The complete chloroplast genome of Carpinus Laxiflora (Betulaceae)

Abstract

Carpinus laxiflora is a member of the family Betulaceae. In the present study, we analyzed the complete chloroplast genome sequence of C. laxiflora using the Ion Torrent Platform. We found that the chloroplast genome of C. laxiflora was 159,255 bp in length with a large single copy (LSC) region of 88,359 bp, a small single copy (SSC) region of 18,764 bp, and a pair of inverted repeats (IRs) of 26,066 bp. The overall GC content of the chloroplast genome was 36.5%. It contained 135 genes, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. A phylogenetic analysis indicated that C. laxiflora is closely related to C. monbeigiana.

Keywords:

• Carpinus laxiflora
• complete chloroplast genome
• Betulaceae
• phylogenetic tree

The genus Carpinus belongs to the family Betulaceae and consists of about 42 species that are mainly distributed between Europe and Eastern Asia (Holstein and Weigend 2017). Four of its species (C. cordata Blume, C. turczaninowii Hance, C. tschonoskii Maxim., and C. laxiflora (Siebold and Zucc.) Blume) are distributed in Korea, China, and Japan (Jeon and Chang 2000). Carpinus laxiflora is widely used as an industrial tree and timber in Korea (Song and Kim 2011). It is a major species of temperate and secondary forests in the temperate zone. Many ecological studies have suggested that C. laxiflora is a representative species of the climax forest in the temperate forests of South Korea (Byeon and Yun 2018). Previous studies on C. laxiflora focused on its phylogenetic relationships and were not based on complete chloroplast genome sequencing data (Yoo and Wen 2007). In the present study, we characterized the chloroplast DNA from C. laxiflora and confirmed its phylogenetic relationships with another 16 species in Betulaceae.

Individual plant materials were collected from Cheongyang, South Korea (N: 36°24′59.9″, E: 126°51′40.6″). Total DNA was isolated using a Plasmid SV mini kit (GeneAll, Seoul, Korea) and stored in a DNA bank (Division of Forest Genetic Resources DNA bank No.0122099500). Whole genome sequencing data were generated using the Ion Torrent Platform (Life Technologies Corporation, Carlsbad, CA). The sequenced fragments were assembled using Geneious 10.2.3. The tRNAs were confirmed using tRNAscan-SE (Lowe and Eddy 1997). A maximum likelihood (ML) tree was conducted using RAxML Blackbox web server, which used the rapid bootstrap method (Stamatakis et al. 2008; Stamatakis 2014). The tree analysis was conducted using 100 bootstrap replicates.

The complete chloroplast genome of C. laxiflora (GenBank: MK425701) was 159,255 bp, with a large single copy (LSC) region of 88,359 bp, a small single copy (SSC) region of 18,764 bp, and 2 inverted repeats (IRa and IRb) of 26,066 bp. The overall GC content was 36.5% (LSC, 34.3%; SSC, 30.1%; IRs, 42.5%). The genome contained 135 genes, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Seven of the protein-coding genes, four rRNA genes, and seven tRNA genes were duplicated in the IR regions. Fifteen genes contained a single intron and two genes had two introns (ycf3 and clpP). The results of the phylogenetic analysis determined from the chloroplast genomes of 17 species of Carpinus with an Ostrya species (using the outgroup). The results indicate that C. laxiflora is most closely related to C. monbeigiana (Figure 1). This information can be used as the basis for a variety of studies using C. laxiflora and population genomic studies of Carpinus species.

Figure 1. The phylogenetic tree of C. laxiflora with 16 species belonging to the Betulaceae based on chloroplast protein-coding sequences. Numbers in the nodes are the bootstrap values from 100 replicates.

Disclosure statement

The authors report no declaration of interest. The authors alone are responsible for the content and writing of this article.