Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae

Abstract

Background: The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy.

Results: The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship.

Conclusions: Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.

Keywords: Rhus; Chloroplast phylogenomics; Genome sequencing; Sumac.

Fig. 1

Chloroplast genome map of Rhus glabra (Accession No. OR800752). Genes encoded in the forward direction are located on the outside of the ring, while those encoded in the reverse direction on the inside of the ring. The gray circles inside represent the GC content

Fig. 2

The type and distribution of SSRs in the three Rhus chloroplast genomes. A: Proportion of SSR distribution in the intergenic spacer, exon and intron; B: Frequency of SSR occurrence in the LSC, SSC, and IR region; C: SSR repeat types and numbers

Fig. 3

Comparison of the borders of the LSC, SSC and IR regions in chloroplast genomes of Rhus. The junction of these parts, i.e., JLB (junction of LSC and IRb), JSB (junction of SSC and IRb), JSA (junction of SSC and IRa) and JLA (junction of LSC and IRa)

Fig. 4

Visualization map of genome alignment of the chloroplast genomes using Rhus glabra (OR800752) as a reference by mVISTA. X-axis: the coordinates in chloroplast genomes; Y-axis: the average percent identity (50–100%)

Fig. 5

Sliding-window analysis of the chloroplast genomes in Rhus genus. Window length: 800 bp; step size: 200 bp; X-axis: position of the midpoint of a window; Y-axis: nucleotide diversity of each window

Fig. 6

The Ka/Ks ratios of 78 protein-coding genes in the Rhus genus taking Pistacia chinensis (MK738124) as a reference

Fig. 7

Maximum likelihood (ML) tree constructed by protein-coding genes of the Anarcadiceae chloroplast genomes. Stars represent nodes with 100% bootstrap values. Dots represent three Rhus individuals in this study