Comparative analysis of mitochondrial genomes of two alpine medicinal plants of Gentiana (Gentianaceae)

Abstract

Gentiana crassicaulis and G. straminea are alpine plants of Gentiana with important medicinal value and complex genetic backgrounds. In this study, the mitochondrial genomes (mtDNAs) of these two species were sequenced. The mtDNAs of G. crassicaulis and G. straminea are 368,808 and 410,086 bp long, respectively, 52 and 49 unique genes are annotated in the two species, and the gene arrangement varies widely. Compared to G. crassicaulis, G. straminea loses three effective genes, namely atp6, trnG-GCC and trnV-GAC. As a pseudogene, the atp6 gene of G. straminea is incomplete, which is rare in higher plants. We detected 1696 and 1858 pairs of long repeats and 213 SSRs and 250 SSs in the mtDNAs of G. crassicaulis and G. straminea, respectively. There are 392 SNPs and 18 InDels between the two genomes, and syntenic sequence and structural variation analysis show low collinearity between the two genomes. Chloroplast DNA transferring to mtDNA is observed in both species, and 46,511 and 55,043 bp transferred segments containing three tRNA genes are identified, respectively. Comparative analysis of mtDNAs of G. crassicaulis, G. straminea and four species of Gentianales determined 18 core genes, and there is no specific gene in G. crassicaulis and G. straminea. The phylogenetic tree based on mtDNAs places Gentianaceae in a branch of Gentianales. This study is the first to analyze the mtDNAs of Gentianaceae, which could provide information for analysis of the structure of mtDNAs of higher plants and phylogenetic research of Gentianaceae and Gentianales.

Fig 1. Mitochondrial genome map of Gentiana crassicaulis (A) and G. straminea (B).

Genes (exons are shown as closed boxes) shown outside the curve are transcribed counterclockwise, whereas those inside are transcribed clockwise. Genes from the same protein complex are colored the same.

Fig 2. Location of atp6 in mitochondrial genomes of Gentiana crassicaulis and G. straminea.

This figure is not to scale.

Fig 3. Large repeat sequence characteristics of mitochondrial genomes of Gentiana crassicaulis and G. straminea.

Fig 4. SSR characteristics of mitochondrial genomes of Gentiana crassicaulis and G. straminea.

Fig 5. Collinear relationship between the mitochondrial genomes of Gentiana crassicaulis and G. straminea.

The upper and lower bars represented the mitochondrial genomes. Dark-orange and blue regions in each bar represented the forward and reverse direction of the aligned genome, respectively. White regions in each bar represent the sequences that could not be aligned to the other genome. Lines between the two bars indicated the syntenic types and locations: magenta, blue-green, dark yellow and light-green represent collinearity, translocation, inversion and translocation+inversion, respectively.

Fig 6. Structural variation map of mitochondrial genomes of Gentiana crassicaulis and G. straminea.

The inner circle is the G. crassicaulis genome, and the outer circle is the G. straminea genome. Collinear: homologous region; translocation: translocation region; inversion: inverted region; tran+inver: translocation and inversion region; insertion: insertion region with length ≥50 bp; deletion: deletion region with length ≥50 bp; complexInDel: region without alignment but corresponding to location; forward_chain: forward chain of a genomic sequence, at which time the gene sitz markers increase clockwise; reverse_chain: the reverse chain of a genomic sequence, where the gene coordinates increase counterclockwise.

Fig 7. Gene exchange in chloroplast genome and mitochondrial genome of Gentiana crassicaulis (A) and G. straminea (B).

The green lines within the circle show the regions of the chloroplast genome those have been inserted into different locations of the mitochondrial genome.

Fig 8. Core and specific genes of six Gentianales plants.

Fig 9. Molecular phylogenetic tree of 33 species based on the complete mitochondrial genomes.

The tree was constructed via a maximum-likelihood analysis using PhyML 3.0 with 1000 bootstrap replications.