Analysis and characterization of the repetitive sequences of T. aestivum chromosome 4D.

JOSÉ ROMERO; INGRID GARBUS; HELGUERA M; TRANQUILI, G; PANIEGO N; CÁCCAMO M; VALARIK M; SIMKOVA H; DOLEZEL J; VIVIANA ECHENIQUE

Yokohama

Simposio; The 12Th International Wheat Genetics Symposium; 2013

International Wheat Genetics Symposium

Much of the nuclear genome of most angiosperms is composed of different repetitive elements. The number and complexity of these elements varies between the different species, being more abundant in species with higher genomes. The aim of this work was the analysis and characterization of the repetitive sequences of Triticumaestivum chromosome 4D arms obtained by flow sorting and sequenced using Next Generation Sequencing technologies (NGS). We have taken advantage of the availability of sequences from individual chromosomes from the International Wheat Genome Sequencing Consortium (IWGSC; www.wheatgenome.org/). DNA from the 4D chromosomes arms, obtained through a flow-sorted approach of Chinese Spring (Triticumaestivum) ditelosomic (DT) lines, was sequenced using the Roche 454 pyrosequencing technology (GS FLX Titanium platform). The 454 sequences were assembled in contigs that were further assembled into 8141 and 7077 scaffolds for the 4DS and 4DL, respectively. The identification of repetitive sequences was performed usingRepeatMasker (RM; www.repeatmasker.org), using the interspersed repeat database mips-REdat_v9.0p. The percentages of masked bases over the total length were similar for both chromosome arms, being 67.4% and 65.5% for 4DS and 4DL, respectively. The RM software was further used to classify recognizable repeat families. The retroelements are the most represented sequences repeats, being ~50% of the total sequences. Moreover, considering the sequence total length covered by sequence repeats in both chromosome arms, retroelements represent the 74% and 80% for 4DS and 4DL, respectively. The retroelements are followed in importance by the DNA elements, which comprise 15.4% and 11.2% for 4DS and 4DL, respectively. The relationship Retroelements/DNA is lower in 4DS (3.2%) than in 4DL (4.7%).  For both chromosomes arms CACTA/En-Spm and Gypsy were the most represented superfamilies of transposons and retrotransposons, respectively.Small RNA, Satellites, Simple repeats and Low complexity sequences represent a small proportion of both chromosomes arms. Unclassified sequences represented less than the 1.4%.. Scaffolds were scanned for LTR retrotransposons using LTR_FINDER (Xu and Wang 2007) and LTR_STRUC (McCarthy et al., 2002). The manual analysis of the candidate LTRs allowed the identification and annotation of novel LTRs.The present study reports wheat repetitive sequences performed at chromosome level, showing a complete landscape of the repeatome of this chromosome.