Population Genetic Characteristics of Hainan Medaka with Whole-genome Resequencing

Overview

Journal Front Genet

Date 2022 Oct 31

PMID 36313474

Authors

Zebin Yao

Shuisheng Long

Chun Wang

Chengqin Huang

Hairui Zhang

Liao Jian

Jingru Huang

Yusong Guo

Zhongdian Dong

Zhongduo Wang

Affiliations

Soon will be listed here.

Abstract

The gene is deleted in all males of the Sanya population (SY-medaka) of the Hainan medaka, , as recently reported by us. However, due to limited knowledge regarding their population genetic background, it is difficult to explore the possible evolutionary pathway. Herein, we resequenced the whole genome of four populations, including SY-medaka. A total of 56 mitogenomes and 32,826,105 SNPs were identified. We found that the genetic differentiation is highest between SY-medaka and the other populations. The results of the population history of the suggest that the SY-medaka has been in a bottleneck period recently. Further analysis shows that SY-medaka are the most strongly affected by environmental selection. Moreover, we screened some potential genomic regions, and the genes contained in these regions may explain the potential mechanism of the selection process of the SY-medaka. In conclusion, our study can provide new clues for the adaptation process of medaka in the new environment of Sanya.

References

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

Brookes B, Jeon H, Derry A, Post J, Rogers S, Humphries S . Neutral and adaptive drivers of genomic change in introduced brook trout () populations revealed by pooled sequencing. Ecol Evol. 2022; 12(2):e8584. PMC: 8820109. DOI: 10.1002/ece3.8584. View

Araki K, Aokic J, Kawase J, Hamada K, Ozaki A, Fujimoto H . Whole Genome Sequencing of Greater Amberjack () for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing. Int J Genomics. 2018; 2018:7984292. PMC: 5896239. DOI: 10.1155/2018/7984292. View

Gaither M, Gkafas G, de Jong M, Sarigol F, Neat F, Regnier T . Genomics of habitat choice and adaptive evolution in a deep-sea fish. Nat Ecol Evol. 2018; 2(4):680-687. DOI: 10.1038/s41559-018-0482-x. View

Yang J, Lee S, Goddard M, Visscher P . GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. 2010; 88(1):76-82. PMC: 3014363. DOI: 10.1016/j.ajhg.2010.11.011. View

Kujovich J . Factor V Leiden thrombophilia. Genet Med. 2010; 13(1):1-16. DOI: 10.1097/GIM.0b013e3181faa0f2. View

Mokodongan D, Yamahira K . Origin and intra-island diversification of Sulawesi endemic Adrianichthyidae. Mol Phylogenet Evol. 2015; 93:150-60. DOI: 10.1016/j.ympev.2015.07.024. View

Kawamura G, Hattori M, Takamatsu K, Tsukada T, Ninomiya Y, Benjamin I . Cooperative interaction among BMAL1, HSF1, and p53 protects mammalian cells from UV stress. Commun Biol. 2018; 1:204. PMC: 6250677. DOI: 10.1038/s42003-018-0209-1. View

Joukov V, Walter J, De Nicolo A . The Cep192-organized aurora A-Plk1 cascade is essential for centrosome cycle and bipolar spindle assembly. Mol Cell. 2014; 55(4):578-91. PMC: 4245277. DOI: 10.1016/j.molcel.2014.06.016. View

10.

Yarham J, Lamichhane T, Pyle A, Mattijssen S, Baruffini E, Bruni F . Defective i6A37 modification of mitochondrial and cytosolic tRNAs results from pathogenic mutations in TRIT1 and its substrate tRNA. PLoS Genet. 2014; 10(6):e1004424. PMC: 4046958. DOI: 10.1371/journal.pgen.1004424. View

11.

Wang X, Wang F, Zhang Z, Yang X, Zhang R . STK3 Suppresses Ovarian Cancer Progression by Activating NF-B Signaling to Recruit CD8 T-Cells. J Immunol Res. 2020; 2020:7263602. PMC: 7542485. DOI: 10.1155/2020/7263602. View

12.

Jin J, Yu W, Yang J, Song Y, dePamphilis C, Yi T . GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020; 21(1):241. PMC: 7488116. DOI: 10.1186/s13059-020-02154-5. View

13.

Nagashima M, Shiseki M, Pedeux R, Okamura S, Kitahama-Shiseki M, Miura K . A novel PHD-finger motif protein, p47ING3, modulates p53-mediated transcription, cell cycle control, and apoptosis. Oncogene. 2003; 22(3):343-50. DOI: 10.1038/sj.onc.1206115. View

14.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

15.

Spivakov M, Auer T, Peravali R, Dunham I, Dolle D, Fujiyama A . Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish. G3 (Bethesda). 2014; 4(3):433-45. PMC: 3962483. DOI: 10.1534/g3.113.008722. View

16.

Zhu F, Lawo S, Bird A, Pinchev D, Ralph A, Richter C . The mammalian SPD-2 ortholog Cep192 regulates centrosome biogenesis. Curr Biol. 2008; 18(2):136-41. DOI: 10.1016/j.cub.2007.12.055. View

17.

Golovko A, Hjalm G, Sitbon F, Nicander B . Cloning of a human tRNA isopentenyl transferase. Gene. 2000; 258(1-2):85-93. DOI: 10.1016/s0378-1119(00)00421-2. View

18.

Wang K, Li M, Hakonarson H . ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010; 38(16):e164. PMC: 2938201. DOI: 10.1093/nar/gkq603. View

19.

Zhang C, Dong S, Xu J, He W, Yang T . PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics. 2018; 35(10):1786-1788. DOI: 10.1093/bioinformatics/bty875. View

20.

Dong Z, Li X, Yao Z, Wang C, Guo Y, Wang Q . in Sanya Does Not Contain the Male Sex-Determining Gene . Animals (Basel). 2021; 11(5). PMC: 8148570. DOI: 10.3390/ani11051327. View