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Complete chloroplast genome sequences of Lagotis yunnanensis (Scrophulariaceae): an Endangered species endemic to the Hengduan Mountains region.

ABSTRACT: Lagotis yunnanensis is a perennial plant in the Scrophulariaceae family with a high value of medicinal in Tibetan medicine. In this study, we assembled and characterized the complete chloroplast genome of L. yunnanensis as a resource for future studies on this species. The chloroplast genome was 152,789 bp in size, with a large single-copy (LSC) region of 83,642 bp, a small single-copy (SSC) region of 17,795 bp, separated by two inverted repeat (IR) regions of 25,676 bp each. A total of 131 genes were predicted. Phylogenetic analysis showed a close relationship between L. yunnanensis and Veronicastrum sibiricum with 100% bootstrap value.

SUBMITTER: Cheng JP

PROVIDER: S-EPMC7748441 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Leptodermis scabrida (Rubiaceae): an endemic shrub in Himalaya-Hengduan Mountains.

Project description:Leptodermis scabrida is an important endemic species in Himalaya-Hengduan Mountains. Here, we report the complete chloroplast genome of L. scabrida. The cp genome was determined to be 154783 bp in length and the GC content was 37.5%. The sequence included a large single copy (LSC) region of 84190 bp, a small single copy (SSC) region of 17183 bp and two separated inverted regions of 26705 bp, respectively. It contained 132 genes, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. This complete genome of L. scabrida will provide valuable information to resolve the complex phylogeny relationship and to elucidate the mechanism of speciation of Leptodermis, as well as for the phylogenetic studies of Rubiaceae.

| S-EPMC7748826 | biostudies-literature

Homoploid hybridization of plants in the Hengduan mountains region.

Project description:The Hengduan Mountains Region (HMR) is a major global biodiversity hotspot. Complex tectonic and historical climatic conditions created opportunities for natural interspecific hybridization. Likewise, anthropogenic disturbance potentially raises the frequency of hybridization. Among species studies to date, the frequency of homoploid hybridization appears in the HMR. Of nine taxa in which natural hybridization has been detected, three groups are involved in homoploid hybrid speciation, and species pairs from the remaining six genera suggest that continuous gene flow occurs in hybrid zones. Reproductive isolation may greatly affect the dynamic and architecture of hybrid zones in the HMR. Asymmetrical hybridization and introgression can primarily be attributed to both prezygotic and postzygotic barriers. The frequent observation of such asymmetry may imply that reproductive barrier contributes to maintaining species boundaries in the alpine region. Ecological isolations with environmental disturbance may promote breeding barriers between parental species and hybrids. Hybrid zones may be an important phase for homoploid hybrid speciation. Hybrid zones potentially provided abundant genetic resources for the diversification of the HMR flora. The ecological and molecular mechanisms of control and mediation for natural hybridization will help biologists to understand the formation of biodiversity in the HMR. More researches from ecological and molecular aspects were required in future studies.

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The complete chloroplast genome sequence of Pellacalyx yunnanensis: an endangered species in China.

Project description:Pellacalyx yunnanensis is an endangered plant species occurring in Yunnan province of China. The first complete chloroplast genome (cpDNA) sequence of P. yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,743?bp in length, contains a large single-copy region (LSC) of 91,075?bp and a small single-copy region (SSC) of 18,668?bp, which were separated by a pair of inverted repeats (IR) regions of 27,000?bp. The genome contains 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 35.7%, and the corresponding values of the LSC, SSC, and IR regions are 33.0%, 29.6%, and 42.3%, respectively. Further phylogenomic analysis showed that P. yunnanensis clustered in a unique clade in family Rhizophoraceae.

| S-EPMC7707691 | biostudies-literature

Westwards and northwards dispersal of Triosteum himalayanum (Caprifoliaceae) from the Hengduan Mountains region based on chloroplast DNA phylogeography.

Project description:The varying topography and environment that resulted from paleoorogeny and climate fluctuations of the Himalaya-Hengduan Mountains (HHM) areas had a considerable impact on the evolution of biota during the Quaternary. To understand the phylogeographic pattern and historical dynamics of Triosteum himalayanum (Caprifoliaceae), we sequenced three chloroplast DNA fragments (rbcL-accD, rps15-ycf1, and trnH-psbA) from 238 individuals representing 20 populations. Nineteen haplotypes (H1-H19) were identified based on 23 single-site mutations and eight indels. Most haplotypes were restricted to a single population or neighboring populations. Analysis of molecular variance revealed that variations among populations were much higher than that within populations for the overall gene pool, as well as for the East Himalayan group (EH group) and the North Hengduan group (NHM group), but not for the Hengduan Mountains group (HM group). Ecoregions representing relatively high genetic diversity or high frequencies of private haplotypes were discovered, suggesting that this alpine herbaceous plant underwent enhanced allopatric divergence in isolated and fragmented locations during the Quaternary glaciations. The current phylogeographic structure of T. himalayanum might be due to heterogeneous habitats and Quaternary climatic oscillations. Based on the phylogeographic structure of T. himalayanum populations, the phylogenetic relationship of identified haplotypes and palaeodistributional reconstruction, we postulated both westwards and northwards expansion from the HM group for this species. The westwards dispersal corridor could be long, narrow mountain areas and/or the Yarlung Zangbo Valley, while the northwards movement path could be south-north oriented mountains and low-elevation valleys.

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Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species.

Project description:BACKGROUND:Phoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus. RESULTS:We sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies. CONCLUSION:This study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

| S-EPMC5597560 | biostudies-literature

Phylogenetic pattern of alpine plants along latitude and longitude in Hengduan Mountains Region.

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Complete chloroplast genome of Angiopteris yunnanensis (Marattiaceae).

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The complete chloroplast genome of Zelkova schneideriana (Rosales: Ulmaceae), an Endangered species endemic to China.

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The complete chloroplast genome of an endangered and endemic species, Acer yangbiense (Aceraceae).

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