Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae

Zelda du Toit, Morne Du Plessis, Desire Lee Dalton, Ray Jansen, J. Paul Grobler, Antoinette Kotze

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Abstract

Background: This study used next generation sequencing to generate the mitogenomes of four African pangolin
species; Temminck’s ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied
pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla).
Results: The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for
S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P. tricuspis. Phylogenetic comparisons of the African pangolins
indicated two lineages with high posterior probabilities providing evidence to support the classification of two genera;
Smutsia and Phataginus. The total GC content between African pangolins was observed to be similar between species
(36.5% – 37.3%). The most frequent codon was found to be A or C at the 3rd codon position. Significant variations in
GC-content and codon usage were observed for several regions between African and Asian pangolin species which may
be attributed to mutation pressure and/or natural selection. Lastly, a total of two insertions of 80 bp and 28 bp in size
respectively was observed in the control region of the black-bellied pangolin which were absent in the other African
pangolin species.
Conclusions: The current study presents reference mitogenomes of all four African pangolin species and thus expands
on the current set of reference genomes available for six of the eight extant pangolin species globally and represents the
first phylogenetic analysis with six pangolin species using full mitochondrial genomes. Knowledge of full mitochondrial
DNA genomes will assist in providing a better understanding on the evolution of pangolins which will be essential for
conservation genetic studies.
Original languageEnglish
Number of pages13
JournalBMC Genomics
Volume18
Issue number746
Publication statusPublished - 21 Sep 2017

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