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Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau.

ABSTRACT: Genus Comastoma (subt. Swertiinae, Gentianaceae) contains species, such as "Zangyinchen," that are important herbs in Tibetan medicine. The phylogenetic relationship of this within Gentianaceae and the circumscriptions of its species have long been controversial with conflicting morphological and molecular data reported. Here, we used whole chloroplast genome sequences for Comastoma species and related taxa to reconstruct their phylogeny and clarify their taxonomic relationships. The results revealed that the length of all plastome sequenced varied from 149 to 151 kb and have high similarity in structure and gene content. Phylogenomic analysis showed that Comastoma is a monophyletic group, closely related to the genus Lomatogonium. The divergence time estimation showed that Gentianaceae diverged at about 21.81 Ma, while the split of Comastoma occurred at 7.70 Ma. However, the results suggested the crown age of species formation in this genus is after 4.19 Ma. Our results suggest that QTP uplift, the alternation of Quaternary glaciation and interglaciation, and monsoon changes might have acted as drivers of speciation in Comastoma.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC8601884 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau.

Zhang Yu Y Yu Jingya J Xia Mingze M Chi Xiaofeng X Khan Gulzar G Chen Shilong S Zhang Faqi F

Ecology and evolution 20211028 22

Genus Comastoma (subt. Swertiinae, Gentianaceae) contains species, such as "Zangyinchen," that are important herbs in Tibetan medicine. The phylogenetic relationship of this within Gentianaceae and the circumscriptions of its species have long been controversial with conflicting morphological and molecular data reported. Here, we used whole chloroplast genome sequences for Comastoma species and related taxa to reconstruct their phylogeny and clarify their taxonomic relationships. T ...[more]

PMID: 34824809

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Project description:BackgroundThe genus Swertia is of great medicinal importance and one of the most taxonomically challenging taxa within Gentianaceae, largely due to the morphological similarities of species within this genus and with its closely related genera. Previous molecular studies confirmed its polyphyly but suffered from low phylogenetic resolutions because only limited sequence loci were used. Thus, we conducted the structural, gene evolutionary, and phylogenetic analyses of 11 newly obtained plastomes of Swertia. Our result greatly improved the phylogenetic resolutions in Swertia, shed new light on the plastome evolution and phylogenetic relationships of this genus.ResultsThe 11 Swertia plastomes together with the published seven species proved highly similar in overall size, structure, gene order, and content, but revealed some structural variations caused by the expansion and contraction of the IRb region into the LSC region, due to the heterogeneous length of the ψycf1. The gene rps16 was found to be in a state flux with pseudogenes or completely lost. Similar situation was also documented in other genera of Gentianaceae. This might imply loss of the gene in the common ancestor of Gentianaceae. The distribution plot of ENC vs. GC3 showed all these plastomes arranging very close in the Wright line with an expected ENC value (49-52%), suggesting the codon usage of Swertia was mainly constrained by a GC mutation bias. Most of the genes remained under the purifying selection, however, the cemA was identified under positive selection, possibly reflecting an adaptive response to low CO2 atmospheric conditions during the Late Miocene. Our phylogenomic analyses, based on 74 protein-coding genes (CDS), supported the polyphyly of Swertia with its close allies in the subtribe Swertiinae, presumably due to recent rapid radiation. The topology inferred from our phylogenetic analyses partly supported the current taxonomic treatment. Finally, several highly variable loci were identified, which can be used in future phylogenetic studies and accurate identification of medicinal genuineness of Swertia.ConclusionsOur study confirmed the polyphyly of Swertia and demonstrated the power of plastome phylogenomics in improvement of phylogenetic resolution, thus contributing to a better understanding of the evolutionary history of Swertia.

Project description:As significant evidence of ice-rich permafrost degradation due to climate warming, thermokarst lake was developing and undergoing substantial changes. Thermokarst lake was an essential ecosystem component, which significantly impacted the global carbon cycle, hydrology process and the stability of the Qinghai-Tibet Engineering Corridor. In this paper, based on Sentinel-2 (2021) and Landsat (1988-2020) images, thermokarst lakes within a 5000 m range along both sides of Qinghai-Tibet Highway were extracted to analyse the spatio-temporal variations. The results showed that the number and area of thermokarst lake in 2021 were 3965 and 4038.6 ha (1 ha = 10,000 m[Formula: see text]), with an average size of 1.0186 ha. Small thermokarst lakes ([Formula: see text]1 ha) accounted for 85.65% of the entire lake count, and large thermokarst lakes ([Formula: see text]10 ha) occupied for 44.92% of the whole lake area. In all sub-regions, the number of small lake far exceeds 75% of the total lake number in each sub-region. R1 sub-region (around Wudaoliang region) had the maximum number density of thermokarst lakes with 0.0071, and R6 sub-region (around Anduo region) had the minimum number density with 0.0032. Thermokarst lakes were mainly distributed within elevation range of 4300 m-5000 m a.s.l. (94.27% and 97.13% of the total number and size), on flat terrain with slopes less than 3[Formula: see text] (99.17% and 98.47% of the total number and surface) and in the north, south, and southeast aspects (51.98% and 50.00% of the total number and area). Thermokarst lakes were significantly developed in warm permafrost region with mean annual ground temperature (MAGT) > - 1.5 [Formula: see text]C, accounting for 47.39% and 54.38% of the total count and coverage, respectively. From 1988 to 2020, in spite of shrinkage or even drain of small portion of thermokarst lake, there was a general expansion trend of thermokarst lake with increase in number of 195 (8.58%) and area of 1160.19 ha (41.36%), which decreased during 1988-1995 (- 702 each year and - 706.27 ha/yr) and then increased during 1995-2020 (184.96-702 each year and 360.82 ha/yr). This significant expansion was attributed to ground ice melting as rising air temperature at a rate of 0.03-0.04 [Formula: see text]C/yr. Followed by the increasing precipitation (1.76-3.07 mm/yr) that accelerated the injection of water into lake.

Dataset Information

Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau.

Publications

Plastome sequencing reveals phylogenetic relationships among <i>Comastoma</i> and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau.

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