Chromosome diversity and evolution in Allium (Allioideae, Amaryllidaceae)

References

• Apg III. 2009. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161: 105–121.
   Web of Science ®Google Scholar
• Auger DL, Sheridan WF. 2012. Plant chromosomal deletions, insertions, and rearrangements. In: Bass HW, Birchler JA, editors. Plant Cytogenetics. Genome Structure and Chromosome Function. Wien: Springer-Verlag. pp. 3–36.
   Google Scholar
• Brandham PE, Doherty MJ. 1998. Genome size variation in the Aloaceae, an angiosperm family displaying karyotypic orthoselection. Ann Bot (London) 82: 67–73.10.1006/anbo.1998.0742
   Web of Science ®Google Scholar
• Brat SV. 1965. Genetic systems in Allium. Heredity 20: 325–339.10.1038/hdy.1965.47
   Web of Science ®Google Scholar
• Brullo S, Guglielmo A, Pavone P, Salmeri C. 2008. Taxonomic study on Allium dentiferum Webb & Berthel (Alliaceae) and its relations with allied species from the Mediterranean. Taxon 57: 243–253.
   Web of Science ®Google Scholar
• Carta A, Peruzzi L. 2015. Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality in Liliaceae. New Phytol, in press. doi:10.1111/nph.13769.
   PubMed Web of Science ®Google Scholar
• Cerbah MJ, Coulaud J, Siljak-Yakovlev S. 1998a. rDNA organization and evolutionary relationships in the genus Hypochaeris (Asteraceae). J Hered 89: 312–318.10.1093/jhered/89.4.312
   Web of Science ®Google Scholar
• Cerbah MJ, Souza-Chies T, Joubier MF, Lejeune B, Siljak-Yakovlev S. 1998b. Molecular phylogeny of the genus Hypochaeris using internal transcribed spacers of nuclear rDNA: Inference for chromosomal evolution. Mol Biol Evol 15: 345–354.10.1093/oxfordjournals.molbev.a025931
   PubMed Web of Science ®Google Scholar
• Chase MW, Reveal JL, Fay MF. 2009. A subfamilial classification for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae. Bot J Linn Soc 161: 132–136.10.1111/(ISSN)1095-8339
   Web of Science ®Google Scholar
• Chen S, Kim DK, Chase MW, Kim JH. 2013. Networks in a large-scale phylogenetic analysis: Reconstructing evolutionary history of Asparagales (Lilianae) based on four plastid genes. PLoS ONE 8: e59472.10.1371/journal.pone.0059472
   PubMed Web of Science ®Google Scholar
• De Azkue D, Martinez A. 1988. DNA content and chromosome evolution in the shrubby Oxalis. Genome 30: 52–57.10.1139/g88-010
   Web of Science ®Google Scholar
• Clarkson JJ, Lim KY, Kovarik A, Chase MW, Knapp S, Leitch AR. 2005. Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae). New Phytol 168: 241–252.10.1111/j.1469-8137.2005.01480.x
   PubMed Web of Science ®Google Scholar
• Fay MF, Chase MW. 1996. Resurrection of Themidaceae for the Brodiaea alliance, and recircumscription of Alliaceae, Amaryllidaceae and Agapanthoideae. Taxon 45: 441–451.10.2307/1224136
   Web of Science ®Google Scholar
• Fedoroff NV. 2012. Transposable Elements, epigenetics, and genome evolution. Science 338: 758–767.10.1126/science.338.6108.758
   PubMed Web of Science ®Google Scholar
• Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat 125: 1–15.10.1086/284325
   Web of Science ®Google Scholar
• Friesen N. 1992. Systematics of the Siberian polyploid complex in subgenus Rhizirideum (Allium). In: Hanelt P, Hammer K, Knüpffer H editors. The genus Allium taxonomic problems and genetic resources. Proceedings of an international symposium held at Gatersleben, Germany, 11–13 June 1991. Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany, 55–66.
   Google Scholar
• Friesen N, Fritsch RM, Blattner FR. 2006. Phylogeny and new intrageneric classification of Allium (Alliaceae) based on nuclear ribosomal DNA its sequences. Aliso 22: 372–395.
   Google Scholar
• Fritsch RM. 2012. Illustrated key to the sections and subsections and brief general circumscription of Allium subg. Melanocrommyum. Phyton (Horn) 52: 1–37.
   Web of Science ®Google Scholar
• Fritsch RM, Astanova SB. 1998. Uniform karyotypes in different sections of Allium L. subgenus Melanocrommyum (Webb & Berth.) Rouy from Central Asia. Feddes Repertorium 109: 539–549.
   Google Scholar
• Fritsch RM, Blattner FR, Gurushidze M. 2010. New classification of Allium L. subg. Melanocrommyum (Webb & Berthel) Rouy (Alliaceae) based on molecular and morphological characters. Phyton (Horn) 49: 145–220.
