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Plastome Announcement

The complete chloroplast genome sequence of Quercus kerrii (Fagaceae), and comparative analysis with related species

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Pages 527-531 | Received 09 Dec 2022, Accepted 13 Apr 2023, Published online: 24 Apr 2023

References

  • Cavender-Bares J. 2019. Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution. New Phytol. 221(2):669–692.
  • Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34(17):i884–i890.
  • Chernomor O, von Haeseler A, Minh BQ. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 65(6):997–1008.
  • Deng M, Jiang XL, Hipp AL, Manos PS, Hahn M. 2018. Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia. Mol Phylogenet Evol. 119:170–181.
  • Denk T, Grimm GW, Manos PS, Deng M, Hipp AL. 2017. An updated infrageneric classification of the oaks: review of previous taxonomic schemes and synthesis of evolutionary patterns. In: Gil-Pelegrín E, Peguero-Pina JJ, Sancho-Knapik D, editors. Oaks physiological ecology. Exploring the functional diversity of genus Quercus L. New York: Springer; p. 13–38.
  • Doyle JJ. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15.
  • Fang YM, Zhu ZY, Li Y, Li X. 2022. Advances and prospects of oak biology based on genomics. J Nanjing Forest Univ. 46:64–72.
  • Hipp AL, Manos PS, Hahn M, Avishai M, Bodénès C, Cavender-Bares J, Crowl AA, Deng M, Denk T, Fitz-Gibbon S, et al. 2020. Genomic landscape of the global oak phylogeny. New Phytol. 226(4):1198–1212.
  • Jiang XL, An M, Zheng SS, Deng M, Su ZH. 2018. Geographical isolation and environmental heterogeneity contribute to the spatial genetic patterns of Quercus kerrii (Fagaceae). Heredity. 120(3):219–233.
  • Jiang X-L, Hipp AL, Deng M, Su T, Zhou Z-K, Yan M-X. 2019. East Asian origins of European holly oaks (Quercus section Ilex Loudon) via the Tibet-Himalaya. J Biogeogr. 46(10):2203–2214.
  • Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
  • Li X, Li Y, Sylvester SP, Zang M, El-Kassaby YA, Fang Y. 2021. Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus. Ecol Evol. 11(19):13401–13414.
  • Li TT, Luo CS, Mou HL, Jiang XL, Xu GB. 2021. The complete chloroplast genome sequence of Quercus schottkyana, and comparative analysis with related species. Mitochondrial DNA B Resour. 6(9):2607–2609.
  • Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H, Liu C. 2023. CPGView: a package for visualizing detailed chloroplast genome structures. Mol Ecol Resour. 23(3):694–704.
  • Pang X, Liu H, Wu S, Yuan Y, Li H, Dong J, Liu Z, An C, Su Z, Li B. 2019. Species Identification of Oaks (Quercus L., Fagaceae) from gene to genome. Int J Mol Sci. 20(23):5940.
  • Qu XJ, Moore MJ, Li DZ, Yi TS. 2019. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods. 15:50.
  • Yang Y, Zhang H, Ren T, Zhao G. 2018. Characterization of the complete plastid genome of Quercus tungmaiensis. Conserv Genet Resour. 10(3):457–460.
  • Yang Y, Zhou T, Qian Z, Zhao G. 2021. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): evidence from plastid genome using low-coverage whole genome sequencing. Genomics. 113(3):1438–1447.
  • Zeng QM, Liu B, Lin RQ, Jiang YT, Liu ZJ, Chen SP. 2019. The complete chloroplast genome sequence of Quercus gilva (Fagaceae). Mitochondrial DNA B Resour. 4(2):2493–2494.
  • Zhou BF, Yuan S, Crowl AA, Liang YY, Shi Y, Chen XY, An QQ, Kang M, Manos PS, Wang BS. 2022. Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nat Commun. 13:1320.