Complete chloroplast genome and phylogenetic analysis of Smallanthus sonchifolius (Asteraceae)

References

• Aybar MJ, Sánchez Riera AN, Grau A, Sánchez SS., 2001. Hypoglycemic effect of the water extract of Smallantus sonchifolius (yacón) leaves in normal and diabetic rats. J Ethnopharmacol. 74(2):125–132. doi: 10.1016/s0378-8741(00)00351-2.
   PubMed Web of Science ®Google Scholar
• Beier S, Thiel T, Münch T, Scholz U, Mascher M., 2017. MISA-web: a web server for microsatellite prediction. Bioinformat. 33(16):2583–2585. doi: 10.1093/bioinformatics/btx198.
   Google Scholar
• Blöch C, Weiss-Schneeweiss H, Schneeweiss GM, Barfuss MHJ, Rebernig CA, Villaseñor JL, Stuessy TF., 2009. Molecular phylogenetic analyses of nuclear and plastid DNA sequences support dysploid and polyploid chromosome number changes and reticulate evolution in the diversification of Melampodium (Millerieae, Asteraceae). Mol Phylogenet Evol. 53(1):220–233. doi: 10.1016/j.ympev.2009.02.021.
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi: 10.1093/bioinformatics/btu170.
   PubMed Web of Science ®Google Scholar
• Delgado GTC, Tamashiro WMdSC, Maróstica Junior MR, Pastore GM., 2013. Yacón (Smallanthus sonchifolius): a functional food. Plant Foods Hum Nutr. 68(3):222–228. doi: 10.1007/s11130-013-0362-0.
   PubMed Web of Science ®Google Scholar
• Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissues. Phytochem Bull. 19:11–15.
   Google Scholar
• Fan W, Wang S, Wang H, Wang A, Jiang F, Liu H, Zhao H, Xu D, Zhang Y., 2022. The genomes of chicory, endive, great burdock and yacón provide insights into Asteraceae palaeo-polyploidization history and plant inulin production. Mol Ecol Resour. 22(8):3124–3140. doi: 10.1111/1755-0998.13675.
   PubMed Web of Science ®Google Scholar
• Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z., 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241. doi: 10.1186/s13059-020-02154-5.
   PubMed Web of Science ®Google Scholar
• Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS., 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589. doi: 10.1038/nmeth.4285.
   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
• Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R., 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29(22):4633–4642. doi: 10.1093/nar/29.22.4633.
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R., 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformat. 25(16):2078–2079. doi: 10.1093/bioinformatics/btp352.
   Google Scholar
• Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274. doi: 10.1093/molbev/msu300.
   PubMed Web of Science ®Google Scholar
• Ojansivu I, Ferreira CL, Salminen S. 2011. Yacón, a new source of prebiotic oligosaccharides with a history of safe use. Trends Food Sci Technol. 22(1):40–46. doi: 10.1016/j.tifs.2010.11.005.
   Web of Science ®Google Scholar
• Qu X-J, Moore MJ, Li D-Z, Yi T-S., 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
• Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformat. 26(6):841–842. doi: 10.1093/bioinformatics/btq033.
   Google Scholar
• Sánchez S, Genta S. 2007. Yacón: un potencial producto natural para el tratamiento de la diabetes. Boletín Latinoamericano y del Caribe de. Plantas Medicinales y Aromáticas. 6(5):162–164.
   Google Scholar
• Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L, Liu C., 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47(W1):W65–W73. doi: 10.1093/nar/gkz345.
   PubMed Web of Science ®Google Scholar
• Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S., 2017. GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. doi: 10.1093/nar/gkx391.
   PubMed Web of Science ®Google Scholar
• Vitali M, Viera Barreto J. 2014. Phylogenetic studies in Smallanthus (Millerieae, Asteraceae): a contribution from morphology. Phytotaxa. 159(2):77. doi: 10.11646/phytotaxa.159.2.2.
   Web of Science ®Google Scholar
• Vos AP, van Esch BC, Stahl B, M'Rabet L, Folkerts G, Nijkamp FP, Garssen J., 2007. Dietary supplementation with specific oligosaccharide mixtures decreases parameters of allergic asthma in mice. Int Immunopharmacol. 7(12):1582–1587. doi: 10.1016/j.intimp.2007.07.024.
   PubMed Web of Science ®Google Scholar
• Wick RR, Schultz MB, Zobel J, Holt KE., 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformat. 31(20):3350–3352. doi: 10.1093/bioinformatics/btv383.
   Google Scholar
• Zardini E. 1991. Ethnobotanical notes on “Yacón,” polymnia sonchifolia (Asteraceae). Econ Bot. 45(1):72–85. doi: 10.1007/BF02860051.
   Web of Science ®Google Scholar
• Zhang C, Huang C-H, Liu M, Hu Y, Panero JL, Luebert F, Gao T, Ma H., 2021. Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation. J Integr Plant Biol. 63(7):1273–1293. doi: 10.1111/jipb.13078.
   PubMed Web of Science ®Google Scholar
• Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT., 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348–355. doi: 10.1111/1755-0998.13096.
   Google Scholar