In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava
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 proport...
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Wiley
2014-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2014/471461 |
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| author | Andrea Vásquez Camilo López |
| author_facet | Andrea Vásquez Camilo López |
| author_sort | Andrea Vásquez |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-56f816322f1a44b5886973deb81f328f |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
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| series | International Journal of Genomics |
| spelling | doaj-art-56f816322f1a44b5886973deb81f328f2025-02-03T01:07:42ZengWileyInternational Journal of Genomics2314-436X2314-43782014-01-01201410.1155/2014/471461471461In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in CassavaAndrea Vásquez0Camilo López1Molecular Biology Laboratory, Biology Department, National University of Colombia, Carrera 30 No. 45-03, Bogotá, ColombiaMolecular Biology Laboratory, Biology Department, National University of Colombia, Carrera 30 No. 45-03, Bogotá, ColombiaWe 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.http://dx.doi.org/10.1155/2014/471461 |
| spellingShingle | Andrea Vásquez Camilo López In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava International Journal of Genomics |
| title | In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava |
| title_full | In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava |
| title_fullStr | In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava |
| title_full_unstemmed | In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava |
| title_short | In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava |
| title_sort | in silico genome comparison and distribution analysis of simple sequences repeats in cassava |
| url | http://dx.doi.org/10.1155/2014/471461 |
| work_keys_str_mv | AT andreavasquez insilicogenomecomparisonanddistributionanalysisofsimplesequencesrepeatsincassava AT camilolopez insilicogenomecomparisonanddistributionanalysisofsimplesequencesrepeatsincassava |