Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA

• Published in: BMC genomics 2019-04, Vol.20 (1), p.262-262, Article 262
• Main Authors: Pamponét, Vanessa Carvalho Cayres, Souza, Margarete Magalhães, Silva, Gonçalo Santos, Micheli, Fabienne, de Melo, Cláusio Antônio Ferreira, de Oliveira, Sarah Gomes, Costa, Eduardo Almeida, Corrêa, Ronan Xavier
• Format: Article
• Language: English
• Subjects: Agricultural production; Agronomy; Bioinformatics; Biological evolution; Chromosome mapping; Chromosomes; Clusters; Computational biology; Cytogenetics; Deoxyribonucleic acid; DNA; DNA sequencing; FISH; Functional morphology; Gene mapping; Genes; Genetic aspects; Genetic diversity; Genetic engineering; Genomes; Genomics; Hybridization; Hybrids; Identification and classification; in tandem repetitive DNA; Long terminal repeat; LTR retrotransposons; Mapping; Markers; Molecular cytogenetics; Morphology; Next-generation sequencing; Nucleotide sequence; Passiflora edulis; Passion fruit; Plant genetics; RepeatExplorer; Ribosomal DNA; Satellite DNA; Sorghum; Studies; Sugarcane; Transposons
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-019-5576-6

The 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. Three 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. P. 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.