Localization of high level of sequence conservation and divergence regions in cotton

Theoretical and Applied Genetics

Volumn 124, Issue 7, 2012, Pages 1173-1182

  Wang, Kai ^a   Zhang, Wenpan ^a   Cao, Yujie ^a   Zhang, Zhongxin ^a   Zheng, Dewei ^a   Zhou, Baoliang ^a   Guo, Wangzhen ^a   Zhang, Tianzhen ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COTTON; FLUORESCENCE MICROSCOPY; PLANTS (BOTANY);

BACTERIAL ARTIFICIAL CHROMOSOMES; CYTOGENETIC MAPS; EXPANSION AND CONTRACTION; FLUORESCENCE IN SITU HYBRIDIZATION; SEQUENCE ANALYSIS; SEQUENCE CONSERVATION; SEQUENCE VARIATIONS; TETRAPLOID COTTON;

CHROMOSOMES;

BACTERIA (MICROORGANISMS); GOSSYPIUM; GOSSYPIUM HIRSUTUM;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME MAP; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC VARIABILITY; GENETICS; GENOME SIZE; GOSSYPIUM; NUCLEOTIDE SEQUENCE; PLANT CHROMOSOME; PLANT GENOME; RETROPOSON; TETRAPLOIDY;

BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; CONSERVED SEQUENCE; GENETIC VARIATION; GENOME SIZE; GENOME, PLANT; GOSSYPIUM; IN SITU HYBRIDIZATION, FLUORESCENCE; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; TETRAPLOIDY;

EID: 84865595107     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-011-1777-3     Document Type: Article

References (33)

1. Bensasson D, Petrov DA, Zhang D-X, Hartl DL, Hewitt GM (2001) Genomic gigantism: DNA loss is slow in mountain grasshoppers. Mol Biol Evol 18: 246-253.
2. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13: 721-731.
3. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
4. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier M-C, Magdelenat G, Gonthier C, Couloux A, Budak H, Breen J, Pumphrey M, Liu S, Kong X, Jia J, Gut M, Brunel D, Anderson JA, Gill BS, Appels R, Keller B, Feuillet C (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22: 1686-1701.
5. Cronn RC, Small RL, Haselkorn T, Wendel JF (2002) Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am J Bot 89: 707-725.
6. Deutsch M, Long M (1999) Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res 27: 3219-3228.
7. Dooner HK, Weil CF (2007) Give-and-take: interactions between DNA transposons and their host plant genomes. Curr Opin Genet Dev 17: 486-492.
8. Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF (2004) Incongruent patterns of local and global genome size evolution in cotton. Genome Res 14: 1474-1482.
9. Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF (2007) Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant J 50: 995-1006.
10. Guo W, Cai C, Wang C, Zhao L, Wang L, Zhang T (2008) A preliminary analysis of genome structure and composition in Gossypium hirsutum. BMC Genomics 9: 314.
11. Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16: 1252-1261.
12. Hawkins JS, Proulx SR, Rapp RA, Wendel JF (2009) Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc Natl Acad Sci USA 106: 17811-17816.
13. Hendrix B, Stewart JM (2005) Estimation of the nuclear DNA content of Gossypium species. Ann Bot 95: 789-797.
14. Hu Y, Guo WZ, Zhang TZ (2009) Construction of a bacterial artificial chromosome library of TM-1, a standard line for genetics and genomics in upland cotton. J Integr Plant Biol 51: 107-112.
15. Jiang J, Birchler JA, Parrott WA, Dawe RK (2003) A molecular view of plant centromeres. Trends Plant Sci 8: 570-575.
16. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
17. Kapuscinski J (1995) DAPI: a DNA-specific fluorescent probe. Biotech Histochem 70: 220-233.
18. Kohany O, Gentles AJ, Hankus L, Jurka J (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7: 474.
19. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532.
20. Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M (2005) Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res 33: 6494-6506.
21. Pearce S, Pich U, Harrison G, Flavell A, Heslop-Harrison J, Schubert I, Kumar A (1996) The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal eterochromatin Chromosome Res 4: 357-364.
22. Peterson-Burch B, Nettleton D, Voytas D (2004) Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae. Genome Biol 5: R78.
23. Petrov DA (2002) Mutational equilibrium model of genome size evolution. Theor Popul Biol 61: 531-544.
24. Sanmiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann Bot 82: 37-44.
25. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
26. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20: 43-45.
27. Seelanan T, Schnabel A, Wendel JF (1997) Congruence and consensus in the cotton tribe (Malvaceae). Syst Bot 22: 259-290.
28. Vitte C, Bennetzen JL (2006) Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci USA 103: 17638-17643.
29. Wang K, Zhang YJ, Guan B, Guo W, Zhang T (2007) Fluorescence in situ hybridization of bacterial artificial chromosome in cotton. Prog Biochem Biophys 34: 1216-1222.
30. Wang K, Yang Z, Shu C, Hu J, Lin Q, Zhang W, Guo W, Zhang T (2009) Higher axial-resolution and sensitivity pachytene fluorescence in situ hybridization protocol in tetraploid cotton. Chromosome Res 17: 1041-1050.
31. Wang K, Guo W, Yang Z, Hu Y, Zhang W, Zhou B, Stelly D, Chen Z, Zhang T (2010) Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton. Chromosoma 119: 255-266.
32. Wendel JF (1989) New World tetraploid cottons contain Old World cytoplasm. Proc Natl Acad Sci USA 86: 4132-4136.
33. Wendel JF, Cronn RC, Alvarez I, Liu B, Small RL, Senchina DS (2002) Intron size and genome size in plants. Mol Biol Evol 19: 2346-2352.