The complete chloroplast genome sequence of Quercus ningangensis and its phylogenetic implication

Abstract

Quercus ningangensis is an economically and ecologically important tree species belonging to the family Fagaceae. In this study, the complete chloroplast (cp) genome of Q. ningangensis was sequenced and assembled, and 18 published cp genomes of Quercus were retrieved for genomic analyses (including sequence divergence, repeat elements, and structure) and phylogenetic inference. With this study, we found that complete cp genomes in Quercus are conserved, and we discovered a codon composition bias, which may be related to genomic content and genetic characteristics. In addition, we detected considerable structural variations in the expansion and contraction of inverted repeat regions. Six regions with relatively high variable (matK-rps16, psbC, ycf3 intron, rbcL, petA-psbJ, and ycf1) were detected by conducting a sliding window analysis, which has a high potential for developing effective genetic markers. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods resulted in a robust phylogenetic tree of Quercus with high resolution for nearly all identified nodes. The phylogenetic relationships showed that the phylogenetic position of Q. ningangensis was located between Q. sichourensis and Q. acuta. The results of this study contribute to future research into the phylogenetic evolution of Quercus section Cyclobalanopsis (Fagaceae).

Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis

“…The results indicated that there were differences in the degree of variation between regions of CPGs, with the single-copy (SC) regions having higher variation than IR regions, simultaneously the IGS regions having higher variation than coding regions. Same phenomena were found in other Quercus species 51 , 52 , 76 , 77 . The copy-dependent repair mechanism of CPGs could guarantee the stability of IRs construction and thereby advance the steadiness and conservation of genomes, which possibly explain the different degree of variation between IRs and SCs.…”

“…160 kb) conformed to the photosynthetic land plant plastid chromosomes, whose size varied from 120 to 160 kb 50 . The same quadripartite circular structure were found in the four assembled CPGs and other Quercus species [51][52][53] . Overall GC content had no distinction within the four species.…”

“…Most of the compared species found no significant expansion or contraction in the IR regions except the Quercus neglecta, which had a only four bp displacement between the JLB and rps19. The conservatism of Quercus section Cyclobalanopsis was demonstrated by the relatively constant length of CPGs and the minor variations in their region borders, as the same conditions with other Quercus species 25,52 .…”

Comparison of Chloroplast Genomes and Phylogenetic Analysis of Four Species in Quercus section Cyclobalanopsis

“…160 kb) conformed to the photosynthetic land plant plastid chromosomes, whose size varied from 120 kb to 160 kb 49 . The same quadripartite circular structure were found in the four assembled CPGs and other Quercus species [50][51][52] . Overall GC content had no distinction within the four species.…”

Complete Chloroplast Genome of an Endangered Species Quercus litseoides, and Its Comparative, Evolutionary, and Phylogenetic Study with Other Quercus Section Cyclobalanopsis Species

“…The number and types of SSRs varied extensively when compared to those of other cp genomes in Quercus . The number of SSRs in Q. litseoides was higher than that in the other Quercus species, whereas fewer SSRs were distributed in the LSC and IGS regions [ 46 , 58 , 59 , 60 , 61 , 62 , 63 ]. These variations support the idea that SSRs can be used as lineage-specific markers for genetic diversity analysis and can be used as markers to understand evolutionary history [ 64 ].…”