Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes

0446928 - ÚEB 2016 RIV US eng J - Journal Article
Garbus, I. - Romero, J.R. - Valárik, Miroslav - Vanžurová, Hana - Karafiátová, Miroslava - Doležel, Jaroslav - Tranquilli, G. - Helguera, M. - Echenique, V. … Total 10 authors
Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes.
BMC Genomics. Roč. 16, MAY 12 (2015). ISSN 1471-2164. E-ISSN 1471-2164
Institutional support: RVO:61389030
Keywords : VIRTUAL GENE ORDER * BAC END SEQUENCES * NEXT-GENERATION
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 3.867, year: 2015

The number and complexity of repetitive elements varies between species, being in general most represented in those with larger genomes. Combining the flow-sorted chromosome arms approach to genome analysis with second generation DNA sequencing technologies provides a unique opportunity to study the repetitive portion of each chromosome, enabling comparisons among them. Additionally, different sequencing approaches may produce different depth of insight to repeatome content and structure. In this work we analyze and characterize the repetitive sequences of Triticum aestivum cv. Chinese Spring homeologous group 4 chromosome arms, obtained through Roche 454 and Illumina sequencing technologies, hereinafter marked by subscripts 454 and I, respectively. Repetitive sequences were identified with the RepeatMasker software using the interspersed repeat database mips-REdat_v9.0p. The input sequences consisted of our 4DS(454) and 4DL(454) scaffolds and 4AS(I), 4AL(I), 4BS(I), 4BL(I), 4DS(I) and 4DL(I) contigs, downloaded from the International Wheat Genome Sequencing Consortium (IWGSC).Repetitive sequences content varied from 55% to 63% for all chromosome arm assemblies except for 4DLI, in which the repeat content was 38%. Transposable elements, small RNA, satellites, simple repeats and low complexity sequences were analyzed. SSR frequency was found one per 24 to 27 kb for all chromosome assemblies except 4DL(I), where it was three times higher. Dinucleotides and trinucleotides were the most abundant SSR repeat units. (GA)n/(TC)n was the most abundant SSR except for 4DLI where the most frequently identified SSR was (CCG/CGG)(n). Retrotransposons followed by DNA transposons were the most highly represented sequence repeats, mainly composed of CACTA/En-Spm and Gypsy superfamilies, respectively. This whole chromosome sequence analysis allowed identification of three new LTR retrotransposon families belonging to the Copia superfamily.
Permanent Link: http://hdl.handle.net/11104/0248880