Complete plastid genome of Gentiana trichotoma (Gentianaceae) and phylogenetic analysis

Abstract

The complete plastid genome of Gentiana trichotoma was determined and analyzed in this work. It had a circular-mapping molecular with the length of 144,759 bp, has similar gene composition with G. section Cruciata but contains 10 more genes than G. section Kudoa. Phylogenetic analysis showed that G. trichotoma clustered together with section Kudoa rather than section Cruciata. The plastome provided in this work would be useful for elucidation of Gentiana evolution.

As a big genus containing 15 sections (Ho and Liu 2001), Gentiana plants are typically alpine and important parts of alpine shrub and meadow. Gentiana trichotoma Kusnezow, belonging to section Frigidae Kusnezow, is endemic to the Qinghai-Tibetan Plateau (Ho and Liu 2001). However, there has been no genomic studies in section Frigidae.

Herein, we reported and characterized the complete G. trichotoma platome (MN089577). One G. trichotoma individual (specimen number: Fu2016163-6) was collected from Daocheng, Sichuan Province of China (29°27′09″N, 100°13′27″E) and its voucher specimens was deposited in the herbarium of School of Life Science, Luoyang Normal University. The fragmented genomic DNA was sequenced using Illumina HiSeq 2500 platform (Novogene, Tianjing, China), yielding approximately 5 Gb of 150-bp paired-end. The plastome was de novo assembled in NOVOPlasty 2.6.1 (Dierckxsens et al. 2016) and then annotated in GeSeq (Tillich et al. 2017) using the default parameters. Comparative analysis was conducted in mVISTA (Frazer et al. 2004) with G. straminea (Ni et al. 2016) and G. lawrencei var. farreri (Fu et al. 2016) which represents the only two plastome-available Gentiana sections, Cruciata Gaudin, and Kudoa (Masamune) Satake & Toyokuni ex Toyokuni, respectively. Shared protein-coding genes in plastomes of available Gentiana species were extracted and concatenated, then aligned using MAFFT (Katoh et al. 2002). The ML phylogeny was performed with IQ-TREE (Nguyen et al. 2015) in PhyloSuite (Zhang et al. 2018) with 1000 replicates. Swertia mussotii (KC875852) and S. verticillifolia (MF795137) were served as the outgroups.

The complete G. trichotoma platome is a circular-mapping molecule with the length of 144,759 bp. The LSC, IR, and SSC regions were 77,430, 25,162, and 17,005 bp, respectively. The overall GC content of the platome was 37.8%. A total of 130 genes were annotated, containing 88 protein-coding genes, 34 tRNA genes, and 8 rRNA genes. Comparison analysis indicated that platome of G. trichotoma has similar gene composition with section Cruciata (Ni et al. 2016; Zhou et al. 2018), with hotspots locating at intergenic regions such as trnK-^UUU–rps16, atpH–atpI, petN–trnD, and trnL-^UAG–ccsA. However, gene loss was not detected in G. trichotoma, which is different with section Kudoa which has almost lost 10 ndh genes (Sun et al. 2018). Phylogenetic analysis showed that G. trichotoma was clustered together with section Kudoa rather than section Cruciata (Figure 1), which is consistent with the previous study (Favre et al. 2016). Gentiana stipitata belonging to section Kudoa was clustered with section Cruciata, which is consistent with the previous study (Sun et al. 2018), indicating that more taxa should be involved for further study. The determination of the G. trichotoma platome sequences provided new molecular data to illuminate the Gentiana evolution.

Figure 1.

Phylogenetic tree (maximum likelihood) based on protein-coding genes of Gentiana plastomes. The asterisks along the branches mean 100% bootstrap supports based on 1000 replicates. The underline located in Genbank accession numbers indicates newly determined plastid genomes.

Disclosure statement

There are no conflicts of interest for all the authors including the implementation of research experiments and writing this article.