Achakkagari SR, Kyriakidou M, Tai HH, Anglin NL, Ellis D, Strömvik MV (2020) Complete plastome assemblies from a panel of 13 diverse potato taxa. PLoS ONE 15:e0240124. https://doi.org/10.1371/journal.pone.0240124
Article PubMed PubMed Central Google Scholar
Amiryousefi A, Hyvönen J, Poczai P (2018) The chloroplast genome sequence of bittersweet (Solanum dulcamara): plastid genome structure evolution in Solanaceae. PLoS ONE 13:e0196069. https://doi.org/10.1371/journal.pone.0196069
Article PubMed PubMed Central Google Scholar
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics. http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Accessed 13 Apr 2024
Anguiano-Constante MA, Dean E, Starbuck T, Rodríguez A, Munguía-Lino G (2021) Diversity, species richness distribution and centers of endemism of Lycianthes (Capsiceae, Solanaceae) in Mexico. Phytotaxa 514:39–60. https://doi.org/10.11646/phytotaxa.514.1.3
Añibarro-Ortega M, Pinela J, Alexopoulos A, Petropoulos SA, Ferreira ICFR, Barros L (2022) Chapter Four - The powerful Solanaceae: Food and nutraceutical applications in a sustainable world. Adv Food Nutr Res 100:131–172. https://doi.org/10.1016/bs.afnr.2022.03.004
Barboza GE, Hunziker AT, Bernardello G, Cocucci AA, Moscone AE, Carrizo-García C, Fuentes V, Dillon MO, Bittrich, Cosa MT, Subils R, Romanutti A, Arroyo S, Anton A (2016) Solanaceae. In: Kadereit JW, Bittrich V (eds) Flowering Plants. Eudicots. The Families and Genera of Vascular Plants 14. Springer International Publishing, Switzerland, pp 295–357
Barboza GE, Carrizo-García C, Bianchetti LB, Romero MV, Scaldaferro M (2022) Monograph of wild and cultivated chili peppers (Capsicum L., Solanaceae). PhytoKeys 200:1–423. https://doi.org/10.3897/phytokeys.200.71667
Article PubMed PubMed Central Google Scholar
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Article PubMed PubMed Central Google Scholar
Carputo D, Aversano R, Ercolano MR (2021) The wild Solanums genomes. Springer Nature Switzeland. https://doi.org/10.1007/978-3-030-30343-3
Carrizo-García C, Barfuss MHJ, Sehr EM, Barboza GE, Samuel R, Moscone EA, Ehrendorfer F (2016) Phylogenetic relationships, diversification and expansion of chili peppers (Capsicum, Solanaceae). Ann Bot 118:35–51. https://doi.org/10.1093/aob/mcw079
Article PubMed PubMed Central Google Scholar
Carrizo García C, Barboza GE, Palombo N, Weiss-Schneeweiss H (2022) Diversification of chiles (Capsicum, Solanaceae) through time and space: new insights from genome-wide RAD-seq data. Front Genet 13:1030536. https://doi.org/10.3389/fgene.2022.1030536
Article PubMed PubMed Central Google Scholar
Causse M, Giovannoni J, Bouzayen M, Zouine M (2016) The Tomato Genome. Compendium of Plant Genomes. Springer, Berlin, Heidelberg
CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci U S A 106:12794–12797. https://doi.org/10.1073/pnas.0905845106
Chakrabarti SK, Xie C, Tiwari JK (2017) The potato genome. Springer, Berlin
Chinnkar M, Jadhav P (2023) Evaluating DNA barcoding using five loci (matK, ITS, trnH- psbA, rpoB, and rbcL) for species identification and phylogenetic analysis of Capsicum frutescens. J App Biol Biotech 11:97–103. https://doi.org/10.7324/JABB.2023.57526
D’Agostino N, Tamburino R, Cantarella C, De Carluccio V, Sannino L, Cozzolino S, Cardi T, Scotti N (2018) The complete plastome sequence of eleven Capsicum genotypes: insights into DNA variation and molecular evolution. Genes (Basel) 9:503. https://doi.org/10.3390/genes9100503
Article PubMed PubMed Central Google Scholar
D’Arcy WG (1986) The calyx in Lycianthes and some other genera. Ann Missouri Bot Gard 73:117–127. https://doi.org/10.2307/2399143
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772. https://doi.org/10.1038/nmeth.2109
Article PubMed PubMed Central Google Scholar
