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View TEs Roya

To analyze the frequency and classes of TE-like elements present in the coffee Rust 454 contigs, we compare two different strategies, de-novo and sequence similarity analysis. De novo searching was conducted as follows. First a dataset of 143 repeat families sequences was generated from all coffee Rust 454 contigs by using RepeatScout (1). Then, using Cap3 (2), related sequences were assembled originating 19 contigs and 93 singletons. These 112 repeated consensus were used as queries in BlastX searches against NR GenBank (3) to identify internal domains like LTR-RT (gypsy and copia), LINE and autonomous DNA TEs. E-value cut off was set to 1e-5. Consensus sequences that could not be annotated as TEs by this way were analyzed manually through dotter (4) comparison with themselves looking for LTRs of LTR-RTs elements, MITEs and other non-autonomous elements, in particular domains like ( PPT, PBS) and Terminal Inverted Repeats (TIR). Finally, all 112 repeat consensus identified as TEs were used as reference library to discover 454 Contigs matching TEs in coffee Rust using RepeatMasker (5) with a 20% divergence and 100 bp coverage of sequence as relevant parameters.

Roya_TEs_Analysis Download

1. Price A.L., Jones N.C. and Pevzner P.A. 2005. De novo identification of repeat families in large genomes. To appear in Proceedings of the 13 Annual International conference on Intelligent Systems for Molecular Biology (ISMB-05). Detroit, Michigan. http://bix.ucsd.edu/repeatscout

2. Huang, X. and Madan, A. (1999) CAP3: A DNA Sequence Assembly Program, Genome Research, 9: 868-877. http://seq.cs.iastate.edu/cap3.html

3. Baxevanis and Oulette, Bioinformatics, Wiley, 1998 Ch.2 :The GenBank Sequence Database. NCBI (National Center for Biotechnology Information) website: http://www.ncbi.nlm.nih.gov

4. “A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis” Erik L.L. Sonnhammer and Richard Durbin Gene 167:GC1-10 (1995). http://sonnhammer.sbc.su.se/Dotter.html

5. Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0.?1996-2004 http://www.repeatmasker.org

Roya TEs family Id TEs Annotation blastX RepeatMasker Censor Dotter
Contig 3 Reverse Transcriptase Gag – Pol X
Contig 4 TY3 – Gypsy X X
Contig 9 Reverse Transcriptase/AFLAV_I X X
Contig 10 Copia /Gypsy X
Contig 11 TY3 – Gypsy X X
Contig 17 TY3 – G / Gag – Pol X X
R_20 INDEFIX_I X
R_23 TY3 – Gypsy X X
R_46 HELITRON4_I X
R_86 Retrotranposon poliprotein X
R_91 Retrotranposon poliprotein X
R_98 DMCR1A X
R_107 Retrotranposon poliprotein/Gypsy X X
R_114 LTR/Retrotranposon poliprotein/Copia X X X
R_125 Gag – Pol Poliprotein X
R_128 TY3 – Gypsy X X X
R_140 TY3 – Gypsy X
R_143 TY3 – Gypsy X X
R_154 ENSPM-2HM X
R_167 TY3 – Gypsy X X
R_180 TY3 – Gypsy X X
R_182 TY3 – Gypsy X X
R_185 TY1 – Copia X X
R_193 TY1 – Copia / ENDOVIR1_I X X
R_197 TY1 – Copia X
R_206 Transposase X
R_247 TY1 – Copia X X
R_296 TY1 – Copia X
R_325 LTR/ERV1 X X
R_334 TY1 – Copia/KOPI2_I X X
R_388 TY1 – Copia X X