ArticleAnnals of botany2019
Comparative analysis of repetitive sequences among species from the potato and the tomato clades.
Article in Annals of botany, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Whole-genome sequencing revealed the genomic origin of Solanum demissum Lindl., a Mexican hexaploid wild potato species.BMC plant biology · 2026Article
- Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication.Annals of botany · 2025Article
- Drought stress responses revealed by genomic and transcriptomic analyses of two macrofungi (IMA fungus · 2025Article
- Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole-genome sequencing.The Plant journal : for cell and molecular biology · 2025Article
- First insight into the genomes of the Pulmonaria officinalis group (Boraginaceae) provided by repeatome analysis and comparative karyotyping.BMC plant biology · 2024Article
- Chromosome-scale genome assembly and annotation of the tetraploid potato cultivar Diacol Capiro adapted to the Andean region.G3 (Bethesda, Md.) · 2024Article
- A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes.G3 (Bethesda, Md.) · 2024Article
- Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina.BMC plant biology · 2024Article
- Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genusFrontiers in plant science · 2024Article
- Comparative analysis of repetitive DNA in dysploid and non-dysploid Phaseolus beans.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- The nuclear lamina is required for proper development and nuclear shape distortion in tomato.Journal of experimental botany · 2023Article
- The nature and organization of satellite DNAs inFrontiers in plant science · 2023Article
- A de novo genome assembly of Solanum verrucosum Schlechtendal, a Mexican diploid species geographically isolated from other diploid A-genome species of potato relatives.G3 (Bethesda, Md.) · 2022Article
- Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species.Planta · 2022Article
- Diverse and mobile: eccDNA-based identification of carrot low-copy-number LTR retrotransposons active in callus cultures.The Plant journal : for cell and molecular biology · 2022Article
- Whole-genome resequencing reveals genomic footprints of Italian sweet and hot pepper heirlooms giving insight into genes underlying key agronomic and qualitative traits.BMC genomic data · 2022Article
- Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View.Plants (Basel, Switzerland) · 2022Review
- Article
- Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2021Article
- Can we have it all? Repurposing target capture for repeat genomics. A commentary on: 'Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA'.Annals of botany · 2021Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND AND
aimsThe genus Solanum includes important vegetable crops and their wild relatives. Introgression of their useful traits into elite cultivars requires effective recombination between hom(e)ologues, which is partially determined by genome sequence differentiation. In this study we compared the repetitive genome fractions of wild and cultivated species of the potato and tomato clades in a phylogenetic context.
methodsGenome skimming followed by a clustering approach was used as implemented in the RepeatExplorer pipeline. Repeat classes were annotated and the sequences of their main domains were compared. KEY
resultsRepeat abundance and genome size were correlated and the larger genomes of species in the tomato clade were found to contain a higher proportion of unclassified elements. Families and lineages of repetitive elements were largely conserved between the clades, but their relative proportions differed. The most abundant repeats were Ty3/Gypsy elements. Striking differences in abundance were found in the highly dynamic Ty3/Gypsy Chromoviruses and Ty1/Copia Tork elements. Within the potato clade, early branching Solanum cardiophyllum showed a divergent repeat profile. There were also contrasts between cultivated and wild potatoes, mostly due to satellite amplification in the cultivated species. Interspersed repeat profiles were very similar among potatoes. The repeat profile of Solanum etuberosum was more similar to that of the potato clade.
conclusionsThe repeat profiles in Solanum seem to be very similar despite genome differentiation at the level of collinearity. Removal of transposable elements by unequal recombination may have been responsible for structural rearrangements across the tomato clade. Sequence variability in the tomato clade is congruent with clade-specific amplification of repeats after its divergence from S. etuberosum and potatoes. The low differentiation among potato and its wild relatives at the level of interspersed repeats may explain the difficulty in discriminating their genomes by genomic in situ hybridization techniques.
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