Characterization of the complete chloroplast genome of Gypsophila huashanensis Y. W. Tsui & D. Q. Lu, an endemic herb species in China

Abstract

Gypsophila huashanensis Y. W. Tsui & D. Q. Lu (Caryophyllaceae) is an endemic herb species to the Qinling Mountains in China. In this study, we characterized its whole plastid genome using the Illumina sequencing platform. The complete plastid genome of G. huashanensis is 152,457 bp in length, including a large single-copy DNA region of 83,476 bp, a small single-copy DNA region of 17,345 bp, and a pair of inverted repeat DNA sequences of 25,818 bp. The genome contains 130 genes comprising 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Evolutionary analysis showed that the non-coding regions of Caryophyllaceae exhibit a higher level of divergence than the exon regions. Gene site selection analysis suggested that 11 coding protein genes (accD, atpF, ndhA, ndhB, petB, petD, rpoCl, rpoC2, rps16, ycfl, and ycf2) have some sites under protein sequence evolution. Phylogenetic analysis showed that G. huashanensis is most closely related to the congeneric species G. oldhamiana. These results are very useful for studying phylogenetic evolution and species divergence in the family Caryophyllaceae.

Keywords: Chloroplast genome; Gypsophila huashanensis; evolutionary selection; phylogenetic relationship.

Figure 1.

Plant characteristics image of Gypsophila huashanensis. The flower characteristics of G. huashanensis is the corymbose cymes terminal or borne in distal leaf axils, in subcapitate clusters; petals pinkish white, oblong-oblanceolate, ca. 5 mm, apex retuse; filaments exserted, linear, flat, unequal, shorter than to longer than petals, base broad. The photograph was taken by the authors in the Qinling Mountains (108°55′23.115756″N, 34°14′58.102116″E, altitude 394.7 m).

Figure 2.

Circular map of the complete chloroplast genome of Gypsophila huashanensis. The center of the figure provides the specific information (genome length, GC content, and number of genes) of the G. huashanensis complete chloroplast genome sequence. From the center to the outside, the first track uses different colors to show the large single-copy (LSC) region (deep blue), small single-copy (SSC) region (light blue), and two inverted repeat (IRa and IRb) regions (gray). The GC content throughout the genome is plotted in the second track. Genes are indicated in the outermost track and color coded according to their functional classifications. The directions of transcription for the inner and outer genes are clockwise and anticlockwise, respectively. Different colors represent different gene types, the detailed gene types are listed in the captions.

Figure 3.

Phylogenetic relationships among Gypsophila huashanensis inferred from (a) maximum-likelihood (ML) method, and (b) maximum parsimony method based on concatenated complete chloroplast genome sequence of 21 species with two outgroups (Phytolaccaceae). *Newly sequenced plastid genome of Gypsophila huashanensis. The number on the branch represents bootstrap support. GenBank accession numbers of the following sequences were used: G. oldhamiana NC058757 (Jeong et al. 2021^a), A. githago NC023357 (Sloan et al. 2014), S. chalcedonica NC023359 (Sloan et al. 2014), S. paradoxa NC023360 (Sloan et al. 2014), S. conoidea NC023358 (Sloan et al. 2014), P. setulosa NC041462 (Kim and Park 2019^a), P. heterantha NC058231 (Kim et al. 2021^a), P. palibiniana MK120981 (Kim et al. 2021^a), P. longipedicellata MH373593 (Kim et al. 2021^a), P. okamotoi NC039974 (Kim et al. 2019^a), C. lycopodioides NC053721 (Androsiuk et al. 2020), C. acicularis NC053724 (Androsiuk et al. 2020), C. nivicola NC053720 (Androsiuk et al. 2020), C. pulvinatus NC053719 (Androsiuk et al. 2020), C. apetalus NC036424 (Androsiuk et al. 2017^a), C. affinis NC053722 (Androsiuk et al. 2020), C. subulatus NC053723 (Androsiuk et al. 2020), C. quitensis NC028080 (Lee et al. 2015^a), Monococcus echinophorus MH286317 (Yao et al. 2019), Phytolacca insularis NC041113 (Yang et al. 2019). ^aDirect submission to NCBI, unpublished.

Figure 4.

Sequence alignment of chloroplast genomes from 19 Caryophyllaceae species. Chloroplast genome sequences were aligned and compared with mVISTA software. The X-axis and Y-axis indicate the coordinates within the chloroplast genome and percentage identity (ranging from 50 to 100%), respectively. The grey arrows indicate the gene directions in the chloroplast genomes. Purple and pink bars represent exons and conserved non-coding sequences in chloroplast genomes, respectively.