Novel evolutionary insights into nemacheilid cavefish: evidence from comparative analysis of mitochondrial genomes

Lei ZHOU; Shihui HUANG; Qing WANG; Zhenhai LI; Zongyang LI; Anyou HE; Jiehu CHEN; Li LIU; Keshu ZOU

doi:10.1007/s00343-021-1047-4

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Novel evolutionary insights into nemacheilid cavefish: evidence from comparative analysis of mitochondrial genomes

Biology | Updated：2023-05-20

- Novel evolutionary insights into nemacheilid cavefish: evidence from comparative analysis of mitochondrial genomes
- Journal of Oceanology and Limnology Vol. 40, Issue 4, Pages: 1640-1653(2022)
- Affiliations：
  
  1.Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
  2.Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
  3.Science Corporation of Gene, Guangzhou 510000, China
- Author bio：
  
  Li LIU, E-mail: liuli@scau.edu.cn
  Keshu ZOU, E-mail: zoukeshu@scau.edu.cn
- Funds：
- DOI：10.1007/s00343-021-1047-4
  CLC：
- Received：24 February 2021，
  
  Accepted：31 May 2021，
  
  Online First：13 September 2021，
  
  Published：2022-07
- Accepted：
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Lei ZHOU, Shihui HUANG, Qing WANG, et al. Novel evolutionary insights into nemacheilid cavefish: evidence from comparative analysis of mitochondrial genomes[J]. Journal of Oceanology and Limnology, 2022, 40(4): 1640-1653.
DOI：

Lei ZHOU, Shihui HUANG, Qing WANG, et al. Novel evolutionary insights into nemacheilid cavefish: evidence from comparative analysis of mitochondrial genomes[J]. Journal of Oceanology and Limnology, 2022, 40(4): 1640-1653. DOI： 10.1007/s00343-021-1047-4.

摘要

Abstract

Cavefish can be important models for understanding the relationships among evolution

adaptation

and development in extreme environments. However

cavefish remain poorly studied

particularly at the genome level. Here

we sequenced the complete mitogenome of three cavefish in the family Nemacheilidae (

Paranemachilus pingguoensis

Oreonectes polystigmus

and

Heminoemacheilus longibarbatus

)

which were collected from karst caves in South China. The mitogenomes each contained 37 genes (13 protein coding

22 tRNA

and two rRNA genes) and a single control region

with the same genetic arrangement and distribution as those found in vertebrates. The non-synonymous/synonymous mutation ratios (Ka/Ks) of the mitogenomes indicated that the protein-coding genes (PCGs) of the three cavefish evolved under purifying selection. The mitogenomes of the three cavefish exhibit nucleotide composition biases for PCGs

tRNAs

rRNAs

and the whole genome

indicating that the mitochondrial DNA might have been subjected to evolutionary selection in response to extreme cave environments. Divergence time and evolutionary history analyses suggested that the speciation and diversification of the cavefish coincided with the Miocene uplift of the southern Qinghai-Tibet Plateau

which greatly changed cave habitats. Overall

our study sheds light on the mitogenomes

phylogeny

and evolutionary history of nemacheilid cavefish.

关键词

Keywords

references

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