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

Abstract

Background 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. Results 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. Conclusion 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 .

Large vs small genomes inPassiflora: the influence of the mobilome and the satellitome

“…In contrast, Ty1/copia retrotransposons showed higher proportion (35.7%) in P. cincinnata, due to an even higher proportion of Angela (29%). This high abundance of Ty1/copia has already been observed in the passion-fruit, Passiflora edulis (16.89% versus 33.33% for Ty3/gypsy, Pamponét et al 2019), another species from the Passiflora subgenus but more closely related to P. quadrangularis than to P. cincinatta (Sader et al 2019a). In Passiflora edulis (1,232…”

“…Thus, the increase in genome size within the genus, so far apparently concentrated in the Passiflora subgenus, was caused by independent patterns of expansions of both Ty3/gypsy, with 33% in P. edulis (Pamponét et al 2019), 18.45% in P. cincinnata and 41.22% in P. quadrangularis, and Ty1/copia, with 35.66% in P. cincinnata, 25.44% in P. quadrangularis and 16.89% in P. edulis.…”

“…In situ localization of the retrotransposons in pericentromeric regions or dispersed throughout the chromosomes is a common feature of plant genomes of similar sizes, small and large, respectively (Miller et al 1998;Cheng and Murata 2003;Nagaki et al 2004¸ Neumann et al 2011 (Pamponét et al 2019;Sader et al 2019b;Stack et al 2009;Dias et al 2020). This distribution pattern suggest that gene-rich regions, and probably recombination, is more evenly distributed in P. organensis, except in pericentromeric regions, while higher in chromosomal ends of larger genome species, such as P. quadrangularis, P. cincinnata, and P.…”

Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species

“…This Athila/Tat dispersion pattern, such as interstitial dots, has been described by Park et al [65] in C. annuum. Using the Passiflora edulis for comparison, members of Ty3/ Gypsy superfamily were the most accumulated, and their sequences appeared scattered along chromosomes, including at the pericentromeric regions [66]. In some Solanaceae species, such as tomato and peppers, elements of the Tekay/Del Gypsy superfamily had a scattered accumulation profile as reported by Park et al [65], with hybridization in the chromosomes of Solanum lycopersicum (tomato) and Capsicum annuum (pepper), in which pepper had a higher number and more intense signals than those observed in tomato.…”

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

“…Following publication of the original article [1], the authors reported that one of the authors’ names was typeset incorrectly. In this Correction the incorrect and correct author name are shown.…”