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Complete chloroplast genome of an endangered endemic tree, handeliodendron bodinieri (levl.) rehder (sapindaceae) from karst forests of southwest China.

ABSTRACT: Handeliodendron bodinieri (Sapindaceae) is an endangered monotypic species endemic to the karst forests in southwest China whose populations are now fragmented and the total number of individuals evidently decreased. In this research, we characterized the chloroplast (cp) genome of H. bodinieri using genome skimming. The whole cp genome was 155,291?bp long and comprised 137 genes, including 8 unique rRNAs, 40 tRNAs, and 89 protein-coding genes. The overall guanine-cytosine content of H. bodinieri cp genome was 37.8%. The phylogenetic analysis suggested that H. bodinieri is closely related to the genus Mangifera. This study will be useful for future studies on conservation genetics of this economically important endemic plant.

SUBMITTER: Tian X

PROVIDER: S-EPMC7707296 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Complete chloroplast genome of an endangered endemic tree, handeliodendron bodinieri (levl.) rehder (sapindaceae) from karst forests of southwest China.

Tian Xinmin X Li Xueli X Miao Haoyu H Xue Chunlin C Wang Bolun B Guo Yu Y Zhang Gucheng G

Mitochondrial DNA. Part B, Resources 20190927 2

Handeliodendron bodinieri (Sapindaceae) is an endangered monotypic species endemic to the karst forests in southwest China whose populations are now fragmented and the total number of individuals evidently decreased. In this research, we characterized the chloroplast (cp) genome of H. bodinieri using genome skimming. The whole cp genome was 155,291 bp long and comprised 137 genes, including 8 unique rRNAs, 40 tRNAs, and 89 protein-coding genes. The overall guanine-cytosine content ...[more]

PMID: 33365952

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Project description:BackgroundHandeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family.ResultsThe chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa.ConclusionThis study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.

Project description:Tropical forests on karstic relief (tropical karst forest) are among the most species-rich biomes. These forests play pivotal roles as global climate regulators and for human wellbeing. Their long-term conservation could be central to global climate mitigation and biodiversity conservation. In Mexico, karst landscapes occupy 20% of the total land surface and are distributed mainly in the southeast of the country, along the eastern slope, and in the Yucatan Peninsula. Within each of these areas, the following types of karst occur: coastal karst, plain karst, hill karst, and mountain karst (low, medium, high). Mountain karst cover 2.07% of Mexico's land surface and are covered by tropical rainforests, montane cloud forests, and tropical deciduous forests. These are probably one of the most diverse biomes in Mexico. However, the mountain karst forests of Mexico have received little attention, and very little is known about their diversity. Here, we evaluated the vascular plant species richness within the mountain karst forests of Mexico. We assembled the first, largest, and most comprehensive datasets of Mexican mountain karst forest species, from different public databases (CONABIO, GBIF, IBdata-UNAM), which included a critical review of all data. We compiled a list of the families, genera, and species present within the mountain karst forests of Mexico. Taxa that best characterize these forests were identified based on their spatial correlation with this biome. We explored biodiversity patterns, identifying areas with the highest species richness, endemism centers, and areas of relatively low sampling intensity. We found that within the mountain karst forests of Mexico there are representatives of 11,771 vascular plant species (253 families and 2,254 genera), ca. 50% of the Mexican flora. We identified 372 species endemic to these forests. According to preliminary IUCN red list criteria, 2,477 species are under some category of conservation risk, of which 456 (3.8%) are endangered. Most of the Mexican mountain karst forests have been extensively explored and six allopatric, species-rich areas were identified. Compared to other regions in the world, the mountain karst forests of Mexico are one of the most diverse biomes. They contain more species than some entire montane systems in Mexico such as Sierra Madre Oriental, and Sierra Madre del Sur. Also, the mountain karst forests of Mexico are most diverse than similar forests of South America and Asia, even if considering the effect of different sampling areas. The fact that mountain karst forests are embedded in areas of high biotic diversity, probably contributes to their great floristic diversity. Thus, the mountain karst forests of Mexico are an important source of diversity and shelters a large percentage of the Mexican flora.

Dataset Information

Complete chloroplast genome of an endangered endemic tree, handeliodendron bodinieri (levl.) rehder (sapindaceae) from karst forests of southwest China.

Publications

Complete chloroplast genome of an endangered endemic tree, <i>handeliodendron bodinieri</i> (levl.) rehder (sapindaceae) from karst forests of southwest China.

Similar Datasets

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