Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping
Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection
Typ dokumentu časopisecké články
PubMed
28591168
PubMed Central
PMC5462415
DOI
10.1371/journal.pone.0179043
PII: PONE-D-17-06508
Knihovny.cz E-zdroje
- MeSH
- chromozomy rostlin genetika MeSH
- diploidie MeSH
- Festuca genetika růst a vývoj MeSH
- fyziologický stres genetika MeSH
- genová knihovna MeSH
- hybridizace genetická MeSH
- hybridizace in situ fluorescenční MeSH
- karyotypizace MeSH
- nízká teplota MeSH
- repetitivní sekvence nukleových kyselin genetika MeSH
- RNA ribozomální 5S genetika MeSH
- tetraploidie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- RNA ribozomální 5S MeSH
The Festuca genus is thought to be the most numerous genus of the Poaceae family. One of the most agronomically important forage grasses, Festuca pratensis Huds. is treated as a model plant to study the molecular mechanisms associated with tolerance to winter stresses, including frost. However, the precise mapping of the genes governing stress tolerance in this species is difficult as its karyotype remains unrecognized. Only two F. pratensis chromosomes with 35S and 5S rDNA sequences can be easily identified, but its remaining chromosomes have not been distinguished to date. Here, two libraries derived from F. pratensis nuclear DNA with various contents of repetitive DNA sequences were used as sources of molecular probes for fluorescent in situ hybridisation (FISH), a BAC library and a library representing sequences most frequently present in the F. pratensis genome. Using FISH, six groups of DNA sequences were revealed in chromosomes on the basis of their signal position, including dispersed-like sequences, chromosome painting-like sequences, centromeric-like sequences, knob-like sequences, a group without hybridization signals, and single locus-like sequences. The last group was exploited to develop cytogenetic maps of diploid and tetraploid F. pratensis, which are presented here for the first time and provide a remarkable progress in karyotype characterization.
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Reheul D, De Cauwer B, Cougnon M. The role of forage crops in multifunctional agriculture In: Boller B, Posselt UK, Veronesi F, editors. Fodder crops and amenity grasses, 2010. pp. 1–12.
Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv. 2014;32: 190–199. 10.1016/j.biotechadv.2013.11.010 PubMed DOI
Zwierzykowski Z, Lukaszewski AJ, Naganowska B, Leśniewska A. The pattern of homoeologous recombination in triploid hybrids of Lolium multiflorum with Festuca pratensis. Genome 1999;42: 720–726.
Kosmala A, Zwierzykowska E, Zwierzykowski Z. Chromosome pairing in triploid intergeneric hybrids of Festuca pratensis with Lolium multiflorum revealed by GISH. J Appl Genet. 2006a;47: 215–220. PubMed
Kosmala A, Zwierzykowski Z, Gasior D, Rapacz M, Zwierzykowska E, Humphreys MW. GISH/FISH mapping of genes for freezing tolerance transferred from Festuca pratensis to Lolium multiflorum. Heredity 2006b;96: 243–251. PubMed
Kosmala A, Zwierzykowski Z, Zwierzykowska E, Łuczak M, Rapacz M, Gąsior D, Humphreys MW. Introgression-mapping of the genes for winter hardiness and frost tolerance transferred from Festuca arundinacea into Lolium multiflorum. J Hered. 2007;98: 311–316. 10.1093/jhered/esm047 PubMed DOI
Betekhtin A, Jenkins G, Hasterok R. Reconstructing the Evolution of Brachypodium Genomes Using Comparative Chromosome Painting. Plos One 2014;12: e115108 10.1371/journal.pone.0115108 PubMed DOI PMC
Mandáková T, Schranz ME, Sharbel TF, de Jong H, Lysak MA. Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes. The Plant J. 2015;82: 785–793. 10.1111/tpj.12849 PubMed DOI
Aliyeva-Schorr L, Stein N, Houben A Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis. Chromosome Res 2016;24: 231–242. 10.1007/s10577-016-9518-8 PubMed DOI
Wolny E, Fidyk W, Hasterok R. Karyotyping of Brachypodium pinnatum (2n = 18) chromosomes using cross-species BAC-FISH. Genome 2013;56: 239–243. 10.1139/gen-2013-0012 PubMed DOI
Iovene M, Cavagnaro PF, Senalik D, Buell CR, Jiang J, Simon PW. Comparative FISH mapping of Daucus species (Apiaceae family). Chrom Res. 2011;19: 493–506. 10.1007/s10577-011-9202-y PubMed DOI
Fonseca A, Pedrosa-Harand A. Karyotype stability in the genus Phaseolus evidenced by the comparative mapping of the wild species Phaseolus microcarpus. Genome 2013;56: 335–343. 10.1139/gen-2013-0025 PubMed DOI
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009;326: 1112–1115. 10.1126/science.1178534 PubMed DOI
Brenchley R, Spannagl M, Pfeifer M, Barker GLA, D'Amore R, Allen AM et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 2012;491: 705–710. 10.1038/nature11650 PubMed DOI PMC
Jia J, Zhao S, Kong X, Li Y, Zhao G, He W et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 2013;496: 91–95. 10.1038/nature12028 PubMed DOI
Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C et al. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 2013;496: 87–90. 10.1038/nature11997 PubMed DOI
Tsujimoto H, Mukai Y, Akagawa K, Nagaki K, Fujigaki J, Yamamoto M, Sasakuma T. Identification of individual barley chromosomes based on repetitive sequences: Conservative distribution of Afa-family repetitive sequences on the chromosomes of barley and wheat. Genes Genet. Syst. 1997;73: 303–309. PubMed
Catalan P, Torrecilla P, Lopez Rodriguez JA, Olmstead RG. Phylogeny of the festucoid grasses of subtribe Loliinae and allies (Poeae, Pooideae) inferred from ITS and trnL–F sequences. Mol Phylogenet Evol. 2004;31: 517–541. 10.1016/j.ympev.2003.08.025 PubMed DOI
Loureiro J, Kopecký D, Castro S, Santos C, Silveira P. Flow cytometric and cytogenetic analyses of Iberian Peninsula Festuca spp. Plant Syst Evol. 2007;269: 89–105.
