The complete chloroplast genome sequence of Begonia gulongshanesis (Begoniaceæ)

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.

Keywords:

• Begonia gulongshanensis
• chloroplast genome
• genome assembly
• phylogenetic tree

Begonia L. (Begoniaceae) was mainly distributed in tropical and subtropical areas (Tian et al. 2018), and 2,039 species in Begonia L. have been published (Hughes et al. 2015–Prensent). As the sixth largest genus in the world, it contains tuberous, semi-tuberous, moniliform, rhizomatous, trailing (scandent), and shrub-like species, and there is a huge diversity in habitat, habit, plant size, leaf type, flower and fruit morphology between different species (Tian et al. 2018). 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 medicine or vegetable (Guan et al. 2007). In the last 20 years, many new species have been discovered because of increasing attention from people (Tian et al. 2018; Dong and Liu 2019; Van et al. 2021) predicted that the number of species of Begonia may actually in total between 2000 and 2500. However, the classification of species in Begonia is still controversial, due to the traditional classification method is mainly based on morphological observations. In recent years, taxonomists have solved some taxonomic problems through a combination of morphology and molecular technology, but there are still a large number of species that lack molecular data, and there is still a lot of work remains to be done.

Begonia gulongshanensis is a newly reported species in 2018 which occurs exclusively in Jingxi county of Guangxi province in Southern China (Chen et al. 2018). It is only grows on the moist surface of shady cliffs at the entrance to shallow caves in a deep valley, with a white area on the leaves (Chen et al. 2018). Due to the rare distribution in the wild, B. gulongshanensis was listed as class II protected plant in the List of National Key Protected Wild Plants in September 2021 (National Forestry and Grassland Administration & Ministry of Agriculture and Rural Affairs of the People’s Republic of China 2021). So far, there have been few studies on the molecular and phylogeny of this species. The purpose of this study was to complete the sequencing of the chloroplast genome of B. gulongshanensis and study its phylogeny, so as to provide reference for the future research on the genetic relationship between it and other Begonia species, and provide a foundation for its conservation, exploitation and utilization, and to provide reference for subsequent intraspecific classification of Begonia.

We collected the leaf samples of B. gulongshanensis from Jingxi county of Guangxi province (106°39’30′’E, 23°0’35′’N, 550 m above sea level). The collected reference samples were deposited in the Flower Research Institute, Guangxi Academy of Agricultural Sciences (http://www.gxaas.net/), and the voucher number was GXAAS-B00158 (collected by Jinye Zhou, [email protected]). The Illumina NovaSeq 6000 platform was used to paired-end sequencing of extracted genomic DNA, and the sequencing read length was 150 bp. Then, we assembled the chloroplast genome by SPAdes v3.10.1 (Bankevich et al. 2012), finally, annotated the chloroplast genome B. gulongshanensis by CPGAVAS 2 (Shi et al. 2019). We submitted the assembled chloroplast genome and the annotations to GenBank, and obtained the accession number MZ671995. In order to construct the phylogenetic tree of B. gulongshanensis, another 21 species (3 species from Begonia L., and 18 species from other families of Rosanae) were compared and analysised by via MAFFT v.7.271 (Katoh et al. 2005) and RAxML v8.0 (Stamatakis 2014).

The assembled chloroplast genome of B. gulongshanensis was 169,153 bp in size, with a typical quarter structure which contained a large single-copy region (LSC) of 75,998 bp, a small single-copy region (SSC) of 18,063 bp, and two inverted repeat regions (IRA and IRB) of the same 37,546 bp. The total GC content is 35.51%. The annotated results showed that there were 140 genes in B. gulongshanensis chloroplast genome, including 42 transfer RNA genes (tRNAs), 8 ribosomal RNA genes (rRNAs) and 90 protein-coding genes (PCGs). The phylogenetic analysis showed that Begoniaceae was closest to Cucurbitaceae and Corynocarpaceae, which also belong to Cucurbitales, followed by Rosales, and had the most distant with Fabales. Although B. gulongshanensis was clustered with the other three begonias, there was still a certain distance between them. We speculated that this was because the B. gulongshanensis belonged to the section Coelocentrum while the other three begonias belonged to the section Platycentrum (Figure 1).

Figure 1. The phylogenetic tree based on the complete chloroplast genome of B. gulongshanensis and 21 other published species. The bootstrap support values are displayed next to the nodes.

Acknowledgment

The authors thank APExBIO Co., Ltd (Shanghai, China) for assistance in sequencing.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The complete sequence of the chloroplast genome of B. gulongshanensis have been deposited in GenBank at https://www.ncbi.nlm.nih.gov/, and the accession no. was MZ671995. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA770846, SRR16311536, and SAMN22241481, respectively.

Correction Statement

This article has been republished with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This word was supported by the Guangxi Natural Science Foundation under Grant [No. 2020GXNSFAA259064], [No. 2020GXNSFAA297068], [No. 2020GXNSFBA297074]; and the Research and Development Fund of Guangxi Academy of Agricultural Sciences under Grant [GUINONGKE-2021YT135], [GUINONGKE-2021JM115], [GUINONGKE-2021YM157], [NKYCZ202107].