Characterization and phylogenetic analysis of the complete chloroplast genome of Saussurea sagittifolia (Asteraceae, Cardueae)

References

• Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. doi: 10.1089/cmb.2012.0021.
   PubMed Web of Science ®Google Scholar
• Doorduin L, Gravendeel B, Lammers Y, Ariyurek Y, Chin-A-Woeng T, Vrieling K. 2011. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res. 18(2):93–105. doi: 10.1093/dnares/dsr002.
   PubMed Web of Science ®Google Scholar
• Downie SR, Jansen RK. 2015. A comparative analysis of whole plastid genomes from the Apiales: expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions. Syst Bot. 40(1):336–351. doi: 10.1600/036364415X686620.
   Web of Science ®Google Scholar
• Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15.
   Google Scholar
• Hereward JP, Werth JA, Thornby DF, Keenan M, Chauhan BS, Walter GH. 2018. Complete chloroplast genome of glyphosate resistant Sonchus oleraceus L. from Australia, with notes on the small single copy (SSC) region orientation. Mitochondrial DNA B Resour. 3(1):363–364. doi: 10.1080/23802359.2018.1450682.
   PubMed Web of Science ®Google Scholar
• Huang L, Wang Z, Wang T, Su YJ. 2016. The complete chloroplast genome sequence of Mikania micrantha (Asteraceae), a noxious invasive weed to South China. Mitochondrial DNA B Resour. 1(1):603–604. doi: 10.1080/23802359.2016.1209090.
   PubMed Web of Science ®Google Scholar
• Jin GZ, Li WJ, Song F, Yang L, Wen ZB, Feng Y. 2023. Comparative analysis of complete Artemisia subgenus Seriphidium (Asteraceae: Anthemideae) chloroplast genomes: insights into structural divergence and phylogenetic relationships. BMC Plant Biol. 23(1):136. doi: 10.1186/s12870-023-04113-1.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. doi: 10.1093/molbev/mst010.
   PubMed Web of Science ®Google Scholar
• Li R, Ma PF, Wen J, Yi TS. 2013. Complete sequencing of five Araliaceae chloroplast genomes and the phylogenetic implications. PLOS One. 8(10):e78568. doi: 10.1371/journal.pone.0078568.
   PubMed Web of Science ®Google Scholar
• Li T, Xu LS, Chen YS. 2022. Saussurea khunjerabensis (Asteraceae, Cardueae), a new species from Pamir. Phytotaxa. 561(1):65–74. doi: 10.11646/phytotaxa.561.1.6.
   Web of Science ®Google Scholar
• 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. doi: 10.1111/1755-0998.13729.
   PubMed Web of Science ®Google Scholar
• Liu XF, Luo JJ, Zhang MK, Wang Q, Liu J, Wu D, Fu ZX. 2023. Phylogenomic analysis of two species of Parasenecio and comparative analysis within tribe Senecioneae (Asteraceae). Diversity. 15(4):563. doi: 10.3390/d15040563.
   Google Scholar
• 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(1):50. doi: 10.1186/s13007-019-0435-7.
   PubMed Web of Science ®Google Scholar
• Seon A, Yun SA, Gil HY, Kim SC. 2017. The complete chloroplast genome sequence of Saussurea polylepis (Asteraceae), a vulnerable endemic species of Korea. Mitochondrial DNA B Resour. 2(2):650–651. doi: 10.1080/23802359.2017.1375881.
   PubMed Web of Science ®Google Scholar
• Shahzadi I, Abdullah  , Mehmood F, Ali Z, Ahmed I, Mirza B. 2020. Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae. Genomics. 112(2):1454–1463. doi: 10.1016/j.ygeno.2019.08.016.
   PubMed Web of Science ®Google Scholar
• Shi Z, Raab-Straube EV. 2011. Saussurea Candolle. In: Wu ZY, Raven PH, Hong DY, editors. Flora of China. Vols. 20–21. Beijing; St. Louis: Science Press; Missouri Botanical Garden Press; p. 56–149.
   Google Scholar
• Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. doi: 10.1093/bioinformatics/btu033.
   PubMed Web of Science ®Google Scholar
• Vargas OM, Ortiz EM, Simpson BB. 2017. Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium). New Phytol. 214(4):1736–1750. doi: 10.1111/nph.14530.
   PubMed Web of Science ®Google Scholar
• Wang AS, Wu HW, Zhu XC, Lin JM. 2018. Species identification of Conyza bonariensis assisted by chloroplast genome sequencing. Front Genet. 9(374):374. doi: 10.3389/fgene.2018.00374.
   PubMedGoogle Scholar
• Wang B, Zhao Q, Wang XH, Fu ZX. 2020. The complete chloroplast genome of Pertya phylicoides (Asteraceae, Pertyeae): a shurby endemic species from China. Mitochondrial DNA B Resour. 5(1):963–964. doi: 10.1080/23802359.2020.1722763.
   PubMed Web of Science ®Google Scholar
• Wang XY, Zhou ZS, Liu G, Qian ZQ. 2018. Characterization of the complete chloroplast genome of the invasive weed Galinsoga quadriradiata (Asterales: Asteraceae). Conserv Genet Resour. 10(1):89–92. doi: 10.1007/s12686-017-0771-8.
   Web of Science ®Google Scholar
• Xu LS, Yi SR, Chen YS. 2020. Saussurea sagittifolia (Asteraceae, Cardueae), a new species from the Bashan Mountains region of China. Phytotaxa. 472(3):295–298. doi: 10.11646/phytotaxa.472.3.9.
   Web of Science ®Google Scholar
• Yun S, Kim S-C. 2022. Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae). BMC Plant Biol. 22(1):550. doi: 10.1186/s12870-022-03946-6.
   PubMed Web of Science ®Google Scholar
• Zhang X, Deng T, Moore MJ, Ji YH, Lin N, Zhang HJ, Meng AP, Wang HC, Sun YX, Sun H. 2019. Plastome phylogenomics of Saussurea (Asteraceae: Cardueae). BMC Plant Biol. 19(1):290. doi: 10.1186/s12870-019-1896-6.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang J, Yang Y, Liu Q. 2017. Complete chloroplast genome of Pluchea indica (L.) Less. (Asteraceae) and its phylogenetic analysis. Mitochondrial DNA B Resour. 2(2):918–919. doi: 10.1080/23802359.2017.1413299.
   PubMed Web of Science ®Google Scholar