Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes

Abstract

Genetic variations from few chloroplast DNA fragments show lower discriminatory power in the delimitation of closely related species and less resolution ability in discerning interspecific relationships than from nrITS. Here we use Orychophragmus (Brassicaceae) as a model system to test the hypothesis that the whole chloroplast genomes (plastomes), with accumulation of more variations despite the slow evolution, can overcome these weaknesses. We used Illumina sequencing technology via a reference-guided assembly to construct complete plastomes of 17 individuals from six putatively assumed species in the genus. All plastomes are highly conserved in genome structure, gene order, and orientation, and they are around 153 kb in length and contain 113 unique genes. However, nucleotide variations are quite substantial to support the delimitation of all sampled species and to resolve interspecific relationships with high statistical supports. As expected, the estimated divergences between major clades and species are lower than those estimated from nrITS probably due to the slow substitution rate of the plastomes. However, the plastome and nrITS phylogenies were contradictory in the placements of most species, thus suggesting that these species may have experienced complex non-bifurcating evolutions with incomplete lineage sorting and/or hybrid introgressions. Overall, our case study highlights the importance of using plastomes to examine species boundaries and establish an independent phylogeny to infer the speciation history of plants.

Plastomes of nine hornbeams and phylogenetic implications

“…They all include 75–77 unique protein‐coding genes, 18 unique tRNA gene sequences, and eight ribosomal RNA genes. In addition, the interspecific variations are clearly higher in the noncoding regions, including the intergenic spacers between genes, than in the coding genes (Figure ), as found in other groups (Hu et al., ; Zhang, Ma, & Li, ). The conserved and well‐aligned plastomes across different species therefore facilitate the further phylogenetic analyses and comparisons based on the whole plastomes, their coding regions, and noncoding regions.…”

“…It should be noted that we obtained identical topological relationships using the whole plastomes or noncoding datasets. However, results based solely on the coding genes suggested different phylogenetic positions for C. betulus and C. caroliniana (Figure ), presumably because the whole plastome and noncoding datasets provided more detailed signals for these two species (Hu et al., ; Zeng et al., ). These findings suggest that it is essential to assess the consistency of phylogenetic relationships based on whole plastomes and both their coding and noncoding regions, as well as their correspondence to phylogenies derived from analyses of nuclear genes or genomes.…”

“…Similar problems have been encountered in phylogenetic analyses of the closely related genus Ostrya (Lu et al., ). The poor resolution of the cited cpDNA phylogeny was probably at least partly due to insufficient informative sites in the sampled sequences, and clearly full plastome sequencing would improve the resolution (e.g., Hu et al., , ). Furthermore, well‐resolved cpDNA phylogenies would greatly facilitate clarification of reticulate evolution during species diversification (Jansen et al., ; Xu et al., ).…”

“…With the development of high‐throughput sequencing technology, it is becoming much cheaper and easier to sequence whole plastomes of plants (Hu et al., ; Zhang & Li, ) and thus increase the resolution of previously ambiguous phylogenetic relationships based on several cpDNA markers (Hu et al., ; Jansen et al., ). For example, Zeng et al.…”

Analyses of genome‐scale variation reveal divergence of two Sinalliaria species (Brassicaceae) with continuous but limited gene flow

“…C, 1D). The genome‐scale variation observed in this work agrees very well with that reported previously based on analyses of SSRs, low‐copy genes, and chloroplast DNA (Hu et al, , ; Zhang et al, ). The two studied species are well differentiated morphologically; notable distinguishing traits include the presence/absence of hairs on leaf blades and stems, the number of flowers produced by each individual, and corolla and flower sizes (Zhang et al, ).…”