New insights into the evolutionary characteristic between the New World and Old World Lupinus species using complete chloroplast genomes

References

• Ainouche A, Bayer RJ. 1999. Phylogenetic relationships in Lupinus(Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA. Am J Bot. 86:590–607. DOI:10.2307/2656820
   PubMed Web of Science ®Google Scholar
• Ainouche A, Bayer RJ, Misset MT. 2004. Molecular phylogeny, diversification and character evolution in Lupinus (Fabaceae) with special attention to Mediterranean and African lupines. Plant Syst Evol. 246:211–222. DOI:10.1007/s00606-004-0149-8
   Web of Science ®Google Scholar
• Alikhan N-F, Petty NK, Zakour NLB, Beatson SA. 2011. BLAST ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 12:402. DOI:10.1186/1471-2164-12-402
   PubMed Web of Science ®Google Scholar
• Ayele TB, Gailing O, Umer M, Finkeldey R. 2009. Chloroplast DNA haplotype diversity and postglacial recolonization of Hagenia abyssinica (Bruce) JF Gmel. in Ethiopia. Plant Syst Evol. 280:175–185. DOI:10.1007/s00606-009-0177-5
   Web of Science ®Google Scholar
• Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573–580. DOI:10.1093/nar/27.2.573
   PubMed Web of Science ®Google Scholar
• Bruneau A, Doyle JJ, Herendeen P, Hughes C, Kenicer G. 2013. Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades. Taxon. 62:217–248. DOI:10.12705/622.8
   Web of Science ®Google Scholar
• Bull LN, Pabón-Peña CR, Freimer NB. 1999. Compound microsatellite repeats: practical and Theoretical features. Genome Res. 9:830–838. DOI:10.1101/gr.9.9.830
   Web of Science ®Google Scholar
• Bupp G, Ricono A, Peterson CL, Pruett CL. 2017. Conservation implications of small population size and habitat fragmentation in an endangered lupine. Conservation Genetics. 18:77–88. DOI:10.1007/s10592-016-0883-9
   Web of Science ®Google Scholar
• Cardoso D, de Queiroz LP, Pennington RT, de Lima HC, Fonty E, Wojciechowski MF, Lavin M. 2012. Revisiting the phylogeny of papilionoid legumes: new insights from comprehensively sampled early-branching lineages. Am J Bot. 99:1991–2013. DOI:10.3732/ajb.1200380
   PubMed Web of Science ®Google Scholar
• Cardoso D, Pennington RT, de Queiroz LP, Boatwright JS, Van Wyk BE, Wojciechowski MF, Lavin M. 2013. Reconstructing the deep-branching relationships of the papilionoid legumes. S Afr J Bot. 89:58–75. DOI:10.1016/j.sajb.2013.05.001
   Web of Science ®Google Scholar
• Cristofolini G. 1989. A serological contribution to the systematics of the genus Lupinus (Fabaceae). Plant Syst Evol. 166:265–278. DOI:10.1007/bf00935955
   Web of Science ®Google Scholar
• Cronk Q, Ojeda I, Pennington RT. 2006. Legume comparative genomics: progress in phylogenetics and phylogenomics. Curr Opin Plant Biol. 9:99–103. DOI:10.1016/j.pbi.2006.01.011
   Web of Science ®Google Scholar
• Cummings MP, King LM, Kellogg EA. 1994. Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae). Molecular Biology Evolution & Development. 11:1–8.
   PubMed Web of Science ®Google Scholar
• Darling AC, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394–1403. DOI:10.1101/gr.2289704
   PubMed Web of Science ®Google Scholar
• Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S, Cheng T, Guo J, Zhou S. 2015. Ycf1, the most promising plastid DNA barcode of land plants. Sci Rep. 5:8348–8353. DOI:10.1038/srep08348
   PubMed Web of Science ®Google Scholar
• Dugas DV, Hernandez D, Koenen EJM, Schwarz E, Straub S, Hughes CE, Jansen RK, Nageswara-Rao M, Staats M, Trujillo JT. 2015. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP. Sci Rep. 5:16958. DOI:10.1038/srep16958
   PubMed Web of Science ®Google Scholar
• Eastwood RJ, Hughes CE. 2008. Origins of domestication of lupinus mutabilis in the Andes. In Proceedings of the 12th International Lupin Conference, Fremantle,Western Australia, 14–18 Sept; pp. 373–379.
