Comparative Genomic and Phylogenetic Analysis of Chloroplast Genomes of Hawthorn (Crataegus spp.) in Southwest China

Abstract

The hawthorns (Crataegus spp.) are widely distributed and famous for their edible and medicinal values. There are ∼18 species and seven varieties of hawthorn in China distributed throughout the country. We now report the chloroplast genome sequences from C. scabrifolia, C. chungtienensis and C. oresbia, from the southwest of China and compare them with the previously released six species in Crataegus and four species in Rosaceae. The chloroplast genome structure of Crataegus is typical and can be divided into four parts. The genome sizes are between 159,654 and 159,898bp. The three newly sequenced chloroplast genomes encode 132 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis of the chloroplast genomes revealed six divergent hotspot regions, including ndhA, rps16-trnQ-UUG, ndhF-rpl32, rps16-psbK, trnR-UCU-atpA and rpl32-trnL-UAG. According to the correlation and co-occurrence analysis of repeats with indels and SNPs, the relationship between them cannot be ignored. The phylogenetic tree constructed based on the complete chloroplast genome and intergenic region sequences indicated that C. scabrifolia has a different origin from C. chungtienensis and C. oresbia. We support the placement of C. hupehensis, C. cuneata, C. scabrifolia in C. subg. Crataegus and C. kansuensis, C. oresbia, C. kansuensis in C. subg. Sanguineae. In addition, based on the morphology, geographic distribution and phylogenetic relationships of C. chungtienensis and C. oresbia, we speculate that these two species may be the same species. In conclusion, this study has enriched the chloroplast genome resources of Crataegus and provided valuable information for the phylogeny and species identification of this genus.

Keywords: Crataegus spp.; chloroplast genome; comparative analysis; hawthorn; phylogenetic analysis.

FIGURE 1

Chloroplast genome maps of Crataegus (C. oresbia, C. scabrifolia, C. chungtienesis). In the diagram, different colors indicate genes with different functions. The genes inside circles are transcribed clockwise and genes outside circles are transcribed counterclockwise. Two inverted repeats (IRa and IRb), a large single copy region (LSC) and small single copy region (SSC) regions are shown in the inner circles. The light gray inner circles indicate A/T content and the dark gray circles indicate G/C content.

FIGURE 2

Heatmap analysis of relative synonymous codon usage (RSCU) values among the 9 species of Crataegus.

FIGURE 3

Complete chloroplast genome comparison of 13 species of Rosaceae. Gray arrows indicate the direction of the gene. The dark blue regions represent exons. Pink regions represent noncoding sequences (CNS), and white peaks represent genomic differences. The Y-axis represents the percentage, from 50 to 100%.

FIGURE 4

Sliding window analysis based on the cp genomes of 9 Crataegus species.

FIGURE 5

Comparison of the borders of the LSC, SSC, and IR regions among 9 Crataegus chloroplast genomes and four species of Rosaceae.

FIGURE 6

Phylogenetic tree of Crataegus within the Rosaceae. The entire genome data set was analyzed using maximum likelihood (ML) and Bayesian information (BI). Different colors represent different clades (A,B).

FIGURE 7

Phylogenetic tree of Crataegus based on the sequences of five intergenic regions. The different colors represent the different evolutionary branches clades (clade A and clade B) in the phylogenetic tree constructed from the complete chloroplast genome. (A) Phylogenetic tree constructed by maximum likelihood (ML). (B) Phylogenetic tree constructed by maximum Bayesian method (BI).