Abstract
BackgroundThis 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).ResultsThe 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.ConclusionsThe 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.
Highlights
This study used 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)
The species identity of samples used in this study was confirmed with Sanger sequencing of the c oxidase I (CoxI) and cytochrome B (Cob) loci which were compared to chain-of-custody voucher specimens available from the National Zoological Gardens of South Africa (NZG) species reference database [68]
The contigs were identified as the mitogenomes of the pangolin species based on the (i) estimated length (≈16.5 kb); (ii) the occurrence of the proteins CoxI, Cob, NADH dehydrogenase V (NadV) and NADH dehydrogenase VI (NadVI) (Table 2) and (iii) correspondence with mitochondrial sequences from other Pholidota based on National Centre for Biotechnology Information (NCBI) BLAST searches
Summary
This study used 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). The taxonomy of pangolins is still under debate, with disagreement regarding the number of genera due to lack of molecular phylogenetic analysis [1, 3, 26,27,28,29]. These species have been placed into six genera by Pocock [26]. Several authors follow the single genus classification [35,36,37,38], an in-depth taxonomic study of pangolin genera is required in order to clarify this issue
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