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The complete chloroplast genome sequence of begonia (Begoniaceae).

ABSTRACT: Begonia L. (Begoniaceae) is the sixth largest genus in the world which consists of more than 2,039 species. Many species of Begonia have highly ornamental leaves and flowers, so they are mainly used for ornamental purposes, and some species can also be used as medicines or vegetables. Begonia gulongshanensis is a newly discovered species in 2018 which occurs exclusively in Jingxi county in Southern China, however, there are few studies on the molecular biology and phylogeny of this species currently. Therefore, we report its complete chloroplast genome sequence for the first time, hoping to provide a foundation for its future phylogenetic analysis. The chloroplast genome of B. gulongshanensis was 169,153 bp in size, which contained a large single-copy region of 75,998 bp, a small single-copy region of 18,063 bp, and two inverted repeat regions of the same 37,546 bp. The total GC content was 35.51%. The genome encodes 42 transfer RNA genes, 8 ribosomal RNA genes and 90 protein-coding genes. The phylogenetic analysis indicated that the genetic relationship between B. gulongshanensis and the other three begonias was very close, but there was still certain distance.

SUBMITTER: Guan S

PROVIDER: S-EPMC8757601 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of Begonia arachnoidea (Begoniaceae).

Project description:There are more than 2035 Begonia species (Begoniaceae) reported currently in the world. Begonia arachnoidea was found as a new species within a small area in Southern China. In this study, we are reporting for the first time its chloroplast genome for the purpose to compare with the chloroplast genomic data from other plant taxa which were closely related to this new species. Our results show that the circular chloroplast genome of B. arachnoidea is 169,725 bp in length, with 35.49% GC content. The whole structure of the genome has 76,431 bp in a large single-copy (LSC) region, 18,146 bp in a small single-copy (SSC) region, and the two inverted repeat (IRs) regions are both 37,574 bp. There are 90 protein-coding genes, 8 rRNA genes, and 42 tRNA genes encoded in this genome. Final phylogenetic analysis revealed that B. arachnoidea is genetically closest to B. pulchrifolia and B. coptidifolia.

| S-EPMC9245980 | biostudies-literature

The complete chloroplast genome sequence of Begonia versicolor Irmsch. (Begoniaceae).

Project description:Begonia versicolor (Code: MK434325) is a perennial plant with unique and precious ornamental value, exhibiting gorgeous leaf morphology and graceful flowers, therefore, it is popular with many horticulturalists and plant hobbyist. The complete chloroplast genome of B. versicolor were reported in this article. It had a typical quarter structure as a circular of 169,506 bp, composed by a large single-copy region (LSC, 75,868 bp), a small single-copy region (SSC, 18,290 bp), and two inverted repeats (IRs, 75,258 bp each). Genome annotations showed that it contained total 185 genes, including 133 protein coding genes (PCGs), 44 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). The percentage of total GC content was 35.57%. Phylogenetic analysis suggested that Begoniaceae was closely related to Cucurbitaceae family.

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Characterization of the complete chloroplast genome of Begonia fimbristipula (Begoniaceae).

Project description:Begonia fimbristipula is a plant of perennial flowering plants in the family Begoniaceae. In this article, the complete chloroplast genome of B. fimbristipula was studied and illustrated to add more genetic information. The chloroplast genome is 169,436 bp in length as the circular, which exhibits a large single-copy region (LSC) of 77,058 bp, a small single-copy region (SSC) of 18,128 bp, and a pair of inverted repeat regions (IRs) of 37,123 bp in each. The overall nucleotide composition of chloroplast genome is: 31.8% A, 32.6% T, 18.0% C, 17.5% G, and the total GC content 35.5%. A total of 142 genes were annotated that included 91 protein-coding genes (PCGs), 43 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). Phylogenetic relationship shows that Begonia fimbristipula is more closely related to Begonia pulchrifolia on genetic relationships using the Maximum-Likelihood (ML) method.

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The complete chloroplast genome and phylogenetic analysis of Begonia pulchrifolia, a near endangered Begoniaceae plant.

Project description:Begonia pulchrifolia is a perennial herb of the genus Begonia and is a near endangered species. Traditional morphological delimitation of B. pulchrifolia is sometimes confused with similar species; therefore, further systematic classification is urgently needed. To enrich the genetic information and guide its molecular identification, the complete chloroplast genome of B. pulchrifolia was sequenced and illustrated. The complete chloroplast genome has a total length of 169,589?bp, containing a large single-copy (LSC, 76,057?bp) and a small single-copy region (SSC, 18,320?bp) separated by a pair of inverted repeat (IRS, 37,606?bp) regions. The overall GC content is 35.56%. A total of 142 genes were annotated, including 91 protein coding genes, 8 rRNA genes and 43 tRNA genes. Phylogenetic analysis showed that B. pulchrifolia is more closely related to Momordica charantia and Gomphogyne cissiformis. This study enriches the genetic information of B. pulchrifolia and contributes to its accurate molecular identification.