Bennett MD, Leitch IJ. Plant DNA C-values Database (Release 6.0, Dec. 2012). http://data.kew.org/cvalues/
Kopecký D, Martis M, Cíhalíková J, Hribová E, Vrána J, Bartoš J, Kopecká J, Cattonaro F, Stočes Š, Novák P, Neumann P, Macas J, Šimková H, Studer B, Asp T, Baird JH, Navrátil P, Karafiátová M, Kubaláková M, Šafář J, Mayer K, Doležel J. Flow Sorting and Sequencing Meadow Fescue Chromosome 4F. Plant Physiol. 2013;163: 1323–1337. 10.1104/pp.113.224105 PubMed DOI PMC
Thomas HM, Harper JA, Meredith MR, Morgan WG, King IP. Physical mapping of ribosomal DNA sites in Festuca arundinacea and related species by in situ hybridization. Genome 1997;40: 406–410. PubMed
Harper JA, Thomas ID, Lovatt JA, Thomas HM. Physical mapping of rDNA sites in possible diploid progenitors of polyploid Festuca species. Plant Syst Evol. 2004;245: 163–168.
Książczyk T, Taciak M, Zwierzykowski Z. Variability of ribosomal DNA sites in Festuca pratensis, Lolium perenne, and their intergeneric hybrids, revealed by FISH and GISH. J Appl Genet. 2010;51: 449–460. 10.1007/BF03208874 PubMed DOI
Kosmala A, Bocian A, Rapacz M, Jurczyk B, Zwierzykowski Z. Identification of leaf proteins differentially accumulated during cold acclimation between Festuca pratensis plants with distinct levels of frost tolerance. J Exp Bot. 2009;60: 3595–3609. 10.1093/jxb/erp205 PubMed DOI
Kopecký D, Lukaszewski AJ, Dolezel J. Meiotic behaviour of individual chromosomes of Festuca pratensis in tetraploid Lolium multiflorum. Chrom Res. 2008;16: 987–998. 10.1007/s10577-008-1256-0 PubMed DOI
Nunome T, Negoro S, Miyatake K, Yamaguchi H, Fukuoka H. A protocol for the construction of microsatellite enriched genomic library. Plant Mol Biol Rep. 2006;24: 305–312.
Gerlach WL, Dyer TA. Sequence organisation of the repeating units in the nucleus of wheat which contain 5S rRNA genes. Nucl Acids Res. 1980;8: 4851–4865. PubMed PMC
Unfried I, Gruendler P. Nucleotide sequence of the 5.8S and 25S rRNA genes and the internal transcribed spacers from Arabidopsis thaliana. Nucl Acids Res. 1990;18: 4011 PubMed PMC
Farrar K, Donnison IS. Construction and screening of BAC libraries made from Brachypodium genomic DNA. Nature Protocols 2007;2: 1661–1674. 10.1038/nprot.2007.204 PubMed DOI
Książczyk T, Apolinarska B, Kulak-Książczyk S, Wiśniewska H, Stojałowski S, Łapiński M. Identification of the chromosome complement and the spontaneous 1R/1V translocations in allotetraploid Secale cereale × Dasypyrum villosum hybrids through cytogenetic approaches. J Appl Genet. 2011;52: 305–311. 10.1007/s13353-011-0048-y PubMed DOI PMC
Heslop-Harrison JS. Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 2000;12: 617–635. PubMed PMC
Thomas HM. The Giemsa C-band karyotypes of six Lolium species. Heredity 1981;46: 263–267.
