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.
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Data Availability Statement
The complete mitochondrial DNA sequences were deposited in GenBank under accession numbers MW043720 (P. pingguoensis), MW043721 (H. longibarbatus), and MW043722 (O. polystigmus). The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
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Acknowledgment
We are very grateful to Jiahu LAN from Du’an Fishery Technique Popularization Station for specimen collection and photographing on the three species.
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Supported by the Open Fund of Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture (No. GXKEYLA2019-05), the National Natural Science Foundation of China (No. 41806170), and the China-ASEAN Maritime Cooperation Fund (No. CAMC-2018F)
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Zhou, L., Huang, S., Wang, Q. et al. Novel evolutionary insights into nemacheilid cavefish: evidence from comparative analysis of mitochondrial genomes. J. Ocean. Limnol. 40, 1640–1653 (2022). https://doi.org/10.1007/s00343-021-1047-4
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DOI: https://doi.org/10.1007/s00343-021-1047-4