   Google Scholar
• Edwards TJ. 2007. Legumes of the world. S Afr J Bot. 73:272–273. DOI:10.1016/j.sajb.2007.02.187
   Web of Science ®Google Scholar
• Georg M, Perlman PS, Lambowitz AM. 1993. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res. 21:4991–4997. DOI:10.1093/nar/21.22.4991
   Web of Science ®Google Scholar
• Gepts P. 2005. Legumes as a model plant family. Genomics for food and feed report of the cross-legume advances through genomics conference. Plant Physiol. 137:1228–1235. DOI:10.1104/pp.105.060871
   PubMed Web of Science ®Google Scholar
• Gladstones J. 1984. Present situation and potential of Mediterranean/African lupins for crop rotation. In Proceedings of the 3rd International Lupin Conference, La Rochelle, France, 4–8 June; pp. 18–37.
   Google Scholar
• Gupta S, Buirchell BJ, Cowling WAJPB. 1996. Interspecific reproductive barriers and genomic similarity among the rough-seeded Lupinus species. Plant Breed. 115:123–127. DOI:10.1111/j.1439-0523.1996.tb00886.x
   Web of Science ®Google Scholar
• Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun C-R, Meng B-Y. 1989. The complete sequence of the rice (oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. MGG Molecular & General Genetics. 217:185–194. DOI:10.1007/bf02464880
   Google Scholar
• Huang L-S, Sun Y-Q, Jin Y-Q, Gao Q. 2018. Development of high transferability cpSSR markers for individual identification and genetic investigation in cupressaceae species. Ecol Evol. 8:4967–4977. DOI:10.1002/ece3.4053
   Web of Science ®Google Scholar
• Ivanova Z, Sablok G, Daskalova E, Zahmanova G, Apostolova E, Yahubyan G, Baev V. 2017. Chloroplast genome analysis of resurrection tertiary relict haberlea rhodopensis highlights genes important for desiccation stress response. Front Plant Sci. 8:15. DOI:10.3389/fpls.2017.00204
   Web of Science ®Google Scholar
• Jeon J-H, Kim S-C. 2019. Comparative analysis of the complete chloroplast genome sequences of three closely related East-Asian wild roses (Rosa sect. Synstylae; Rosaceae). Genes (Basel). 10:23.
   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. 14:587–589. DOI:10.1038/nmeth.4285
   PubMed Web of Science ®Google Scholar
• Käss E, Wink M. 1997. Molecular phylogeny and phylogeography of Lupinus (Leguminosae) inferred from nucleotide sequences of therbcL gene and ITS 1 + 2 regions of rDNA. Plant Syst Evol. 208:139–167. DOI:10.1007/BF00985439
   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. 30:772–780. DOI:10.1093/molbev/mst010
   PubMed Web of Science ®Google Scholar
• Kelchner SA. 2000. The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann Mo Bot Gard. 87:482–498. DOI:10.2307/2666142
   Web of Science ®Google Scholar
• Keller J, Rousseau-Gueutin M, Martin GE, Morice J, Boutte J, Coissac E, Ourari M, Ainouche M, Salmon A, Cabello-Hurtado F, et al. 2017. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. DNA Res. 24:343–358. DOI:10.1093/dnares/dsx006
   PubMed Web of Science ®Google Scholar
• Kikuchi S, Bedard J, Hirano M, Hirabayashi Y, Oishi M, Imai M, Mai T, Ide T, Nakai M. 2013. Uncovering the protein translocon at the chloroplast inner envelope membrane. Science. 339:571–574. DOI:10.1126/science.1229262
   PubMed Web of Science ®Google Scholar
• Kim M, Christopher DA, Mullet JE. 1993. Direct evidence for selective modulation of psbA, rpoA, rbcL and 16S RNA stability during barley chloroplast development. Plant Mol Biol. 22:447–463. DOI:10.1007/BF00015975
   PubMed Web of Science ®Google Scholar
• Kimura M. 1989. The neutral theory of molecular evolution and the world view of the neutralists. Genome. 31:24–31. DOI:10.1139/g89-009
   PubMed Web of Science ®Google Scholar
• Kode V, Mudd EA, Iamtham S, Day A. 2005. The tobacco plastid accD gene is essential and is required for leaf development. Plant J. 44:237–244. DOI:10.1111/j.1365-313X.2005.02533.x
   PubMed Web of Science ®Google Scholar
• Kuang DY, Wu H, Wang YL, Gao LM, Lu L. 2011. Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): Implication for DNA barcoding and population genetics. Genome. 54:663–673. DOI:10.1139/g11-026
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 33:1870–1874. DOI:10.1093/molbev/msw054
   PubMed Web of Science ®Google Scholar
• Kurtz S, Schleiermacher C. 1999. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics. 15:426–427. DOI:10.1093/bioinformatics/15.5.426
   PubMed Web of Science ®Google Scholar
• Li X, Zuo Y, Zhu X, Liao S, Ma J. 2019. Complete chloroplast genomes and comparative analysis of sequences evolution among seven Aristolochia (Aristolochiaceae) medicinal species. Int J Mol Sci. 20:1045–1068.