Dean E, Poore J, Anguiano-Constante MA, Nee MH, Kang H, Starbuck T, RodríguezA, Conner M (2020) The genus Lycianthes (Solanaceae, Capsiceae) in Mexico and Guatemala. Phytokeys 168:1-333. https://doi.org/10.3897/phytokeys.168.51904
Deanna R, Martínez C, Manchester S, Wilf P, Campos A, Knapp S, Franco EC, Barboza GE, Bernardello G, Sauquet H, Dean E, Orejuela A, Smith SD (2023) Fossil berries reveal global radiation of the nightshade family by the early Cenozoic. New Phytol 238:2685–2697. https://doi.org/10.1111/nph.18904
Deanna R, Barboza GE, Bohs L, Dodsworth S, Gagnon E, Giacomin LL, Knapp S, Orejuela A, Pczai P, Särkinen T, Smith SD, Olmstead RG (2026a) A new phylogeny and phylogenetic classification for Solanaceae. Taxon 75:e70129. https://doi.org/10.1002/tax.70129
Deanna R, Hvlj AV, Martinetto E, Knapp S, Sadowski EM, Manchester S, Campos A, Fernandez V, Barboza GE, Sauquet H, Dean E, Särkinen T, Chiarini F, Bernardello G, Smith SD (2026b) Seed fossil record of Solanaceae revisited. Taxon 75:e70096. https://doi.org/10.1002/tax.70096
FAOSTAT (2022) www.faostat.fao.org. Accessed 24 Apr 2024
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:W273–W279. https://doi.org/10.1038/nmeth.2109
Article PubMed PubMed Central Google Scholar
Gao L, Su YJ, Wang T (2010) Plastid genome sequencing, comparative genomics, and phylogenomics: current status and prospects. J Syst Evol 48:77–93. https://doi.org/10.1111/j.1759-6831.2010.00071.x
Ghimiray D, Sharma BC (2014) Comparative and bioinformatics analyses of the Solanaceae chloroplast genomes: plastome organization is more or less conserved at family level. J Appl Biol Biotech 2:21–06. https://doi.org/10.7324/JABB.2014.2305
Gitzendanner MA, Soltis PS, Yi TS, Li DZ, Soltis DE (2018) Plastome phylogenetics: 30 years of inferences into plant evolution. Adv Bot Res 85:293–313. https://doi.org/10.1016/bs.abr.2017.11.016
González-Ramírez IS, Deanna R, Smith SD (2026) Late Cretaceous origins for major nightshade lineages from total-evidence timetree analysis. Ann Bot. https://doi.org/10.1093/aob/mcag011
Article PubMed PubMed Central Google Scholar
Greiner S, Lehwark P, Bock R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res 47:W59–W64. https://doi.org/10.1093/nar/gkz238
Article PubMed PubMed Central Google Scholar
Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ (2023) Phylogenomics and the flowering plant tree of life. J Integr Plant Biol 65:299–323. https://doi.org/10.1111/jipb.13415
He S, Siman Y, Li G, Lv J, Zhao K, Deng M (2024) Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae). BMC Genomics 25:1052. https://doi.org/10.1186/s12864-024-10980-1
Article PubMed PubMed Central Google Scholar
Jarret RL (2008) DNA barcoding in a crop genebank: the Capsicum annuum species complex. Open Biol J. https://doi.org/10.2174/1874196700801010035
Jia X, Feng S, Zhang H, Liu X (2022) Plastome Phylogenomics Provide Insight into the evolution of Taxus. Forest 13:1590. https://doi.org/10.3390/f13101590
Jin JJ, Yu WB, Yang JB, Song Y, de Pamphilis CW, Yi TS, Li DZ (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21:241. https://doi.org/10.1186/s13059-020-02154-5
Article PubMed PubMed Central Google Scholar
Kahlau S, Aspinall S, Gray JC, Bock R (2006) Sequence of the tomato chloroplast DNA and evolutionary comparison of Solanaceus plastid genomes. J Mol Evol 63:194-207. https://doi.org/10.1007/s00239-005-0254-5
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. MBE 30:772–780. https://doi.org/10.1093/molbev/mst010
Kress WJ, Erickson DL (2007) A two locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2:508. https://doi.org/10.1371/journal.pone.0000508
Li X, Zhao Y, Tu X, Li C, Zhu Y, Zhong H, Liu ZJ, Wu S, Zhai J (2021) Comparative analysis of plastones in Oxalidaceae: phylogenetic relationships and potential molecular markers. Plant Divers 43:281–291.
Comments (0)