Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: Citogenomic characterization of transposable elements and satellite DNA
| Autor: | Sárah Gomes de Oliveira, Gonçalo Santos Silva, Cláusio Antônio Ferreira de Melo, Vanessa de Carvalho Cayres Pamponet, Fabienne Micheli, Eduardo Almeida Costa, Ronan Xavier Corrêa, Margarete Magalhães Souza |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Chromosome mapping
0106 biological sciences Genome evolution lcsh:QH426-470 transposon Satellite DNA Sequence analysis LTR retrotransposons lcsh:Biotechnology chromosome mapping [EN] Retrotransposon Biology 01 natural sciences Genome F50 - Anatomie et morphologie des plantes ADN satellite DNA sequencing F30 - Génétique et amélioration des plantes 03 medical and health sciences FISH lcsh:TP248.13-248.65 Genetics in tandem repetitive DNA RepeatExplorer Cytogénétique Repeated sequence Technique analytique 030304 developmental biology 0303 health sciences Molecular cytogenetics phytogénétique Chromosome Passiflora edulis lcsh:Genetics Evolutionary biology 010606 plant biology & botany Biotechnology |
| Zdroj: | BMC Genomics BMC Genomics, Vol 20, Iss 1, Pp 1-17 (2019) |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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