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De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs

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Abstract

Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.

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Acknowledgements

This Project was supported by National Natural Science Foundation of China (NSFC-CGIAR, No. 31361140365), Foshan University Initiative Scientific Research Program (No. 31702088) and the Fundamental Research Funds for the Central Universities (Grant ID: 2662015JC010 and 2662017JC027).

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Author notes

  1. Pan Ni and Ali Akbar Bhuiyan contributed equally to this work.

Authors and Affiliations

  1. College of Life Science, Foshan University, Foshan, 528231, Guangdong, People’s Republic of China

    Pan Ni, Hua Li, Hui Yu & Kui Li

  2. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    Pan Ni, Ali Akbar Bhuiyan, Jian-Hai Chen, Jingjin Li, Shuhong Zhao, Xiaoyong Du & Xiangdong Liu

  3. Bangladesh Livestock Research Institute, Savar, Dhaka, 1341, Bangladesh

    Ali Akbar Bhuiyan

  4. College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    Cheng Zhang & Xiaoyong Du

Authors
  1. Pan Ni
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  2. Ali Akbar Bhuiyan
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Contributions

KL and SZ conceived and designed the experiments; PN, CZ and HY downloaded and compiled the public data; PN, JHC, AAB, JL, XL and XD analyzed the data; AAB, PN and JHC wrote the manuscript; KL, and SZ finalized the manuscript.

Corresponding authors

Correspondence to Xiangdong Liu or Kui Li.

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The authors declare that they have no conflict of interest and responsible for the content and authorship of this paper.

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Ni, P., Bhuiyan, A.A., Chen, JH. et al. De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs. Genetica 146, 277–285 (2018). https://doi.org/10.1007/s10709-018-0018-y

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  • DOI: https://doi.org/10.1007/s10709-018-0018-y

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