Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution

Abstract

Urophysa is a Chinese endemic genus comprising two species, Urophysa rockii and Urophysa henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these two species and of their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare sequences, elucidate the intra- and interspecies variations, and infer the phylogeny relationship with other Ranunculaceae family species. A typical quadripartite structure was detected, with a genome size from 158,473 to 158,512 bp, consisting of a pair of inverted repeats separated by a small single-copy region and a large single-copy region. We analyzed the nucleotide diversity and repeated sequences components and conducted a positive selection analysis by the codon-based substitution on single-copy coding sequence (CDS). Seven regions were found to possess relatively high nucleotide diversity, and numerous variable repeats and simple sequence repeats (SSR) markers were detected. Six single-copy genes (atpA, rpl20, psaA, atpB, ndhI, and rbcL) resulted to have high posterior probabilities of codon sites in the positive selection analysis, which means that the six genes may be under a great selection pressure. The visualization results of the six genes showed that the amino acid properties across each column of all species are variable in different genera. All these regions with high nucleotide diversity, abundant repeats, and under positive selection will provide potential plastid markers for further taxonomic, phylogenetic, and population genetics studies in Urophysa and its relatives. Phylogenetic analyses based on the 79 single-copy genes, the whole complete genome sequences, and all CDS sequences showed same topologies with high support, and U. rockii was closely clustered with U. henryi within the Urophysa genus, with S. adoxoides as their closest relative. Therefore, the complete cp genomes in Urophysa species provide interesting insights and valuable information that can be used to identify related species and reconstruct their phylogeny.

Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution

“…Future phylogenomic studies require more extensive taxonomic sampling, especially subgenus Liliorhiza of genus Fritillaria to discern the relationships among the Old and New World clades of Fritillaria and Lilium. Moreover, some efforts should focus on the evolutionary and adaptive researches of Fritillaria species in the future as the recent studies suggested [63,64]. In conclusion, our results will be valuable to understand the evolutionary relationship between Fritillaria and Lilium, especially plastid gene evolution of Fritillaria.…”

Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

“…Due to these advantages, plastid genomes have been widely applied to molecular identification, divergence dating and phylogenetic analysis [20,[24][25][26][27].The rapid development of high-throughput sequencing technology has greatly facilitated the acquisition of genome data. With the advantages of high-throughput and low cost-effectiveness, an increasing number of plastid genomes of plants have been sequenced and assembled in recent years, and more genetic resources are analyzed via different bioinformatics approaches [28,29]. The high-throughput sequencing technology and vast information of plastid genomes mark a new era of population genomics and phylogenetic studies.In our study, we used the NGS to obtain the complete plastid DNA sequences of two Bupleurum species (B. chinense and B. commelynoideum), then counted and analyzed their gene content, order and structure.…”

“…The rapid development of high-throughput sequencing technology has greatly facilitated the acquisition of genome data. With the advantages of high-throughput and low cost-effectiveness, an increasing number of plastid genomes of plants have been sequenced and assembled in recent years, and more genetic resources are analyzed via different bioinformatics approaches [28,29]. The high-throughput sequencing technology and vast information of plastid genomes mark a new era of population genomics and phylogenetic studies.…”

Characteristics of the Completed Chloroplast Genome Sequence of Xanthium Spinosum: Comparative Analyses, Identification of Mutational Hotspots and Phylogenetic Implications

“…The repeat units, that are dispersed in chloroplast genomes with high frequency, play a signi cant role in genome evolution [25][26][27][28]. The X. spinosum chloroplast consists of 264 direct, 256 palindromic, 251 reverse and 228 complement repeats.…”