   Web of Science ®Google Scholar
• Garbari F, Bedini G, Peruzzi L. 2012. Chromosome numbers of the Italian flora. From the Caryologia foundation to present. Caryologia 65: 62–71.10.1080/00087114.2012.678090
   Web of Science ®Google Scholar
• Grif VG. 2000. Some aspects of plant karyology and karyosystematics. Int Rev Cytol 196: 131–175.10.1016/S0074-7696(00)96004-2
   PubMed Web of Science ®Google Scholar
• Hanelt P. 1990. Taxonomy, evolution and history. In: Rabinowitch HD, Brewster JL, editors. Onions and allied crops, Vol. 1. Boca Raton, FL: CRC Press. pp. 1–26.
   Google Scholar
• Hanelt P, SchulzeMotel J, Fritsch RM, et al. 1992. Infrageneric grouping of Allium—the Gatersleben approach. In: Hanelt P, Hammer K, Knüpffer H. eds., The genus Allium: taxonomic problems and genetic resources Proceedings of an international symposium held at Gatersleben, Germany, 11–13 June 1991. Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany. pp. 107–123.
   Google Scholar
• Huang RF, Xu JM, Yu H. 1995. A study on karyotypes and their evolutionary trends in Allium Sect. Bromatorrhiza Ekberg (Liliaceae). Cathaya 7: 133–145.
   Google Scholar
• Jang TS, Emadzade K, Parker J, Temsch EM, Leitch AR, Speta F, et al. 2013. Chromosomal diversification and karyotype evolution of diploids in the cytologically diverse genus Prospero (Hyacinthaceae). BMC Evol Biol 13: 136.10.1186/1471-2148-13-136
   PubMed Web of Science ®Google Scholar
• Kamelin RV. 1973. Florogeneticheskij analiz estestvennoj flory gornoj Srednej Azii. Leningrad: Nauka, p. 354.
   Google Scholar
• Kim S, Park YI, Yang TJ. 2015. Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the Pink allele of the ANS gene in onion (Allium cepa L.). Mol Genet Genom 290: 1027–1037. doi:10.1007/s00438-014-0973-7.
   PubMed Web of Science ®Google Scholar
• Levan A. 1931. Cytological studies in Allium. Hereditas 15: 347–356.
   Google Scholar
• Levan A. 1932. Cytological studies in Allium II. Chromosome morphological contributions. Hereditas 16: 257–294.
   Google Scholar
• Levan A. 1935. Cytological studies in Allium VI. The chromosome morphology of some diploid species of Allium. Hereditas 20: 289–330.
   Google Scholar
• Levan A, Fredga K, Sandberg AA. 1964. Nomenclature for centromeric position on chromosomes. Hereditas 52: 201–220.
   Web of Science ®Google Scholar
• Levin DA. 2002. The role of chromosome change in plant evolution. New York, NY: Oxford University Press.
   Google Scholar
• Li QQ, Zhou SD, He XJ, Yu Y, Zhang YC, Wei XQ. 2010. Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Ann. Bot. (London) 106: 709–733.10.1093/aob/mcq177
   PubMed Web of Science ®Google Scholar
• Linnaeus C. 1753. Species plantarum, Vol. 1. Stockholm: Laurentiis Salvii.
   Google Scholar
• Lysak MA, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I. 2006. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. PNAS USA 103: 5224–5229.10.1073/pnas.0510791103
   PubMed Web of Science ®Google Scholar
• Mensinkai SW. 1939. Cytogenetic studies in the genus Allium. J Genet 39: 1–45.10.1007/BF02982816
   Google Scholar
• Orme D, Freckleton RP, Thomas GH, Petzoldt T, Fritz S, Isaac N, Pearse W. 2012. Caper: Comparative analyses of phylogenetics and evolution in R. Met. Ecol. Evol 3: 145–151.
   Web of Science ®Google Scholar
• Pagel M. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877–884.10.1038/44766
   PubMed Web of Science ®Google Scholar
• Paradis E, Claude J, Strimmer K. 2004. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289–290.10.1093/bioinformatics/btg412
   PubMed Web of Science ®Google Scholar
• Parida A, Raina SN, Narayan RKJ. 1990. Quantitative DNA variation between and within chromosome complements of Vigna species (Fabaceae). Genetica 82: 125–133.10.1007/BF00124642
   Web of Science ®Google Scholar
• Pastor J. 1982. Karyology of Allium species from the Iberian peninsula. Phyton (Horn) 22: 171–200.
