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3 Biotech

, 9:233 | Cite as

Phylogenetic analyses of human 1/2/8/20 paralogons suggest segmental duplications during animal evolution

  • Farhan HaqEmail author
  • Usman Saeed
  • Rida Khalid
  • Muhammad Qasim
  • Maryam Mehmood
Original Article

Abstract

Susumu Ohno hypothesized that the diversity of vertebrate gene families and genome is due to two rounds of whole genome duplications (also referred as 2R hypothesis). The quadruplicate paralogous blocks present on 1/2/8/20 chromosomes are taken as one of the evidences in favor of the 2R. In this study, we investigated that whether 2R has shaped the vertebrate evolution using gene families residing on chromosomes 1/2/8/20. Evolutionary history of 22 gene families (11 from the current study and 11 from the previous study) was evaluated by the phylogenetic analysis with triplicated or quadruplicated distribution on these human chromosomes 1/2/8/20. The phylogenetic analysis was performed using high-quality whole genomic sequence data of multiple species with neighbor-joining (NJ) and maximum likelihood (ML) methods. The phylogenetic tree topology of these gene families revealed variable duplication time points during invertebrate–vertebrate evolution. Topology comparison approach categorized 22 gene families into three groups. Tree topologies of ten gene families fell into Group 1 (duplications prior to invertebrate–vertebrate split), four in Group 2 (i.e., (AB) (C) (D), topology incongruent with 2R) and eight in Group 3 (((AB) (CD)), 2R congruent topology). Therefore, taken together the current and previous data of 1/2/8/20 paralogons, we propose that, in addition to whole genome duplications events, current developmental, morphological and genomic complexity of the vertebrate genomes may also have originated through segmental duplications occurring at varying time points during the course of animal evolution.

Keywords

Phylogenetics 2R hypothesis Segmental duplications Paralogous blocks Tree topology 

Notes

Acknowledgements

Special thanks to the teams behind UCSC, NCBI and Ensembl genome browsers, for making all the data publically available for different analyses.

Compliance with ethical standards

Conflict of interest

Authors have no conflict of interests.

Supplementary material

13205_2019_1768_MOESM1_ESM.pdf (546 kb)
Supplementary material 1 (PDF 546 kb)
13205_2019_1768_MOESM2_ESM.pdf (402 kb)
Supplementary material 2 (PDF 403 kb)
13205_2019_1768_MOESM3_ESM.docx (209 kb)
Supplementary material 3 (DOCX 403 kb)

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Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  • Farhan Haq
    • 1
    Email author
  • Usman Saeed
    • 2
  • Rida Khalid
    • 1
  • Muhammad Qasim
    • 3
  • Maryam Mehmood
    • 1
  1. 1.Department of BiosciencesCOMSATS University IslamabadIslamabadPakistan
  2. 2.Department of Genome Oriented BioinformaticsTechnische Universität MünchenMunichGermany
  3. 3.Ajou University School of MedicineSuwonSouth Korea

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