Complete chloroplast genome of Ulleung Island endemic basswood, Tilia insularis (Malvaceae), in Korea

Abstract

The first complete chloroplast genome sequences of Korean endemic basswood in Ulleung Island, Tilia insularis, were reported in this study. The T. insularis plastome was 162,565 bp long, with the large single-copy (LSC) region of 91,100 bp, the small single-copy (SSC) region of 20,381 bp, and two inverted repeat (IR) regions of 25,542 bp. The plastome contained 131 genes, including 86 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. The overall GC content was 36.5%. Phylogenetic analysis of 14 representative plastomes within the family Malvaceae suggests that T. insularis is closely related to other congeneric species in subfamily Tilioideae.

Keywords:

• Chloroplast genome
• Korean endemic basswood
• Tilia insularis
• Ulleung Island
• Malvaceae

The basswood genus Tilia L. belongs to subfamily Tilioideae of Malvaceae and consists of 23 species widely distributed in the temperate northern hemisphere (Alverson et al. 1999; APG III 2009; Pigott 2012). Tilia is an ecologically important genus as one of the dominant deciduous tree species in the broad-leaved temperate forests and economically as useful timbers, honey resources, and ornamental trees (Pigott 2012; Cai et al. 2015; Bu and Park 2016). Of 23 species of Tilia, nine native and two cultivated species are known in Korea (Chung and Kim 1983; Kim and Chung 1986). Of nine native species, T. insularis Nakai is endemic to young volcanic Ulleung Island, which is located approximately 130 km east of the Korean peninsula (Nakai 1917; Kim 1985). Taxonomic status of T. insularis and its relationship to other species have long been controversial. For example, Yoon et al (2003) investigated the vegetative and reproductive morphology among T. amurensis, T. insularis, and T. taquetii in Korea and T. japonica in Japan, and concluded that the morphological differentiation among them were not sufficient enough to be recognized as distinct species. A similar morphological study between T. amurensis and T. insularis by Pigott (2008) also concluded that the two should be treated as conspecific. However, recent molecular phylogenetic study suggested that T. insularis is more closely related to T. japonica than T. amurensis (Bu and Park 2016). It is still required to determine the taxonomic status of T. insularis and its phylogenetic position (Chung and Kim 1983; Choi 2008). In this study, we sequenced the complete chloroplast genome of T. insularis and compared it to congeneric species.

Total DNA (Voucher specimen: KNU-Lee171010) was isolated using the DNeasy plant Mini Kit (Quiagen, Carlsbad, CA) and sequenced by the Illumina HiSeq 4000 (Illumina Inc., San Diego, CA). A total of 31,656,366 paired-end reads were obtained and assembled de novo with Velvet v. 1.2.10 using multiple k-mers (Zerbino and Birney 2008). The tRNAs were confirmed using tRNAsacn-SE (Lowe and Eddy 1997). The total plastome length of T. insularis (MH169579) was 162,565 bp, with large single copy (LSC; 91,100 bp), small single copy (SSC; 20,381 bp), and two inverted repeats (IRa and IRb; 25,542 bp each). The overall GC content was 36.5% (LSC, 34.2%; SSC, 31.0%; IRs, 43.0%) and the plastome contained 131 genes, including 86 protein-coding, eight rRNA, and 37 tRNA genes. A total of 17 genes were duplicated in the inverted repeat regions including seven tRNA, four rRNA, and six protein-coding genes. The complete ycf1 gene was included in the IR at the SSC/IRa junction and the infA gene located in LSC became a pseudogene.

To confirm the phylogenetic position of T. insularis, 14 representative species of Malvaceae were aligned using MAFFT v.7 (Katoh and Standley 2013) and maximum likelihood (ML) analysis was conducted based on the concatenated 77 coding genes using IQ-TREE v.1.4.2 (Nguyen et al. 2015). The ML tree showed that T. insularis formed polytomy with T. manshurica, T. paucicostata, and T. oliveri.

Figure 1. The maximum-likelihood (ML) tree based on 77 protein-coding genes in the 14 representative chloroplast genomes of Malvaceae. The bootstrap value based on 1000 replicates is shown on each node.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education [2011-0023620 and 2017RID1A3B03034296].