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The complete chloroplast genome sequence of Begonia coptidifolia.

Project description:Begonia (Begoniaceae) is a large, pantropically distributed genus, comprising more than 1900 species. Due to poorly available genome resources, the phylogeny of this species-rich genus is still challenged. B. coptidifolia is a newly discovered species of restricted distribution in Southern China, and its genetic relationship with the other Begonia species has not been reported. Therefore, in this study, we report for the first time its chloroplast genome for future phylogenetic analysis. The circular chloroplast genome of B. coptidifolia is 169,412 bp in length, with a GC content of 35.57%. Its large single-copy region is 75,937 bp, a small single-copy region is 18,362 bp, and two inverted repeat regions are 37,556 bp and 37,557 bp, respectively. The genome encodes 82 protein-coding genes, 8 ribosomal RNA genes, and 40 transfer RNA genes. Phylogenetic analysis indicated that B. coptidifolia is genetically closest to B. pulchrifolia.

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The complete plastid genome sequence of Begonia guangxiensis.

Project description:Begonia guangxiensis was assessed as endangered according to Red List of Chinese Plants. In this study, we described the complete plastid genome of B. guangxiensis. The plastid genome sequence of B. guangxiensis is 157,648?bp in size, having a large single-copy region (LSC) of 86,514?bp, a small single-copy region (SSC) of 18,076?bp, and two inverted repeat (IR) regions of 26,529?bp. The complete plastid genome of B. guangxiensis encoding 112 unique genes including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. The overall GC content of the plastid genome is 35.9%. Phylogenetic analysis confirmed that B. guangxiensis is closely related to B. varipeltata.

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Three new species of Begonia (Begoniaceae) from Bahia, Brazil.

Project description:The taxonomic treatment of Begoniaceae for the state of Bahia, Brazil, led to the recognition of three new species of Begonia with narrow distributions, which are described and illustrated here: Begoniadelicata Gregório & J.A.S. Costa, sp. nov. is a herb restricted to the region of the Recôncavo; Begoniaelianeae Gregório & J.A.S. Costa, sp. nov. is a shrub endemic to the Atlantic forest of the southern part of the state; and Begoniapaganuccii Gregório & J.A.S. Costa, sp. nov. is a subshrub known only from the type material, collected in the Piedmont of Paraguaçu. Notes on morphology, comparisons with morphologically similar species, etymology, geographic distribution, habitat and phenological data for each species are also presented. Furthermore, keys are provided as an aid to separating the new species from congeneric species that occur in their surroundings. Due to the sparse knowledge of the new species, there is as yet insufficient data to accurately assess their conservation status.

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Begonia guangdongensis, a new species of Begonia (Begoniaceae) from Guangdong, China.

Project description:A new species of Begonia section Coelocentrum, B. guangdongensis W.H. Tu, B.M. Wang & Y.L. Li from Guangdong Province, China, is described and illustrated here. Morphologically, the new species is most similar to B. biflora T. C. Ku and B. longistyla Y. M. Shui & W. H. Chen, but differs from B. biflora by its rugose leaves and glabrous capsules and from B. longistyla by its glabrous stipules without ciliate margin, densely hirsute-pilose leaves and obtuse apex of bracts. Additionally, it is also somewhat similar to B. chongzuoensis Yan Liu, S. M. Ku & C.-I Peng, but there are significant distinctions in their stipules, leaves and bracts. The conservation status of B. guangdongensis is assessed as Critically Endangered (CR), according to the IUCN Red List Categories and Criteria.

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Recircumscription of Begonia sect. Baryandra (Begoniaceae): evidence from molecular data.

Project description:BACKGROUND:Begonia sect. Diploclinium is a 'dust-bin' section for species retaining pleisiomorphic characters and lacking novel synapomorphic characters used to delimit other Asian sections in Begonia. Part of this large and polymorphous section is transferred to Begonia sect. Baryandra in a move towards a more natural classification for the genus. RESULTS:Phylogenetic analysis of nuclear ribosomal ITS DNA sequences show a strongly supported monophyletic group containing Philippine and Bornean species previously in Begonia sect. Diploclinium, and the type of Begonia sect. Baryandra, B. oxysperma. This clade forms the basis for the now much-expanded Begonia sect. Baryandra, which as defined here contains 49 species and has its centre of diversity in the Philippines. CONCLUSIONS:A natural classification for a much expanded Begonia sect. Baryandra has been provided. This paper highlights the feasibility of moving towards a natural classification of Asian Begonia step by step as information comes to light through building upon previous framework phylogenies with denser sampling.

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Development and characterization of EST-SSR markers for Begonia luzhaiensis (Begoniaceae).

Project description:Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa. The expressed sequence tag-simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis.

| S-EPMC5435407 | biostudies-literature

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