Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae
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...
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BMC
2017-09-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-4140-5 |
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| author | Zelda du Toit Morné du Plessis Desiré L. Dalton Raymond Jansen J. Paul Grobler Antoinette Kotzé |
| author_facet | Zelda du Toit Morné du Plessis Desiré L. Dalton Raymond Jansen J. Paul Grobler Antoinette Kotzé |
| author_sort | Zelda du Toit |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T17:00:29Z |
| format | Article |
| id | doaj.art-b9c09f259f8241da919a7bb1024e58a0 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T17:00:29Z |
| publishDate | 2017-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b9c09f259f8241da919a7bb1024e58a02022-12-21T18:19:21ZengBMCBMC Genomics1471-21642017-09-0118111310.1186/s12864-017-4140-5Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family ManidaeZelda du Toit0Morné du Plessis1Desiré L. Dalton2Raymond Jansen3J. Paul Grobler4Antoinette Kotzé5Department of Genetics, University of the Free StateCentre for Conservation Science, National Zoological Gardens of South AfricaDepartment of Genetics, University of the Free StateDepartment of Environmental, Water and Earth Sciences, Tshwane University of TechnologyDepartment of Genetics, University of the Free StateDepartment of Genetics, University of the Free StateAbstract 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.http://link.springer.com/article/10.1186/s12864-017-4140-5Mitochondrial DNAPhylogeneticsPholidotaAfrican pangolins |
| spellingShingle | Zelda du Toit Morné du Plessis Desiré L. Dalton Raymond Jansen J. Paul Grobler Antoinette Kotzé Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae BMC Genomics Mitochondrial DNA Phylogenetics Pholidota African pangolins |
| title | Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae |
| title_full | Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae |
| title_fullStr | Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae |
| title_full_unstemmed | Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae |
| title_short | Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae |
| title_sort | mitochondrial genomes of african pangolins and insights into evolutionary patterns and phylogeny of the family manidae |
| topic | Mitochondrial DNA Phylogenetics Pholidota African pangolins |
| url | http://link.springer.com/article/10.1186/s12864-017-4140-5 |
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