Dataset Information

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.

SUBMITTER: Pamponet VCC

PROVIDER: S-EPMC6444444 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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

Pamponét Vanessa Carvalho Cayres VCC Souza Margarete Magalhães MM Silva Gonçalo Santos GS Micheli Fabienne F de Melo Cláusio Antônio Ferreira CAF de Oliveira Sarah Gomes SG Costa Eduardo Almeida EA Corrêa Ronan Xavier RX

BMC genomics 20190402 1

<h4>Background</h4>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 ...[more]

PMID: 30940088

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Project description:Purple passion fruit, Passiflora edulis Sims f. edulis, is an important semi-perennial, fruit bearing vine originating in South America that produces a commercial tropical juice pulp for international and national consumption. Within the round purple passion fruit are a large number of membranous seed sacs each containing individual seeds. Little is known about the seed anatomy of the commercial passion fruit, differences between wild collected and commercial types, and its effect on seedling germination. Therefore, our main objective for this study was to analyze the seed anatomy variability of different germplasm as well as the effect on viability and germination of the seeds of this species. Germplasm was evaluated from three sources: (1) commercial cultivars grown in current production areas, (2) genebank accession from the national seed bank, and (3) landraces collected across different high and mid-elevation sites of the Andean region. A total of 12 morphometric descriptors related to seed anatomy were evaluated on the 56 genotypes, of which three were most informative: Angle to the vertex which is related to the shape of the seed, the thickness of the tegument and the horizontal length; separating the seed according to its source of origin. Germination was found to be positively correlated with the number (r = 0.789) and depth (r = 0.854) of seed pitting. Seeds of the commercial cultivars had more seed pits and higher germination compared to seeds of landraces or genebank accessions showing a possible effect of domestication on the crop. Interestingly, passion fruits often germinate during the rainy season as escaped or wild seedlings especially in the disturbed landscapes of coffee plantations, so some dormancy is needed but faster germination is needed for intensive cultivation. Harnessing passion fruit diversity would be useful as the semi-domesticated landraces have valuable adaptation characteristics to combine with rapid germination selected in the commercial cultivars. The variability of seed pitting with cultivars more pitted than landraces possibly resulting in faster germination may indicate that purple passion fruit is still undergoing a process of selection and domestication for this trait.

Dataset Information

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

Publications

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

Similar Datasets

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