A high level of chloroplast genome sequence variability in the Sawtooth Oak Quercus acutissima

Zhang, Rusong; Yang, Jian; Hu, Hualei; Xia, Run-Xi; Li, Yuping; Su, Junfang; Qun, LI; Liu, Yanping; Qin, Li

doi:10.1016/j.ijbiomac.2020.02.201

Cited by 27 publications

(33 citation statements)

References 40 publications

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“…The complete assembled cp genome of Q. ningangensis was 160,736 bp in length with a typical quadripartite structure. Gene content and order were similar to those of other published cp genomes in Fagaceae (Dane et al 2015;Yang et al 2018;Zhang et al 2020). The base composition of the cp genome was asymmetric (31.15% A, 18.78 C, 18.11% G, 31.96% T) with an overall guanine-cytosine (GC) content of 36.89% and the corresponding values of the inverted repeat (IR), large single copy (LSC), and small single copy (SSC) regions were 42.76%, 34.74%, and 31.09%, respectively.…”

Section: Resultssupporting

confidence: 78%

“…The IR regions exhibited lower variability than the LSC and SSC regions. This result was similar to other cp genomes (Han et al 2016;He et al 2017;Zhang et al 2020).…”

Section: Chloroplast Sequence Variation and Evolutionsupporting

confidence: 90%

“…To determine the nucleotide diversity of the ten complete cp genomes of section Cyclobalanopsis, sliding window analysis was conducted to generate nucleotide diversity (Pi) of the cp genomes using DnaSP (DNA Sequence Polymorphism v.5.10.01) software (Librado & Rozas 2009). The step size was set to 200 bp with an 800 bp window length (Zhang et al 2020).…”

Section: Intraspecific Sequence Divergence Hotspot Identificationmentioning

confidence: 99%

“…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%

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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: Resultssupporting

confidence: 78%

“…The IR regions exhibited lower variability than the LSC and SSC regions. This result was similar to other cp genomes (Han et al 2016;He et al 2017;Zhang et al 2020).…”

Section: Chloroplast Sequence Variation and Evolutionsupporting

confidence: 90%

Section: Intraspecific Sequence Divergence Hotspot Identificationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Wang¹,

Wang²,

Kozlowski³

2021

pfs

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“…The degree of overall plastome sequence variation among the three Rhus accessions is similar to what is observed in other intraspecific studies of plastid genomic variation among photosynthetic angiosperms, for example, in: Silene vulgaris (Moench) Garcke (Krüger et al, 2019), Macadamia integrifolia Maiden & Betche (Nock et al, 2019), Quercus acutissima Carruth. (Zhang et al, 2020), Utricularia amethystina Salzm. ex A. St.-Hil.…”

Section: Plastid Phylogeonomics Of Rhus and Order Sapindalesmentioning

confidence: 99%

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

Barrett¹

2020

PeerJ

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Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.

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Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

Tian,

Guo,

Song

et al. 2024

Ecology and Evolution

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Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis‐related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.

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A high level of chloroplast genome sequence variability in the Sawtooth Oak Quercus acutissima

Cited by 27 publications

References 40 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

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

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