ArticleMolecular biology reports2019
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis.
Article in Molecular biology reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 8 citations in OpenAlex.
- Multi-integrated genomic data for Passiflora foetida provides insights into genome size evolution and floral development in Passiflora.Molecular horticulture · 2023Article
- PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons.Frontiers in plant science · 2023Article
- A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis.The plant genome · 2021Article
- Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome.Planta · 2021Article
- CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.PloS one · 2021Article
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Authors and funding
8 authors at 4 institutions in 2 countries.
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Abstract
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 (< 2.0 Mya), and with the exception of the Athila lineage, all LTR-RTs are transcriptionally active. Moreover, functional analyses disclosed that the Angela, Del, CRM and Tork lineages are conserved in wild Passiflora species, supporting the idea of a common expansion of Copia and Gypsy superfamilies. Overall, this is the first study describing the P. edulis TE repertoire, and it also lends weight to the suggestion that LTR-RTs had a recent expansion into the analyzed gene-rich region of the P. edulis genome, possibly along WGD (Whole genome duplication) events, but are under negative selection due to their potential deleterious impact on gene regions.
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