Genetic diversity of the captive Asian tapir population in Thailand, based on mitochondrial control region sequence data and the comparison of its nucleotide structure with Brazilian tapir

Muangkram, Yuttamol; Amano, Atsushi; Wajjwalku, Worawidh; Pinyopummintr, Tanu; Thongtip, Nikorn; Kaolim, Nongnid; Sukmak, Manakorn; Kamolnorranath, Sumate; Siriaroonrat, Boripat; Tipkantha, Wanlaya; Maikaew, Umaporn; Thomas, W. Kelley; Polsrila, Kanda; Dongsaard, Kwanreaun; Sanannu, Saowaphang; Wattananorrasate, Anuwat

doi:10.3109/24701394.2016.1149828

Cited by 3 publications

(2 citation statements)

References 28 publications

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“…The CSB domain was A-T rich, with 56.3% A-T composition. The large tandem repeat found to be from position 16,152 to 16,420–between CSB-1 and CSB-2–is similar to others in Perissodactyla ( Xu & Arnason, 1994 ; Muangkram et al, 2017 ). The function of the CSB is still unclear, but their occurrence in vertebrate mitogenomes in general suggests that they play a critical role in genome replication and transcription ( Satoh et al, 2016 ).…”

Section: Resultssupporting

confidence: 84%

“…The full 1,247 bp long putative CR ranges from position 15,451 to 16,697 and is located between the trnP and trnF genes. The CR has a slight A-T skew, with an overall nucleotide composition of A = 33.2%, T = 25.6%, C = 28.7%, and G = 12.5%, which has been observed in other organisms ( Muangkram et al, 2017 ). Stem-loop structures are located within this putative control region as well as microsatellite repeats.…”

Section: Resultsmentioning

confidence: 54%

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First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii)

Ennis

Ortega

Baeza

2022

PeerJ

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Baird’s tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America, and is categorized as ‘endangered’ on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG’s). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length consisting of 13 protein-coding genes (PCG’s), two ribosomal RNA genes (rrnS (12s ribosomal RNA and rrnL (16s ribosomal RNA)), and 22 transfer RNA (tRNA) genes. A 33 bp long region was identified to be the origin of replication for the light strand (OL), and a 1,247 bp long control region (CR) contains the origin of replication for the heavy strand (OH). A majority of the PCG’s and tRNA genes are encoded on the positive, or heavy, strand. The gene order in T. baiirdi is identical to that of T. indicus and T. terrestris, the only two other species of extant tapirs with assembled mitochondrial genomes. An analysis of Ka/Ks ratios for all the PCG’s show values <1, suggesting that all these PCGs experience strong purifying selection. A maximum-likelihood phylogenetic analysis supports the monophyly of the genus Tapirus and the order Perissodactyla. The complete annotation and analysis of the mitochondrial genome of T. bairdii will contribute to a better understanding of the population genomic diversity and structure of this species, and it will assist in the conservation and protection of its dwindling populations.

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Section: Resultssupporting

confidence: 84%

Section: Resultsmentioning

confidence: 54%

First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii)

Ennis

Ortega

Baeza

2022

PeerJ

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Genetic diversity and phylogenetic relationships of Malayan tapir (Tapirus indicus) populations in the Malay Peninsula based on mitochondrial DNA control region

Lim

Yong

et al. 2021

Biodivers Conserv

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The Malayan tapir (Tapirus indicus) is an endangered species in Southeast Asia (SEA). Over the years, there has only been a few reports on its population genetic structure and evolutionary history in SEA. In particular, while the captive Malayan tapir population in Thailand has received fairly more research in recent years, there has not been any widescale population genetic study in the Malay Peninsula since the last decade. In this study, we report on the genetic diversity and attempt to make inferences on the phylogeography of the Malayan tapir in the Malay Peninsula, using the mitochondrial DNA control region, including also data from previous studies. We identified 12 novel haplotypes and two distinct Malayan tapir clades with a divergence time of 14.6 million years ago (mya) in the Peninsular Malaysia (i.e. southern Malay Peninsula) samples, as opposed to only one clade found in the Thai (i.e. Thailand western border and northern Malay Peninsula) captive individuals, with an almost two-fold higher nucleotide diversity compared to the latter. The co-occurrence of the two lineages in southern Malay Peninsula suggested past historical events of population isolation, migration and admixture as a result of episodic glacial periods and paleoenvironmental changes in SEA. Only one haplotype shared between the populations of the two regions suggested further gene flow restriction at the narrow corridor of the Malay Peninsula as of present day. Keywords D-loop • Asian tapir • Peninsular Malaysia • Thailand • Population genetic structure Communicated by Pradeep Kumar Divakar.

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The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia

Muangkram

Wajjwalku

Amano

et al. 2016

Mitochondrial DNA Part A

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We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.

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Genetic diversity of the captive Asian tapir population in Thailand, based on mitochondrial control region sequence data and the comparison of its nucleotide structure with Brazilian tapir

Cited by 3 publications

References 28 publications

First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii)

First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii)

Genetic diversity and phylogenetic relationships of Malayan tapir (Tapirus indicus) populations in the Malay Peninsula based on mitochondrial DNA control region

The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia

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