Remarkably conserved plastid genomes of Quercus group Cerris in China: comparative and phylogenetic analyses

Abstract

Quercus is one of the most important plant genera in terms of economic and ecological values, with approximately 500 species worldwide. Quercus group Cerris is endemic to Eurasia (with 11 species), and three species (Quercus acutissima, Quercus chenii and Quercus variabilis) are widely distributed in China. Here, we sequenced the complete plastid genomes of Q. acutissima and Q. chenii by Illumina pair‐end sequencing and obtained an additional plastome of Q. variabilis from GenBank. In spite of geographically distant sampling, the three available plastomes of Cerris were remarkably conserved with regard to genome size, gene organization, GC content, and IR/SC boundary regions. A phylogenetic analysis showed that the Cerris group is nested within the Ilex group, forming a Cerris‐Ilex clade. The current study provide plastid genomic‐scale data for the less intensively studied Cerris group, which should be useful for studying speciation processes, geographical structure and phylogeny within the group in the future.

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

“…Higher nucleotide diversity has been found in SCs compared with IRs and in noncoding regions compared with coding regions, which is in accordance with the results found for other taxa [43][44][45]63,68], although exceptions have been identified [32,69]. A cp genome has a copy-dependent repair mechanism that ensures the uniformity and stability of two IR regions in sequence and enhances the stability and conservation of the genome [70,71], which might explain the lower sequence divergence in the IRs compared with the LSC or SSC regions, because natural selection coding regions are more conserved than non-coding regions [72].…”

“…Efficient molecular markers might be selected by using auxiliary information from the uneven distribution of cpSSRs for phylogenetic and phylogeographical studies [38,96,97]. In addition, the majority of cpSSRs in the Q. bawanglingensis cp genome mononucleotides and dinucleotides are formed by A and T, which might be related to the high AT richness in the nucleotide composition, similar to the results found for other cp genomes [39,43,46,98].…”

“…In general, the complete cp genome of Q. bawanglingensis has a strong resemblance to those of other Quercus species in the aspects of genome size and structure, GC content, genes and gene order, which illustrates that the cp genomes are conserved in Quercus [43][44][45]62,63]. Nonetheless, changes in the border of LSC/IRb and the nucleotide variability were detected, which are relatively common in plants [15,46,64].…”

“…Thus, a high-resolution and supported molecular phylogenetic tree is necessary. Obtaining cp genome information is necessary due to the lack of data on Q. bawanglingensis, and the importance and availability of information on the plastid genomes of oaks for detailed comparisons are increasing [40,[43][44][45][46]. Polymorphic chloroplast microsatellite markers designed based on a cp genome analysis can be utilised to comprehend the levels and patterns of the geographical structure and genetic diversity of Q. bawanglingensis, and this information can subsequently be used formulate an effective protection strategy.…”

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

“…Nucleotide diversity (Pi) can indicate the magnitude of variation in various species' nucleic acid sequences, and locations with higher variability can be used as molecular markers in population genetics [43,44]. In this study, the results of nucleotide diversity (Pi) assessment showed that the gene sequences of the LSC/SSC region were more variable than those in the IR region, which was consistent with the results found in other genera [13,41,[45][46][47]. The same conclusion has been reached in the study of Lagerstroemia and Adrinandra plants [48,49].…”