: Biomarker Technologies, Beijing 101300, China (H. Zheng). Center for Genomics and Biotechnology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China (J. Zhang).
Xiaohan Chen: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; Corresponding authors at: Biomarker Technologies, Beijing 101300, China (H. Zheng). Center for Genomics and Biotechnology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China (J. Zhang).

Journal volume & issue: Vol. 65
pp. 1 – 17

Abstract

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Introduction: Golden pompano (Trachinotus ovatus) is economically significant important for offshore cage aquaculture in China and Southeast Asian countries. Lack of high-quality genomic data and accurate gene annotations greatly restricts its genetic breeding progress. Objectives: To decode the mechanisms of sex determination and rapid growth in golden pompano and facilitate the sex- and growth-aimed genetic breeding. Methods: Genome assemblies of male and female golden pompano were generated using Illumina, PacBio, BioNano, genetic maps and Hi-C sequencing data. Genomic comparisons, whole genome re-sequencing of 202 F1 individuals, QTL mapping and gonadal transcriptomes were used to analyze the sex determining region, sex chromosome evolution, SNP loci, and growth candidate genes. Zebrafish model was used to investigate the functions of growth candidate gene. Results: Female (644.45 Mb) and male (652.12 Mb) genomes of golden pompano were assembled and annotated at the chromosome level. Both genomes are highly conserved and no new or highly differentiated sex chromosomes occur. A 3.5 Mb sex determining region on LG15 was identified, where Hsd17b1, Micall2 and Lmx1a were putative candidates for sex determination. Three SNP loci significantly linked to growth were pinpointed, and a growth-linked gene gpsstr1 was identified by locus BSNP1369 (G → C, 17489695, Chr23). Loss of sstr1a (homologue of gpsstr1) in zebrafish caused growth retardation. Conclusion: This study provides insights into sex chromosome evolution, sex determination and rapid growth of golden pompano.

Published in Journal of Advanced Research

ISSN: 2090-1232 (Print); 2090-1224 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Medicine: Medicine (General); Science: Science (General)
Website: http://www.journals.elsevier.com/journal-of-advanced-research/

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