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Phylogenetic studies of Hylopetes alboniger based on complete mitochondrial DNA sequences.

ABSTRACT: The complete mitochondrial genome sequence of the Hylopetes alboniger was sequenced and reported for the first time using muscle tissue. The mitochondrial genome is 16,584?bp in size, including 22 tRNA genes, 13 protein-coding genes, 12S rRNA, 16S rRNA, and one control region. Phylogenetic analysis was performed using whole mitogenome sequences with other 15 closely related taxa to assess their phylogenetic relationship. This mitochondrial genome sequence will provide a better understanding for H. alboniger evolution in the future.

SUBMITTER: Yang Y

PROVIDER: S-EPMC7800767 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Phylogenetic studies of <i>Hylopetes alboniger</i> based on complete mitochondrial DNA sequences.

Yang Yumin Y Sun Jungang J Chen Qizhu Q Wu Zhijiu Z Yang Zaijun Z Hu Jie J Li Dayong D

Mitochondrial DNA. Part B, Resources 20161018 1

The complete mitochondrial genome sequence of the <i>Hylopetes alboniger</i> was sequenced and reported for the first time using muscle tissue. The mitochondrial genome is 16,584 bp in size, including 22 tRNA genes, 13 protein-coding genes, 12S rRNA, 16S rRNA, and one control region. Phylogenetic analysis was performed using whole mitogenome sequences with other 15 closely related taxa to assess their phylogenetic relationship. This mitochondrial genome sequence will provide a better understandi ...[more]

PMID: 33473605

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Project description:Walnuts (Juglans of the Juglandaceae) are well-known economically important resource plants for the edible nuts, high-quality wood, and medicinal use, with a distribution from tropical to temperate zones and from Asia to Europe and Americas. There are about 21 species in Juglans. Classification of Juglans at section level is problematic, because the phylogenetic position of Juglans cinerea is disputable. Lacking morphological and DNA markers severely inhibited the development of related researches. In this study, the complete chloroplast genomes and two nuclear DNA regions (the internal transcribed spacer and ubiquitin ligase gene) of 10 representative taxa of Juglans were used for comparative genomic analyses in order to deepen the understanding on the application value of genetic information for inferring the phylogenetic relationship of the genus. The Juglans chloroplast genomes possessed the typical quadripartite structure of angiosperms, consisting of a pair of inverted repeat regions separated by a large single-copy region and a small single-copy region. All the 10 chloroplast genomes possessed 112 unique genes arranged in the same order, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A combined sequence data set from two nuclear DNA regions revealed that Juglans plants could be classified into three branches: (1) section Juglans, (2) section Cardiocaryon including J. cinerea which is closer to J. mandshurica, and (3) section Rhysocaryon. However, three branches with a different phylogenetic topology were recognized in Juglans using the complete chloroplast genome sequences: (1) section Juglans, (2) section Cardiocaryon, and (3) section Rhysocaryon plus J. cinerea. The molecular taxonomy of Juglans is almost compatible to the morphological taxonomy except J. cinerea (section Trachycaryon). Based on the complete chloroplast genome sequence data, the divergence time between section Juglans and section Cardiocaryon was 44.77 Mya, while section Rhysocaryon diverged from other sections in the genus Juglans was 47.61 Mya. Eleven of the 12 small inversions in the chloroplast genomes provided valuable phylogenetic information for classification of walnut plants at section and species levels. Our results are valuable for future studies on Juglans genetic diversity and will enhance the understanding on the phylogenetic evolution of Juglandaceae.

Project description:BackgroundThe taxonomic distinctiveness of Ascaris lumbricoides and A. suum, two of the world's most significant nematodes, still represents a much-debated scientific issue. Previous studies have described two different scenarios in transmission patterns, explained by two hypotheses: (1) separated host-specific transmission cycles in highly endemic regions, (2) a single pool of infection shared by humans and pigs in non-endemic regions. Recently, A. suum has been suggested as an important cause of human ascariasis in endemic areas such as China, where cross-infections and hybridization have also been reported. The main aims of the present study were to investigate the molecular epidemiology of human and pig Ascaris from non-endemic regions and, with reference to existing data, to infer the phylogenetic and phylogeographic relationships among the samples.Methodology151 Ascaris worms from pigs and humans were characterized using PCR-RFLP on nuclear ITS rDNA. Representative geographical sub-samples were also analysed by sequencing a portion of the mitochondrial cox1 gene, to infer the extent of variability at population level. Sequence data were compared to GenBank sequences from endemic and non-endemic regions.Principal findingsNo fixed differences between human and pig Ascaris were evident, with the exception of the Slovak population, which displays significant genetic differentiation. The RFLP analysis confirmed pig as a source of human infection in non-endemic regions and as a corridor for the promulgation of hybrid genotypes. Epidemiology and host-affiliation seem not to be relevant in shaping molecular variance. Phylogenetic and phylogeographical analyses described a complex scenario, involving multiple hosts, sporadic contact between forms and an ancestral taxon referable to A. suum.Conclusions/significanceThese results suggest the existence of homogenizing gene flow between the two taxa, which appear to be variants of a single polytypic species. This conclusion has implications on the systematics, transmission and control programs relating to ascariasis.

Dataset Information

Phylogenetic studies of Hylopetes alboniger based on complete mitochondrial DNA sequences.

Publications

Phylogenetic studies of <i>Hylopetes alboniger</i> based on complete mitochondrial DNA sequences.

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