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. 2017 Apr 18:11:1177932217702388.
doi: 10.1177/1177932217702388. eCollection 2017.

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

Jaire Alves Ferreira Filho  1   2   3 , Lucas Soares de Brito  2 , André Pereira Leão  2 , Alexandre Alonso Alves  2 , Eduardo Fernandes Formighieri  2 , Manoel Teixeira Souza Júnior  1   2
Affiliations

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

Jaire Alves Ferreira Filho et al. Bioinform Biol Insights. .

Abstract

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microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm).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.

Keywords: Elaeis guineensis; Elaeis oleifera; Phoenix dactylifera; bioinformatics; transposable elements.

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Conflict of interest statement

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.

Figures

Figure 1
Figure 1
Distribution of transposable elements in the genome of Elaeis oleifera, Amazonian genotype. Transposable elements in silico identified in the draft genome (version 1.0) of a Manicoré genotype from the Germplasm Bank of Caiaué (E oleifera) at Embrapa Amazônia Ocidental. LTR indicates long terminal repeat.
Figure 2
Figure 2
Frequency (%) of the most common simple sequence repeat (SSR) motifs in the genome of Elaeis oleifera, Amazonian genotype. Frequency was estimated for each class of SSRs.
Figure 3
Figure 3
Comparison of simple sequence repeat (SSR) amount among oil and date palm genomes. Amount of mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide in EoAG (scaf.), EgMG (scaf.), EgMG (Chr.), and PdG (scaf.). EgMG indicates Elaeis guineensis MPOB genome; EoAG, Elaeis oleifera Amazonian genome; EoMG, Elaeis oleifera MPOB genome; PdG, Phoenix dactylifera genome; Scaf., scaffolds; Chr., chromosomes.
Figure 4
Figure 4
Chromosomal distribution of TEs in Elaeis guineensis, the African oil palm. Each chromosome of E guineensis MPOB genotype was analyzed for the proportion of the types of TEs. LINE indicates long interspersed nuclear element, LTR, long terminal repeat; MPOB, Malaysian Palm Oil Board; TE, transposable element.
Figure 5
Figure 5
Chromosomal distribution of the most represented transposable elements (TEs) in Elaeis guineensis, the African oil palm. (A) DNA/MuLE-MuDR and DNA/CMC-EnSpm families are the most represented DNA transposons. (B) LINE/RTE-BovB and LINE/L1 families are the 2 most represented LINE superfamilies. (C) LTR/Gypsy and LTR/Copia families are the 2 most represented LTR superfamilies. (D) Unknown and unspecified are the 2 most represented unclassified repeats. LINE indicates long interspersed nuclear element; LTR, long terminal repeat.
Figure 6
Figure 6
The plot of the divergence of transposable element (TEs) in Elaeis guineensis, the African oil palm. The divergence has been plotted for the most represented families of DNA transposons (upper panel), LINE-like elements (half panel), and LTR retrotransposons (lower panel). (A) DNA/hAT-AC, (B) DNA/CMC-EnSpm, (C) LINE/L1, (D) LINE/L1-Tx1, (E) LTR/Copia, and (F) LTR/Gypsy. Each point corresponds to a copy. Copies with divergence close to 0 and ratio close to 1 correspond to potentially active and full-length copies. LINE indicates long interspersed nuclear element; LTR, long terminal repeat.
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