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BMC evolutionary biology
06 20, 2019;19 (1): 128.

Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals.

Nashaiman Pervaiz, Nazia Shakeel, Ayesha Qasim, Rabail Zehra, Saneela Anwar, Neenish Rana, Yongbiao Xue, Zhang Zhang, Yiming Bao, Amir Ali Abbasi
Author Information
  1. Nashaiman Pervaiz: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  2. Nazia Shakeel: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  3. Ayesha Qasim: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  4. Rabail Zehra: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  5. Saneela Anwar: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  6. Neenish Rana: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  7. Yongbiao Xue: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101; University of Chinese Academy of Sciences, Beijing, 100049, China.
  8. Zhang Zhang: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101; University of Chinese Academy of Sciences, Beijing, 100049, China.
  9. Yiming Bao: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101; University of Chinese Academy of Sciences, Beijing, 100049, China. baoym@big.ac.cn.
  10. Amir Ali Abbasi: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan. abbasiam@qau.edu.pk.
PMID: 31221090 DOI: 10.1186/s12862-019-1441-0

Abstract

BACKGROUND: The hypothesis that vertebrates have experienced two ancient, whole genome duplications (WGDs) is of central interest to evolutionary biology and has been implicated in evolution of developmental complexity. Three-way and Four-way paralogy regions in human and other vertebrate genomes are considered as vital evidence to support this hypothesis. Alternatively, it has been proposed that such paralogy regions are created by small-scale duplications that occurred at different intervals over the evolution of life.
RESULTS: To address this debate, the present study investigates the evolutionary history of multigene families with at least three-fold representation on human chromosomes 1, 2, 8 and 20. Phylogenetic analysis and the tree topology comparisons classified the members of 36 multigene families into four distinct co-duplicated groups. Gene families falling within the same co-duplicated group might have duplicated together, whereas genes belong to different co-duplicated groups might have distinct evolutionary origins.
CONCLUSION: Taken together with previous investigations, the current study yielded no proof in favor of WGDs hypothesis. Rather, it appears that the vertebrate genome evolved as a result of small-scale duplication events, that cover the entire span of the animals' history.

Keywords

Human Multigene families Paralogons Paralogy regions Phylogenetic analysis Segmental duplications Vertebrate Whole genome duplications

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MeSH Term

Animals
Chromosomes, Human
Evolution, Molecular
Gene Duplication
Genome, Human
Humans
Invertebrates
Multigene Family
Phylogeny
Vertebrates
Journal Article Research Support, Non-U.S. Gov't

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