Jones ES, Mahoney NL, Hayward MD, Armstead IP, Jones JG, Humphreys MO, King IP, Kishida T, Yamada T, Balfourier F, Charmet G, Forster JW. An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes. Genome 2002;45: 282–295. PubMed
Idziak D, Hazuka I, Poliwczak B, Wiszynska A, Wolny E, Hasterok R. Insight into the karyotype evolution of Brachypodium species using comparative chromosome barcoding. Plos One 2014;9: e93503 10.1371/journal.pone.0093503 PubMed DOI PMC
Fransz P, Armstrong S, Alonso-Blanco C, Fischer TC, Torres-Ruiz RA, Jones G. Cytogenetics for the model system Arabidopsis thaliana. Plant J. 1998;13: 867–876. PubMed
Hasterok R, Marasek A, Donnison IS, Armstead I, Thomas A, King IP, Wolny E, Idziak D, Draper J, Jenkins G. Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 2006;173: 349–362. 10.1534/genetics.105.049726 PubMed DOI PMC
Pedrosa A, Sandal N, Stougaard J, Schweizer D, Bachmair A. Chromosomal map of the model legume Lotus japonicus. Genetics 2002;161: 1661–1672. PubMed PMC
Han Y, Zhang Z, Huang S, Jin H. An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2. BMC Genetics 2011;12: 18 10.1186/1471-2156-12-18 PubMed DOI PMC
Sun J, Zhang Z, Zong X, Huang S, Li Z, Han Y. A high-resolution cucumber cytogenetic map integrated with the genome assembly. BMC Genomics 2013;14: 461 10.1186/1471-2164-14-461 PubMed DOI PMC
Houben A, Schroeder-Reiter E, Nagaki K, Nasuda S, Wanner G, Murata M, Endo TR. CENH3 interacts with the centromeric retrotransposon cereba and GC-rich satellites and locates to centromeric substructures in barley. Chromosoma 2007;116: 275–283. 10.1007/s00412-007-0102-z PubMed DOI
He Q, Cai Z, Hu T, Liu H, Bao C, Mao W, Jin W. Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.). BMC Plant Biol. 2015;15:105 10.1186/s12870-015-0480-y PubMed DOI PMC
Langdon T, Seago C, Mende M, Leggett M, Thomas H, Forster JW, Jones RN, Jenkins G. Retrotransposon Evolution in Diverse Plant Genomes. Genetics 2000;156: 313–325. PubMed PMC
Sharma A, Wolfgruber TK, Presting GG. Tandem repeats derived from centromeric retrotransposons. BMC Genomics 2013;14: 142 10.1186/1471-2164-14-142 PubMed DOI PMC
Zhang P, Li W, Friebe B, Gill BS. Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH. Genome 2004;47: 979–987. 10.1139/g04-042 PubMed DOI
Yagi K, Siedlecka E, Pawełkowicz M, Wojcieszek M, Przybecki Z, Tagashira N, Hoshi Y, Malepszy S, Pląder W. Karyotype analysis and chromosomal distribution of repetitive DNA sequences of Cucumis metuliferus using fluorescence in situ hybridization. Cytogenet Gen Res. 2014;144: 237–242. PubMed
Houben A, Banaei-Moghaddam AM, Klemme S, Timmis JN. Evolution and biology of supernumerary B chromosomes. Cell Mol Life Sci. 2014;71: 467–476. 10.1007/s00018-013-1437-7 PubMed DOI PMC
Banaei-Moghaddam AM, Martis MM, Macas J, Gundlach H, Himmelbach A, Altschmied L, Mayer KF, Houben A. Genes on B chromosomes: Old questions with new tools. Biochim Bioph Acta 2015;1849: 64–70. PubMed
Renny-Byfield S, Wendel JF. Doubling down on genomes: Polyploidy and crop plants Am J Bot. 2014;101: 1711–1725. 10.3732/ajb.1400119 PubMed DOI
Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM. Rapid elimination of low-copy DNA sequences in polyploidy wheat: A possible mechanism for differentiation of homoeologous chromosomes. Genetics 1997;147: 1381–1387. PubMed PMC
Weiss H, Maluszynska J. Chromosomal rearrangements in autotetraploid plants of Arabidopsis thaliana. Hereditas 2000;133: 255–261. PubMed
Murat F, Zhang R, Guizard S, Flores R, Armero A, Pont C, Steinbach D, Quesneville H, Cooke R, Salse J. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome Biol Evol. 2013;6: 12–33. PubMed PMC
Byrne SL, Nagy I, Pfeifer M, Armstead I, Swain S, Studer B, Mayer K, Campbell JD, Czaban A, Hentrup S, Panitz F, Bendixen C, Hedegaard J, Caccamo M, Asp T. A synteny-based draft genome sequence of the forage grass Lolium perenne. Plant J. 2015;84: 816–826. 10.1111/tpj.13037 PubMed DOI