   Web of Science ®Google Scholar
• Paszko B. 2006. A critical review and a new proposal of karyotype asymmetry indices. Pl Syst Evol 258: 39–48.10.1007/s00606-005-0389-2
   Web of Science ®Google Scholar
• Peruzzi L. 2013. “x” is not a bias, but a number with real biological significance. Plant Biosyst 147: 1238–1241.10.1080/11263504.2013.861533
   Web of Science ®Google Scholar
• Peruzzi L, Altınordu F. 2014. A proposal for a multivariate quantitative approach to infer karyological relationships among taxa. Comp Cytogen 8: 337–349.10.3897/CompCytogen.v8i4.8564
   PubMed Web of Science ®Google Scholar
• Peruzzi L, Eroğlu HE. 2013. Karyotype asymmetry: Again, how to measure and what to measure? Comp Cytogen 7: 1–9.10.3897/compcytogen.v7i1.4431
   PubMed Web of Science ®Google Scholar
• Peruzzi L, Leitch IJ, Caparelli KF. 2009. Chromosome diversity and evolution in Liliaceae. Ann Bot (London) 103: 459–475.
   PubMed Web of Science ®Google Scholar
• R Development Core Team. 2015. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
   Google Scholar
• Raina SN, Rees H. 1983. DNA variation between and within chromosome complements of vicia species. Heredity 51: 335–346.10.1038/hdy.1983.38
   Web of Science ®Google Scholar
• Regel E. 1875. Alliorum adhuc cognitorum monographia. Acta Horti Petrop 3: 1–266.
   Google Scholar
• Regel E. 1887. Allii species Asiae Centralis in Asia Media a Turcomania desertisque Araliensibus et Caspicis usque ad Mongolian crescentes. Acta Horti Petrop 10: 278–362.
   Google Scholar
• Revell LJ. 2012. Phytools: An R package for phylogenetic comparative biology (and other things). Meth Ecol Evol 3: 217–223.10.1111/j.2041-210X.2011.00169.x
   Web of Science ®Google Scholar
• Schneeweiss GM, Palomeque T, Colwell AE, Weiss-Schneeweiss H. 2004. Chromosome numbers and karyotype evolution in holoparasitic Orobanche (Orobanchaceae) and related genera. Am J Bot 91: 439–448.10.3732/ajb.91.3.439
   PubMed Web of Science ®Google Scholar
• Schubert I. 2007. Chromosome evolution. Current Opinions in Plant Biology 10: 109–115.10.1016/j.pbi.2007.01.001
   PubMed Web of Science ®Google Scholar
• Srivastava S, Lavania UC. 1991. Evolutionary DNA variation in Papaver. Genome 34: 763–768.10.1139/g91-118
   Web of Science ®Google Scholar
• Stearn WT. 1980. Allium L. In: Tutin TG, Heywood VH, Burges NA, et al., editors. Flora Europaea, Vol. 5. Cambridge: Cambridge University Press. pp. 49–69.
   Google Scholar
• Stebbins GL. 1971. Chromosomal evolution in higher plants. London: Edward Arnold.
   Google Scholar
• Traub HP. 1968. The subgenera, sections and subsections of Allium L. Plant Life 24: 147–163.
   Google Scholar
• Vvedensky AI. 1935. Rod 267. Luk – Allium L. In: Komarov VL, editor. Flora URSS, Vol. 4. Leningrad: Izd. Akad. Nauk SSSR. pp. 112–280.
   Google Scholar
• Webb C, Ackerly D, Kembel S. 2009. Phylocom. Software for the analysis of phylogenetic community structure and character evolution. [WWW document] URL. Available: http://phylodiversity.net/phylocom/. Accessed Feb 3 2015.
   Google Scholar
• Weiss-Schneeweiss H, Tremetsberger K, Schneeweiss GM, Parker JS, Stuessy TF. 2008. Karyotype diversification and evolution in diploid and polyploidy South American Hypochaeris (Asteraceae) inferred from rDNA localization and genetic fingerprint data. Ann Bot (London) 101: 909–918.10.1093/aob/mcn023
   PubMed Web of Science ®Google Scholar
• Weiss-Schneeweiss H, Schneeweiss GM. 2013. Karyotype diversity and evolutionary trends in angiosperms. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF, editors. Plant genome diversity. Volume 2. Physical structure, behavior and evolution of plant genomes. Wien: Springer-Verlag. pp. 209–230.
   Google Scholar
• Wheeler EJ, Mashayekhi S, McNeal DW, Columbus JT, Pires JC. 2013. Molecular systematics of Allium subgenus Amerallium (Amaryllidaceae) in North America. Am J Bot 100: 701–711.10.3732/ajb.1200641
   PubMed Web of Science ®Google Scholar
• Xu JM, Yang L, He XJ. 1998. A study on karyotype differentiation of Allium fasciculatum (Liliaceae). Acta Phytotax Sinica 36: 346–352.
   Google Scholar
• Zhou SD, He XJ, Yu Y, Xu JM. 2007. Karyotype studies on twenty-one populations of eight species in Allium section Rhiziridium. Acta Phytotax Sinica 45: 207–216.
   Google Scholar
• Zuo J, Yuan G. 2011. The difference between the heterogeneity of the centromeric index and intrachromosomal asymmetry. Pl Syst Evol 297: 141–145.10.1007/s00606-011-0528-x
   Web of Science ®Google Scholar