Morphological Characteristics and Comparative Chloroplast Genome Analyses between Red and White Flower Phenotypes of Pyracantha fortuneana (Maxim.) Li (Rosaceae), with Implications for Taxonomy and Phylogeny

Abstract

Pyracantha fortuneana (Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western Hubei, China, showing great ornamental potential. In this study, the complete chloroplast genome of the red flower phenotype of P. fortuneana was reported for the first time, using high-throughput sequencing technology. The complete chloroplast genome was 160,361 bp in length and showed a typical quadripartite structure with a pair of inverted repeat (IR) regions (26,350 bp) separated by a large single-copy (LSC) region (88,316 bp) and a small single-copy (SSC) region (19,345 bp). A total of 131 functional genes were annotated in this chloroplast genome, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. Comparative chloroplast genome analyses revealed that high genome similarity existed not only between red and white flower phenotypes of P. fortuneana, but also among Pyracantha species. No evidence for positive selection was found in any PCG, suggesting the evolutionary conservation of Pyracantha chloroplast genomes. Furthermore, four mutational hotspots (trnG-trnR-atpA, psbZ-trnG-trnfM-rps14, ycf3-trnS-rps4, and ndhF-rpl32) with π > 0.004 were identified as potential molecular markers for Pyracantha species. Phylogenomic analysis strongly supported that the red flower phenotype of P. fortuneana was nested within the common white flower phenotype. Based on both morphological and molecular evidence, we suggest that the red flower phenotype of P. fortuneana could be considered as a new forma. Overall, the availability of these genetic resources will not only offer valuable information for further studies on molecular taxonomy, phylogeny, and population genetics of Pyracantha species but also could be used as potential genetic resources for Chinese firethorn breeding.

Keywords: Pyracantha fortuneana; chloroplast genome; comparative analysis; red flower phenotype; taxonomic investigation.

Figure 1

Morphological comparison between red and white flower phenotypes of P. fortuneana. (A) (B) the flowers and young fruits of individual with the red flower phenotype; (C,D) the flowers and mature fruits of individual with the white flower phenotype (photographed by Shi-Xiong Ding).

Figure 2

The circular chloroplast genome map of P. fortuneana (red). The genes drawn inside the circle are transcribed counterclockwise while those outside are transcribed clockwise. Different functional genes are differently colored on the outer circle. The dashed darker gray area in the inner circle denotes GC content, and the lighter gray area corresponds to AT content.

Figure 3

Comparative junction characteristics of LSC, SSC, and IR regions of chloroplast genomes between three accessions of P. fortuneana and two other Pyracantha species. JLB, JSB, JSA, and JLA represent four different junction regions in the chloroplast genome boundaries.

Figure 4

Comparative analysis plots of RSCU values for the six Pyracantha chloroplast genomes. Each amino acid corresponds to six histograms, and their heights represent the RSCU value. The histograms from left to right are P. atalantioides, P. angustifolia, P. coccinea, P. fortuneana (red), P. fortuneana-1 (white), and P. fortuneana-2 (white).

Figure 5

The predicted RNA editing sites in protein-coding genes of P. fortuneana chloroplast genomes.

Figure 6

Analyses of SSRs in six Pyracantha chloroplast genomes. (A) Frequency of SSR types. (B) Frequency of different SSR units. (C) Frequency of SSRs in LSC, SSC, and IR regions.

Figure 7

The nucleotide diversity (Pi) of six Pyracantha chloroplast genomes.

Figure 8

Distance-based NJ tree of the genus Pyracantha inferred from chloroplast genome sequences.

Figure 9

The phylogenetic tree of the genus Pyracantha inferred from chloroplast genome sequences based on the methods of maximum likelihood (ML) and Bayesian inference (BI). The BI posterior probabilities/ML bootstrap values are displayed above the lines.