Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea

Yu, Tao; Gao, Jian; Huang, Bing; Dayananda, Buddhi; Bao, Wenbin; Zhang, Yu-Yang; Liao, Pei Chun; Li, Jun Qing

doi:10.3390/f11040462

Cited by 10 publications

(10 citation statements)

References 44 publications

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“…2). The variation region of petA-psbJ has been found in previous studies to be highly variable (Timme et al 2007;Yu et al 2020) and the mutation hotspots identified with matK are recommended regions for DNA barcoding in plants (CBOL Plant Working Group 2009; Hollingsworth et al 2011). Furthermore, most divergent hotspot loci are located in the LSC region, which allows for the proper design of genetic markers for classification and revealing the genetic divergence of the Quercus taxa.…”

Section: Chloroplast Sequence Variation and Evolutionmentioning

confidence: 99%

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

Wang¹,

Wang²,

Kozlowski³

2021

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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: Chloroplast Sequence Variation and Evolutionmentioning

confidence: 99%

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

Wang¹,

Wang²,

Kozlowski³

2021

pfs

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“…A. catalpifolium is located in the rainy zone of western China ( Yu et al 2020 ). As part of the Hengduan Mountains, this region has a special climate and unique vegetation types, with perennial rain and insufficient sunshine duration ( Zhuang and Gao 2002 ).…”

Section: Discussionmentioning

confidence: 99%

“…For example, in China, some Acer species are widely distributed ( A. amplum , A. longipes , A. mono , and A. truncatum ), whereas others are endangered ( A. catalpifolium , A. miaotaiense , and A. yangjuechi ) ( Bi et al 2016 ). Acer catalpifolium is a deciduous tree that is under threat of extinction ( Yu et al 2020 ) and is narrowly distributed in the rainy zone of western China (28°30′–33°N, 102°30′–104°E). Acer catalpifolium has a straight tree trunk and umbrella-shaped crown and usually grows up to 25 m tall ( fig.…”

Section: Introductionmentioning

confidence: 99%

Whole-Genome Sequencing ofAcer catalpifoliumReveals Evolutionary History of Endangered Species

Zhang

et al. 2021

Genome Biology and Evolution

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Acer catalpifolium is an endangered species restricted to remote localities of West China. Understanding the genomic content and evolution of A. catalpifolium is essential to conservation efforts of this rare and ecologically valuable plant. Here, we report a high-quality genome of A. catalpifolium consisting of ∼654 Mbps and ∼35,132 protein-coding genes. We detected 969 positively-selected genes in two Acer genomes compared with four other eudicots, 65 of which were transcription factors. We hypothesize that these positively-selected mutations in transcription factors might affect their function and thus contribute to A. catalpifolium’s decline-type population. We also identified 179 significantly expanded gene families compared to 12 other eudicots, some of which are involved in stress responses, such as the FRS-FRF family. We inferred that A. catalpifolium has experienced gene family expansions to cope with environmental stress in its evolutionary history. Finally, 109 candidate genes encoding key enzymes in the lignin biosynthesis pathway were identified in A. catalpifolium; of particular note were the large range and high copy number of cinnamyl alcohol dehydrogenase genes. The chromosome-level genome of A. catalpifolium presented here may serve as a fundamental genomic resource for better understanding endangered Acer species, informing future conservation efforts.

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“…mono is traditionally considered sister to A. truncatum but not to A. yangjuechi (van Gelderen et al, 1994;Xu et al, 2008). However, Yu et al (2020) proposed A. pictum subsp. mono and A. yangjuechi as sister species according to the "local varieties."…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

Gao

Liao

et al. 2022

Front. Genet.

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Acer L. (Sapindaceae) is one of the most diverse and widespread plant genera in the Northern Hemisphere. It comprises 124–156 recognized species, with approximately half being native to Asia. Owing to its numerous morphological features and hybridization, this genus is taxonomically and phylogenetically ranked as one of the most challenging plant taxa. Here, we report the complete chloroplast genome sequences of five Acer species and compare them with those of 43 published Acer species. The chloroplast genomes were 149,103–158,458 bp in length. We conducted a sliding window analysis to find three relatively highly variable regions (psbN-rps14, rpl32-trnL, and ycf1) with a high potential for developing practical genetic markers. A total of 76–103 SSR loci were identified in 48 Acer species. The positive selection analysis of Acer species chloroplast genes showed that two genes (psaI and psbK) were positively selected, implying that light level is a selection pressure for Acer species. Using Bayes empirical Bayes methods, we also identified that 20 cp gene sites have undergone positive selection, which might result from adaptation to specific ecological niches. In phylogenetic analysis, we have reconfirmed that Acer pictum subsp. mono and A. truncatum as sister species. Our results strongly support the sister relationships between sections Platanoidea and Macrantha and between sections Trifoliata and Pentaphylla. Moreover, series Glabra and Arguta are proposed to promote to the section level. The chloroplast genomic resources provided in this study assist taxonomic and phylogenomic resolution within Acer and the Sapindaceae family.

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Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea

Cited by 10 publications

References 44 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

Whole-Genome Sequencing ofAcer catalpifoliumReveals Evolutionary History of Endangered Species

Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

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