Abstract
BackgroundThe cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its genome sequenced by next generation sequencing and bioinformatics analysis performed by RepeatExplorer pipeline. The clusters allowed the identification and characterization of repetitive elements (predominant contributors to most plant genomes). The aim of this study was to identify, characterize and map the repetitive DNA of P. edulis, providing important cytogenomic markers, especially sequences associated with the centromere.ResultsThree clusters of satellite DNAs (69, 118 and 207) and seven clusters of Long Terminal Repeat (LTR) retrotransposons of the superfamilies Ty1/Copy and Ty3/Gypsy and families Angela, Athila, Chromovirus and Maximus-Sire (6, 11, 36, 43, 86, 94 and 135) were characterized and analyzed. The chromosome mapping of satellite DNAs showed two hybridization sites co-located in the 5S rDNA region (PeSat_1), subterminal hybridizations (PeSat_3) and hybridization in four sites, co-located in the 45S rDNA region (PeSat_2). Most of the retroelements hybridizations showed signals scattered in the chromosomes, diverging in abundance, and only the cluster 6 presented pericentromeric regions marking. No satellite DNAs and retroelement associated with centromere was observed.ConclusionP. edulis has a highly repetitive genome, with the predominance of Ty3/Gypsy LTR retrotransposon. The satellite DNAs and LTR retrotransposon characterized are promising markers for investigation of the evolutionary patterns and genetic distinction of species and hybrids of Passiflora.
Highlights
The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution
Our work focused on the analysis of TEs and satellite DNA (SatDNA) associated to centromeres, considering that they are species-specific markers widely used for the identification of chromosomal alterations, an important tool for genetic improvement programs and evolutionary studies of passion fruit
Graph-based identification of repetitive DNA, classification and chromosomal mapping of satellite DNA Among the total of 11,493,782 paired-end reads obtained by sequencing using Illumina MiSeq® platform, 2,368,626 reads were analyzed by RepeatExplorer [42, 43]
Summary
The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. The aim of this study was to identify, characterize and map the repetitive DNA of P. edulis, providing important cytogenomic markers, especially sequences associated with the centromere. In tandem repeated DNAs represent the main component of heterochromatic regions, and can be associated with specific functions in the chromosome, such as centromeres and telomeres. They can be classified based on the repeated unit (monomer), and cluster repetition sizes. Despite the many studies focusing on SatDNA, little is known about their functions [8], in contrast to studies involving ribosomal DNA (rDNA), which consist of in tandem moderated repeats, and represent sequences preserved between species and have well-defined functions [13]
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