Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis

A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome evolution. However, not much information is available on the structure and evolutionary role of TEs in the Passifloraceae family (Malpighial...

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Bibliographic Details
Published in:Molecular biology reports 2019-12, Vol.46 (6), p.6117-6133
Main Authors: da Costa, Zirlane Portugal, Cauz-Santos, Luiz Augusto, Ragagnin, Geovani Tolfo, Van Sluys, Marie-Anne, Dornelas, Marcelo Carnier, Berges, Hélène, de Mello Varani, Alessandro, Vieira, Maria Lucia Carneiro
Format: Article
Language:English
Subjects:
Animal Anatomy
Animal Biochemistry
Biomedical and Life Sciences
DNA Transposable Elements
Evolution
Evolution, Molecular
Fruit - genetics
Fruits
Genomes
Histology
Life Sciences
Morphology
Mutagenesis, Insertional
Negative selection
Original Article
Passiflora - classification
Passiflora - genetics
Passiflora edulis
Phylogeny
Retroelements
RNA-directed DNA polymerase
Species
Terminal Repeat Sequences
Transcription
Transcription, Genetic
Transposons
Vegetal Biology
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Summary:A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome evolution. However, not much information is available on the structure and evolutionary role of TEs in the Passifloraceae family (Malpighiales order). Against this backdrop, we identified, characterized, and inferred the potential genomic impact of the TE repertoire found in the available genomic resources for Passiflora edulis , a tropical fruit species. A total of 250 different TE sequences were identified (96% Class I, and 4% Class II), corresponding to ~ 19% of the P. edulis draft genome. TEs were found preferentially in intergenic spaces (70.4%), but also overlapping genes (30.6%). LTR-RTs accounted for 181 single elements corresponding to ~ 13% of the draft genome. A phylogenetic inference of the reverse transcriptase domain of the LTR-RT revealed association of 37 elements with the Copia superfamily ( Angela , Ale , Tork , and Sire ) and 128 with the Gypsy ( Del , Athila , Reina , CRM , and Galadriel ) superfamily, and Del elements were the most frequent. Interestingly, according to insertion time analysis, the majority (95.9%) of the LTR-RTs were recently inserted into the P. edulis genome (
ISSN:0301-4851
1573-4978
DOI:10.1007/s11033-019-05047-4