1,325
Views
5
CrossRef citations to date
0
Altmetric
Articles

The complete chloroplast genome provides insight into the polymorphism and adaptive evolution of Garcinia paucinervis

, , , &
Pages 377-391 | Received 21 Oct 2020, Accepted 19 Jan 2021, Published online: 28 Feb 2021

References

  • Hu G, Zhang ZH, Yang P, et al. Development of microsatellite markers in Garcinia paucinervis (Clusiaceae), an endangered species of karst habitats. Appl Plant Sci. 2017;5(1):1600131.
  • Hemshekhar M, Sunitha K, Santhosh MS, et al. An overview on genus Garcinia: phytochemical and therapeutical aspects. Phytochem Rev. 2011; 10(3):325–351.
  • Wang S, Xie Y. China Species Red List, 366. Beijing, China: Higher Education Press; 2004.
  • Ovalle-Magallanes B, Eugenio-Pérez D, Pedraza-Chaverri J. Medicinal properties of mangosteen (Garcinia mangostana L.): A comprehensive update. Food Chem Toxicol. 2017;109(Pt 1):102–122.
  • Nie L, Cui Y, Chen X, et al. Complete chloroplast genome sequence of the medicinal plant Arctiumlappa. Genome. 2020; 63(1):53–60.
  • Sabater B. Evolution and function of the chloroplast. Current investigations and perspectives. IJMS. 2018; 19(10):3095.
  • Zha X, Wang X, Li J, et al. Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis. J Genet. 2020;99(1):30.
  • Cheon KS, Kim KA, Kwak M, et al. The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species. PLoS One. 2019; 14(3):e0214162
  • Zhou T, Ruhsam M, Wang J, et al. The complete chloroplast genome of Euphrasia regelii, pseudogenization of ndh genes and the phylogenetic relationships within. Orobanchaceae Front Genet. 2019; 10:444.
  • Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987; 19:11–15.
  • Arya M, Shergill IS, Williamson M, et al. Basic principles of real-time quantitative PCR. Expert Rev Mol Diagn. 2005; 5(2):209–219.
  • Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455–477.
  • Zhao K, Chu X. G-BLASTN: accelerating nucleotide alignment by graphics processors. Bioinformatics. 2014;30(10):1384–1391.
  • Li R, Zhu H, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010; 20(2):265–272.
  • Tillich M, Lehwark P, Pellizzer T, et al. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6–W11.
  • Mower JP. JP. The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic Acids Res. 2009;37(Web Server):W253–W259.
  • Kurtz S, Choudhuri JV, Ohlebusch E, et al. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001; 29(22):4633–4642.
  • Mayor C, Brudno M, Schwartz JR, et al. VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 2000; 16(11):1046–1047.
  • Amiryousefi A, Hyvönen J, Poczai P. IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 2018; 34(17):3030–3031.
  • Yang Z. Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–1591.
  • Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780.
  • Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22(21):2688–2690.
  • Gui L, Jiang S, Xie D, et al. Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution. Gene. 2020; 732:144355
  • Qian J, Song J, Gao H, et al. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PloS One. 2013; 8(2):e57607
  • Nakamura Y, Wada K, Wada Y, et al. Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 1996; 24(1):214–215.
  • Oresic M, Shalloway D. Specific correlations between relative synonymous codon usage and protein secondary structure. J Mol Biol. 1998; 281(1):31–48.
  • Zandueta-Criado A, Bock R. Surprising features of plastid ndhD transcripts: addition of non-encoded nucleotides and polysome association of mRNAs with an unedited start codon. Nucleic Acids Res. 2004; 32(2):542–550.
  • Hirose T, Sugiura M. Both RNA editing and RNA cleavage are required for translation of tobacco chloroplast ndhD mRNA: a possible regulatory mechanism for the expression of a chloroplast operon consisting of functionally unrelated genes. EMBO J. 1997; 16(22):6804–6811.
  • Suwabe K, Tsukazaki H, Iketani H, et al. Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance. Genetics. 2006; 173(1):309–319.
  • Li HT, Yi TS, Gao LM, et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nat Plants. 2019;5(5):461–470.
  • Anne HE, Staton ME, Dattilo AJ, et al. Population structure and genetic diversity within the endangered species Pityopsis ruthii (Asteraceae). Front Plant Sci. 2018; 9:943.
  • Jian HY, Li SF, Guo JL, et al. High genetic diversity and differentiation of an extremely narrowly distributed and critically endangered decaploid rose (Rosa praelucens): implications for its conservation. Conserv Genet. 2018; 19(4):761–776.
  • Terrab A, Talavera S, Arista M, et al. Genetic diversity at chloroplast microsatellites (cpSSRs) and geographic structure in endangered west mediterranean firs (Abies spp. pinaceae). Taxon. 2007; 56(2):409–416.
  • Ebert D, Peakall R. Chloroplast simple sequence repeats (cpSSRs): Technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol Ecol Resour. 2009; 9(3):673–690.
  • Ichinose M, Sugita M. RNA editing and its molecular mechanism in plant organelles. Genes. 2016; 8(1):5.
  • Tulshiram WS. RNA Editing and its Potential Role in Evolution. Biotecharticles2017. Available from: https://www.biotecharticles.com/Microbiology-Article/RNA-Editing-and-its-Potential-Role-in-Evolution-3799.html.
  • Adams KL, Qiu YL, Stoutemyer M, et al. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci U S A. 2002; 99(15):9905–9912.
  • Maier RM, Zeltz P, Kossel H, et al. RNA editing in plant mitochondria and chloroplasts. Plant Mol Biol. 1996;32(1-2):343–365.
  • Mower JP. JP. Modeling sites of RNA editing as a fifth nucleotide state reveals progressive loss of edited sites from angiosperm mitochondria. Mol Biol Evol. 2008;25(1):52–61.
  • Bock R. Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing. Biochimie. 2000; 82(6-7):549–557.
  • Tangphatsornruang S, Uthaipaisanwong P, Sangsrakru D, et al. Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships. Gene. 2011;475(2):104–112.
  • Kahlau S, Aspinall S, Gray JC, et al. Sequence of the tomato chloroplast DNA and evolutionary comparison of Solanaceous plastid genomes. J Mol Evol. 2006;63(2):194–207.
  • Sasaki T, Yukawa Y, Miyamoto T, et al. Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): Comparative analysis shows the involvement of distinct trans-factors for ndhB editing. Mol Biol Evol. 2003; 20(7):1028–1035.
  • Ivanova Z, Sablok G, Daskalova E, et al. Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response. Front Plant Sci. 2017; 8:204.
  • Xie DF, Yu Y, Deng YQ, et al. Comparative analysis of the chloroplast genomes of the Chinese endemic genus Urophysa and their contribution to chloroplast phylogeny and adaptive evolution. IJMS. 2018; 19(7):1847.
  • Zhao B, Li JJ, Yuan RW, et al. Adaptive evolution of the rbcL gene in the genus Rheum (polygonaceae.). Biotechnol Biotec Eq. 2017; 31(3):493–498.
  • Barthet MM, Hilu KW. Expression of matK: functional and evolutionary implications. Am J Bot. 2007; 94(8):1402–1412.
  • UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015; 43(Database issue):D204-212. Available link: https://www.uniprot.org/uniprot/P60147.
  • Ramundo S, Rahire M, Schaad O, et al. Repression of essential chloroplast genes reveals new signaling pathways and regulatory feedback loops in chlamydomonas. Plant Cell. 2013;25(1):167–186.