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An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia.

ABSTRACT: Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.

SUBMITTER: Kloss-Brandstatter A

PROVIDER: S-EPMC8144189 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia.

Kloss-Brandstätter Anita A Summerer Monika M Horst David D Horst Basil B Streiter Gertraud G Raschenberger Julia J Kronenberg Florian F Sanguansermsri Torpong T Horst Jürgen J Weissensteiner Hansi H

Scientific reports 20210524 1

Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup ...[more]

PMID: 34031453

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Project description:BackgroundNeocinnamomum plants are considered a promising feedstock for biodiesel in China, due to the richness in long-chain fatty acids (LCFAs) found in their seeds. However, the mitochondrial genome (mitogenome) of this genus has not yet been systematically described, and the exploration of species relationships within this genus using mitogenome sequences is also an uncharted territory. This has hindered our understanding of mitogenome diversity and the evolutionary relationships within Neocinnamomum.ResultsIn this study, a total of 24 individuals representing seven distinct taxa from the genus Neocinnamomum were subjected to Illumina sequencing, and the species N. delavayi was sequenced using Oxford Nanopore sequencing technology. We successfully assembled the mitogenome of N. delavayi, which is 778,066 bp in size and exhibits a single circular structure. The analysis identified 659 dispersed repeats, 211 simple sequence repeats (SSRs), and 30 tandem repeats within the mitogenome. Additionally, 37 homologous fragments, totaling 9929 bp, were found between the mitogenome and the plastid genome (plastome). The codons of 41 protein-coding genes (PCGs) had a preference for ending in A/T, and the codon usage bias of the majority of these genes was influenced by natural selection pressures. Comparative genomic analysis revealed low collinearity and significant gene rearrangements between species. Phylogenetic analysis resulted in the classification of Neocinnamomum into six distinct clades, contradicting previous findings which based on complete plastomes and nuclear ribosomal cistron (nrDNA). In the PCGs of 24 individuals, 86 mutation events were identified, which included three indels and 83 SNPs. Notably, the ccmC gene underwent positive selection in pairwise comparisons of three species pairs. Furthermore, 748 RNA editing sites were predicted within the PCGs of the N. delavayi mitogenome.ConclusionsThis study enriches our knowledge of the mitogenomes in the family Lauraceae, and provides valuable data and a foundation for genomic evolution research, genetic resource conservation, and molecular breeding in Neocinnamomum.

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An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia.

Publications

An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia.

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