Chloroplast genome features and phylogenomic placement of Lespedeza bicolor (Fabaceae)

Abstract

The complete chloroplast genome (plastome) of a deciduous shrub Lespedeza bicolor (commonly called bush clover) was determined in this study. The plastome was 148,930 bp in size with a canonical quadripartite structure, including two inverted repeats regions of 23,827 bp for each, a large single-copy region of 82,338 bp in length, and a small single-copy region of 18,938 bp in length. The overall guanine-cytosine (GC) content of this plastome was 35.0%. A total of 112 unique genes was annotated in this plastome, including four rRNA genes, 30 tRNA genes, and 78 protein-coding genes. Among them, two protein-coding genes (clpP and ycf3) contained two introns, and eight protein-coding genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpoC1, and rps16) and six tRNA genes (trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) contained one intron. ML phylogenetic analysis showed that L. bicolor was sister to other Lespedeza species.

Keywords:

• Lespedeza bicolor plastome
• phylogeny

The genus Lespedeza, belonging to Fabaceae family, contained ca. 40 species with high economic and medicinal value (Xu, et al. 2012). Species in this genus are mainly distributed in eastern Asia and eastern North America. Species identification for this genus is difficult if only using morphological evidence. L. bicolor, commonly called bush clover, is a deciduous shrub. Its native range is eastern Asia. It is hermaphrodite and is pollinated by insects. L. bicolor is an important ornamental plant due to its inflorescence. As a semi-woody perennial legume, it can fix nitrogen and may be used to prevent soil erosion. In this study, we reported the plastome of L. bicolor and resolved its phylogenetic relationship with other Lespedeza species.

Fresh leaves of L. bicolor were collected from Qianfo Mountain (Shandong, China; 36°37′N, 117°2′E). Voucher specimen (SD149) was deposited at College of Life Sciences, Shandong Normal University. Total genomic DNA was extracted by using the modified CTAB method, and was sequenced by the Novaseq platform at Novogene (Beijing, China). Plastome assembly was performed with Organelle Genome Assembler (OGA) as described in Qu, Fan, et al. (2019). Plastome annotation was performed with Plastid Genome Annotator (PGA) (Qu, Moore, et al. 2019), with manual correction with Geneious v9.1.4. The annotated complete plastome was submitted to GenBank under accession number MT083894.

Complete plastome of L. bicolor was 148,930 bp in size with a canonical quadripartite structure, including two inverted repeats regions of 23,827 bp for each, a large single-copy region of 82,338 bp in length, and a small single-copy region of 18,938 bp in length. The overall guanine-cytosine (GC) content was 35.0%. A total of 112 unique genes was annotated in this plastome, including four rRNA genes, 30 tRNA genes, and 78 protein-coding genes. Among them, two protein-coding genes (clpP and ycf3) contained two introns, and eight protein-coding genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpoC1, and rps16) and six tRNA genes (trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) contained one intron.

A maximum likelihood (ML) tree was reconstructed to determine the phylogenetic relationships of L. bicolor with other Lespedeza species by using RAxML v8.2.10 (Stamatakis 2014), including tree robustness assessment with 1,000 rapid bootstrap replicates, and GTRGAMMA substitution model. Alignment of 78 shared protein-coding genes was conducted by using MAFFT v7.313 (Katoh and Standley 2013). ML phylogenetic analysis showed that L. bicolor was sister to other Lespedeza species (Figure 1).

Figure 1. A maximum likelihood (ML) tree based on alignment of 78 shared protein-coding genes in plastome. Mucuna macrocarpa is used as outgroup. The numbers behind each node are bootstrap support values.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The study was financially supported by “Collection, Preservation and Accurate Identification of Stress-Resistant Tree Species Germplasm Resources” of Shandong Provincial Agricultural Elite Varieties Project [2019LZGC01803].