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International Journal of Genomics
Volume 2014 (2014), Article ID 471461, 9 pages
http://dx.doi.org/10.1155/2014/471461
Research Article

In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava

Molecular Biology Laboratory, Biology Department, National University of Colombia, Carrera 30 No. 45-03, Bogotá, Colombia

Received 2 May 2014; Accepted 8 September 2014; Published 13 October 2014

Academic Editor: Margarita Hadzopoulou-Cladaras

Copyright © 2014 Andrea Vásquez and Camilo López. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We conducted a SSRs density analysis in different cassava genomic regions. The information obtained was useful to establish comparisons between cassava’s SSRs genomic distribution and those of poplar, flax, and Jatropha. In general, cassava has a low SSR density (~50 SSRs/Mbp) and has a high proportion of pentanucleotides, (24,2 SSRs/Mbp). It was found that coding sequences have 15,5 SSRs/Mbp, introns have 82,3 SSRs/Mbp, 5′ UTRs have 196,1 SSRs/Mbp, and 3′ UTRs have 50,5 SSRs/Mbp. Through motif analysis of cassava’s genome SSRs, the most abundant motif was AT/AT while in intron sequences and UTRs regions it was AG/CT. In addition, in coding sequences the motif AAG/CTT was also found to occur most frequently; in fact, it is the third most used codon in cassava. Sequences containing SSRs were classified according to their functional annotation of Gene Ontology categories. The identified SSRs here may be a valuable addition for genetic mapping and future studies in phylogenetic analyses and genomic evolution.