   PubMed Web of Science ®Google Scholar
• Liu LX, Li R, Worth JRP, Li X, Li P, Cameron KM, Fu CX. 2017. The complete chloroplast genome of Chinese bayberry (Morella rubra, Myricaceae): implications for understanding the evolution of fagales. Front Plant Sci. 8:968. DOI:10.3389/fpls.2017.00968
   PubMed Web of Science ®Google Scholar
• Maciel HS, Schifino-Wittmann MT. 2002. First chromosome number determinations in south-eastern South American species of Lupinus L. (Leguminosae). Bot J Linn Soc. 139:395–400. DOI:10.1046/j.1095-8339.2002.00071.x
   Web of Science ®Google Scholar
• Mehmood F, Abdullah UZ, Bao Y, Poczai P, Mirza B. 2020b. Comparative plastomics of Ashwagandha (Withania, Solanaceae) and identification of mutational hotspots for barcoding medicinal plants. Plants-Basel. 9. DOI:10.3390/plants9060752
   Web of Science ®Google Scholar
• Mehmood F, Abdullah, Shahzadi I, Ahmed I, Waheed MT, Mirza B. 2020a. Characterization of Withania somnifera chloroplast genome and its comparison with other selected species of Solanaceae. Genomics. 112:1522–1530. DOI:10.1016/j.ygeno.2019.08.024
   PubMed Web of Science ®Google Scholar
• Mehmood F, Abdullah UZ, Shahzadi I, Ahmed I, Waheed MT, Poczai P, Mirza B. 2020c. Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica). Peerj. 8:30. DOI:10.7717/peerj.9552
   Web of Science ®Google Scholar
• Naydenov KD, Naydenov MK, Alexandrov A, Vasilevski K, Gyuleva V, Matevski V, Nikolic B, Goudiaby V, Bogunic F, Paitaridou D, et al. 2016. Ancient split of major genetic lineages of european black pine: evidence from chloroplast DNA. Tree Genetics & Genomes. 12:61–68. DOI:10.1007/s11295-016-1022-y
   Web of Science ®Google Scholar
• Neuhaus H, Link G. 1987. The chloroplast tRNALys(UUU) gene from mustard (sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Curr Genet. 11:251–257. DOI:10.1007/BF00355398
   PubMed Web of Science ®Google Scholar
• Njuguna AW, Li Z-Z, Saina JK, Munywoki JM, Gichira AW, Gituru RW, Wang Q-F, Chen J-M. 2019. Comparative analyses of the complete chloroplast genomes of nymphoides and menyanthes species (menyanthaceae). Aquat Bot. 156:73–81. DOI:10.1016/j.aquabot.2019.05.001
   Web of Science ®Google Scholar
• Planchuelo-Ravelo AM. 1984. Taxonomic studies of Lupinus in South America. In Proceedings of the 3rd International Lupin Conference, La Rochelle, France, 4–8 June; pp. 39–53.
   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. 15:12. DOI:10.1186/s13007-019-0435-7
   PubMed Web of Science ®Google Scholar
• Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sanchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 34:3299–3302. DOI:10.1093/molbev/msx248
   PubMed Web of Science ®Google Scholar
• Schwarz EN, Ruhlman TA, Weng ML, Khiyami MA, Sabir JSM, Hajarah NH, Alharbi NS, Rabah SO, Jansen RK. 2017. Plastome-Wide nucleotide substitution rates reveal accelerated rates in Papilionoideae and correlations with genome features across legume subfamilies. J Mol Evol. 84:187–203. DOI:10.1007/s00239-017-9792-x
   Web of Science ®Google Scholar
• Silva SR, Diaz YC, Penha HA, Pinheiro DG, Fernandes CC, Miranda VF, Michael TP, Varani AM. 2016. The chloroplast genome of utricularia reniformis sheds light on the evolution of the ndh gene complex of terrestrial carnivorous plants from the lentibulariaceae family. PLoS One. 11:e0165176. DOI:10.1371/journal.pone.0165176
   PubMed Web of Science ®Google Scholar
• Tang J, Xia HA, Cao M, Zhang X, Zeng W, Hu S, Tong W, Wang J, Wang J, Yu J, et al. 2004. A comparison of rice chloroplast genomes. Plant Physiol. 135:412–420. DOI:10.1104/pp.103.031245
   PubMed Web of Science ®Google Scholar
• Thiel T, Michalek W, Varshney RK, Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 106:411–422. DOI:10.1007/s00122-002-1031-0
   PubMed Web of Science ®Google Scholar
• Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA. 91:9794–9798. DOI:10.1073/pnas.91.21.9794
   PubMed Web of Science ®Google Scholar
• Wang YH, Susann W, Hong W, Jin JJ, Chen SY, Zhang SD, Li DZ, Yi TSJ. 2018. Plastid Genome evolution in the early-diverging legume subfamily cercidoideae (fabaceae). Front Plant Sci. 9:138–149. DOI:10.3389/fpls.2018.00138
   PubMed Web of Science ®Google Scholar
• Williams CA, Demissie A, Harborne JB. 1983. Flavonoids as taxonomic markers in old world Lupinus species. Biochem Syst Ecol. 11:221–231. DOI:10.1016/0305-1978(83)90058-3
   Web of Science ®Google Scholar
• Wolko B, Clements JC, Naganowska B, Nelson MN, Yang H. 2011. Lupinus. In: Kole C., editor. Wild crop relatives: genomic and breeding resources, Legume crops and forages. Germany: Springer Berlin Heidelberg; p. 153–206.
