Abstract
Main conclusions
While two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome analysed.
Abstract
Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a tenfold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of this genus representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicates that while large genomes evolved by an accumulation of retrotransposons, the smallest genome known for the genus has evolved by diversification of different repeat types, particularly satDNAs.
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Abbreviations
- Cy3-dUTP:
-
5-Amino-propargyl-2′-deoxyuridine 5′-triphosphate coupled to red cyanine fluorescent dye
- DAPI:
-
4′,6-Diamidino-2-phenylindole
- FISH:
-
Fluorescent in situ hybridization
- LTR:
-
Long terminal repeat
- NGS:
-
Next-generation sequencing
- rDNA:
-
Ribosomal DNA
- RT:
-
Retrotransposons
- satDNA:
-
Satellite DNA
- TAREAN:
-
TAndem REpeat ANalyser
- TEs:
-
Transposable elements
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Acknowledgements
We are grateful to Dr. Alessandro Varani for bioinformatics support and Dr. Francisco Ruiz-Ruano for bioinformatics support and for critical reading of the manuscript. This study was partially supported by Fundação de Amparo à Pesquisa do Estado de Pernambuco (FACEPE) through scholarships awarded to MAS (IBPG-1086-2.03/15 and FACEPE AMD-0128-2.00/17) and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) through fellowship awarded to AP-H (310804/2017-5). This study was supported in part by the Coordenacão de Aperfeiçoamento de Pessoal de Nıvel Superior—Brasil (CAPES, Finance Code 001); EMBRAPA (Embrapa SEG-02.16.04.007.00.03) and FAPESP (2019/07838-6).
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Communicated by Anastasios Melis.
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Fig. S1. Similarity analysis of Passiflora superfamily 1 satDNA. a) Alignment and b) dotplot of satDNAs PorSat01-161 and PorSat01-162 sequences, showing a high similarity (84% identity) between them. c) dotplot of PorSat01-161, PquSat02-145 and PciSat01-145 sequences and d) Alignment of satDNA PquSat02-145 and PciSat01-145 and MF401644.1 from P. edulis sequences (TIF 5039 KB)
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Fig. S2. Organization of the 35S ribosomal DNA (rDNA) sequence of Passiflora quadrangularis assembled by NOVOPlasty. Comparison of the sequence similarity between the consensus sequence of the satDNA PquSat01-100 and the intergenic spacer (IGS) region of 35S rDNA, showing detail of repeats and subrepeats and the dotplot analysis of the complex structure of satDNA PquSat01-100 (TIF 3277 KB)
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Fig. S3. Chromosomal distribution of scattered satellite DNA repeats in Passiflora quadrangularis and P. cincinnata (TIF 13448 KB)
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Sader, M., Vaio, M., Cauz-Santos, L.A. et al. Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. Planta 253, 86 (2021). https://doi.org/10.1007/s00425-021-03598-0
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DOI: https://doi.org/10.1007/s00425-021-03598-0