In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.

Autor: Filho JAF; Graduate Program in Plant Biotechnology, Federal University of Lavras (UFLA), Lavras, Brazil.; Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil.; Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil., de Brito LS; Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil., Leão AP; Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil., Alves AA; Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil., Formighieri EF; Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil., Júnior MTS; Graduate Program in Plant Biotechnology, Federal University of Lavras (UFLA), Lavras, Brazil.; Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil.
Jazyk: angličtina
Zdroj: Bioinformatics and biology insights [Bioinform Biol Insights] 2017 Apr 18; Vol. 11, pp. 1177932217702388. Date of Electronic Publication: 2017 Apr 18 (Print Publication: 2017).
DOI: 10.1177/1177932217702388
Abstrakt: Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm). The estimated total coverage of TEs was 50.96% (523 572 kb) and 42.31% (593 463 kb), 39.41% (605 015 kb), and 33.67% (187 361 kb), respectively. A total of 155 726 microsatellite loci were identified in the genomes of oil and date palms. This is the first detailed description of repeats in the genomes of oil and date palms. A relatively high diversity and abundance of TEs were found in the genomes, opening a range of further opportunities for applied research in these genera. The development of molecular markers (mainly simple sequence repeat), which may be immediately applied in breeding programs of those species to support the selection of superior genotypes and to enhance knowledge of the genetic structure of the breeding and natural populations, is the most notable opportunity.
Competing Interests: DECLARATION OF CONFLICTING INTERESTS: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Databáze: MEDLINE
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