   Google Scholar
• Wolko B, Weeden NF. 1990. Isozyme number as an indicator of phylogeny in Lupinus. Genetica Polonica. 31:179–187.
   Google Scholar
• Wunderlin R. 1982. The leguminosae: A source book of characteristics, uses, and nodulation. Econ Bot. 36:224–224. DOI:10.1007/BF02858721
   Google Scholar
• Xiao Z, Tao Z, Nazish K, Zhao Y, Bai G, Zhao G. 2017. Completion of eight gynostemma BL. (Cucurbitaceae) chloroplast genomes: characterization, comparative analysis, and phylogenetic relationships. Front Plant Sci. 8:1583. DOI:10.3389/fpls.2017.01583
   Web of Science ®Google Scholar
• Xu Z, Zhao Y, Dong M, Dong C, Xue Y, Yang G. 2019. Characterization and phylogenetic analysis of the chloroplast genome of Lupinus westianus, a endemic species to Florida, United States. Conserv Genet Resour. 11:51–54. DOI:10.1007/s12686-017-0965-0
   Web of Science ®Google Scholar
• Yan X, Cui ming L, Shu fang W, Ning ning W, Yong W. 2002. Chloroplast genome and the regulation of chloroplast-encoded gene expression. J Plant Physiol. 38:264–269. DOI:10.13592/j.cnki.ppj.2002.03.030
   Google Scholar
• Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586–1591. DOI:10.1093/molbev/msm088
   PubMed Web of Science ®Google Scholar
• Yi Z, Cui YL, Zhang XL, Yu QB, Xi W, Yuan XB, Qin XM, He XF, Chao H, Yang ZN. 2018. A nuclear-encoded protein, mTERF6, mediates transcription termination of rpoA polycistron for plastid-encoded RNA polymerase-dependent chloroplast gene expression and chloroplast development. Sci Rep. 8:11929–11941. DOI:10.1038/s41598-018-30166-6
   Web of Science ®Google Scholar
• Yin K, Zhang Y, Li Y, Du FK. 2018. Different natural selection pressures on the atpF gene in evergreen sclerophyllous and deciduous Oak species: evidence from comparative analysis of the complete chloroplast genome of Quercus aquifolioides with other Oak species. Int J Mol Sci. 19. DOI:10.3390/ijms19041042
   Web of Science ®Google Scholar
• Yuka M, Ken-Ichi T, Junya M, Ikuo N, Yukio N, Yukiko S. 2002. Chloroplast transformation with modified accD operon increases acetyl-CoA carboxylase and causes extension of leaf longevity and increase in seed yield in tobacco. Plant Cell Physiology. 43:1518–1525. DOI:10.1093/pcp/pcf172
   Web of Science ®Google Scholar
• Zhang X, Zhou T, Yang J, Sun J, Ju M, Zhao Y, Zhao G. 2018. Comparative analyses of chloroplast genomes of cucurbitaceae species: lights into selective pressures and phylogenetic relationships. Molecules. 23. DOI:10.3390/molecules-23092165
   Web of Science ®Google Scholar
• Zheng XM, Wang J, Li F, Sha L, Pang H, Lan Q, Jing L, Yan S, Qiao W, Zhang LJSR. 2017. Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants. Sci Rep. 7:1555–1565. DOI:10.1038/s41598-017-01518-5
   Web of Science ®Google Scholar