The complete plastid genome sequence of <i>Quercus ciliaris</i> (Fagaceae)

Li, Yao; Wang, Lu; Liu, Qingliang; Fang, Yanming

doi:10.1080/23802359.2020.1756955

Cited by 4 publications

(3 citation statements)

References 5 publications

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“…With the rapid development of next-generation sequencing, cp genomes are increasingly being used for phylogenetic relationship reconstruction (Li et al 2020a;Mu et al 2020;Zhao et al 2020;Uckele et al 2021). Since the first oak cp genome for Q. rubra was published in 2014, up to 30 species have been sequenced (Alexander & Woeste 2014;Li et al 2020b;Zhang et al 2020). Although angiosperm cp genomes exhibit a remarkably conserved gene content and order (Jansen & Ruhlman 2012), complete cp genome data will provide more valuable information for understanding the phylogenetic relationships and intraspecific diversity of Quercus (Li et al 2018).…”

Section: Introductionmentioning

confidence: 99%

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

Wang¹,

Wang²,

Kozlowski³

2021

pfs

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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).

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Section: Introductionmentioning

confidence: 99%

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

Wang¹,

Wang²,

Kozlowski³

2021

pfs

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“…A total of 131 genes, including 86 PCGs, 37 tRNAs and 8 rRNA genes, were annotated in the chloroplast genomes of 50 species (Tables 1 and 2). Previous studies of the chloroplast genome sequences downloaded from NCBI database have found that using different annotation software and reference genome sequences can lead to differences in the annotation results [74][75][76]. The ycf15 gene is de ned as a pseudogene because it does not encode proteins; therefore, it is not annotated in most chloroplast genomes of Quercus.…”

Section: Discussionmentioning

confidence: 99%

Structural conservation and functional genetic adaptive evolution of chloroplast genomes in Cycle-cup Oaks

Li,

Zheng,

Wang

et al. 2023

Preprint

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Background: Cycle-cup oaks (Quercus section Cyclobalanopsis) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the course, tempo, and mode of genome evolution in cycle-cup oaks remain largely unknown; in particular, how plant plastome genes and genomes evolve during rapid speciation. To address this question, we analyzed the complete plastomes of 50 species of Quercus section Cyclobalanopsis, 36 newly sequenced and 14 published species. Results: Based on a series of analyses, including genome structure, genome annotation, GC content, repeat sequences, SSR components, codon usage bias, and comparative genomics, we found that Quercus section Cyclobalanopsishad a conserved plastome structure. Highly divergent regions, such as the ndhFand ycf1 gene regions and the petN—psbM and rpoB—trnC-GCA gene spacer regions, provided potential molecular markers for subsequent analysis. The maximum likelihood phylogenetic tree based on complete chloroplast genomes, coding DNA sequences, and highly divergent regions produced a poorly resolved genetic relationship of the plastid lineages of section Cyclobalanopsis. We identified nine protein-coding genes containing sites for positive selection: ndhA, ndhD, ndhF, ndhH, rbcL, rpl32, accD, ycf1, and ycf2. Conclusions: We compared and analyzed the chloroplast genomes of 50 species of Quercus section Cyclobalanopsis to explore their diversity structure, phylogenetic relationships, and ecological adaptative evolution. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in Quercus.

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“…Phylogenetic analyses were conducted using 53 cp genome sequences belonging to six white oaks (section Quercus) [66][67][68][69], three Cerris oaks (section Cerris) [68,[70][71][72][73], six ringcupped oaks (section Cyclobalanopsis) [74][75][76][77][78][79], 11 Ilex oaks (section Ilex) [67][68][69]71,[80][81][82][83], and two outgroups in Fagus [78,84] (Table S2). The HomBlocks v.1.0 pipeline [85] was applied to identify shared locally collinear blocks and generate a phylogenetically informative matrix of 83,130 bp.…”

Section: Phylogenetic Analyses Of Chloroplast Genome Sequencesmentioning

confidence: 99%

Interspecific Sharing of Closely Related Chloroplast Genome Haplotypes among Sclerophyllous Oaks in the Hot-Dry Valley of the Jinsha River, Southwestern China

Li,

Tan,

Zhang

et al. 2024

Forests

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Evergreen sclerophyllous oak forests (ESOFs) in southwestern China are a special vegetation type developed in response to the expansion of arid habitats after the uplift of the Himalayas. Here, we used chloroplast (cp) DNA and nuclear ribosomal (nr) DNA to investigate the fine-scale genetic variation patterns of six sympatric oaks (Quercus, Fagaceae) in the hot-dry valley ESOFs of the Jinsha River, southwestern China. Three cp genomes were assembled for each species. Nine cp genome haplotypes and 16 nrDNA haplotypes were identified based on single-nucleotide variants and indels. Our results demonstrated that discordance existed between the cpDNA and nrDNA phylogenies of the sclerophyllous oaks in section Ilex. The nrDNA phylogeny was consistent with species boundaries, while the cpDNA phylogeny was decoupled from taxonomy. Interspecific sharing of closely related cp genome haplotypes was detected between Quercus cocciferoides and the other two sclerophyllous oaks, Q. longispica and Q. franchetii. Specifically, Q. cocciferoides and Q. longispica sampled in a mixed stand exhibited two haplotypes that differed by a 9 bp indel. The local distribution of the two highly similar haplotypes suggested that they may have arisen from ancient introgression. Given that the two species have diverged for a long time, it is possible that the ancestral cp genome of one species was captured by another species through asymmetric introgression in early times, and an indel event occurred subsequently. Phylogenetic analyses using more previously published cp genome sequences indicated that Q. cocciferoides and Q. franchetii shared multiple cpDNA lineages of Ilex oaks, which may be caused by shared ancestral polymorphism and/or ancient introgression. Our study showed that at least three highly variable regions (ψycf1, ndhF-rpl32, and trnKUUU-rps16 or rpl32-trnLUAG) can distinguish the nine haplotypes identified by whole-cp genome sequences. These markers are useful for the evolutionary studies of the maternal lineages of oaks in hot-dry valley ESOFs.

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The complete plastid genome sequence of Quercus ciliaris (Fagaceae)

Cited by 4 publications

References 5 publications

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

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

Structural conservation and functional genetic adaptive evolution of chloroplast genomes in Cycle-cup Oaks

Interspecific Sharing of Closely Related Chloroplast Genome Haplotypes among Sclerophyllous Oaks in the Hot-Dry Valley of the Jinsha River, Southwestern China

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