Abstract
BACKGROUND AND AIMS: The 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. METHODS: Genome 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 RESULTS: Repeat 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. CONCLUSIONS: The 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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Claims 15
Claim · model-written summary
Repeat abundance correlated with genome size in Solanum.
SolanumNot reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Repeat abundance and genome size were correlated”
e1“Within the potato clade, early branching Solanum cardiophyllum showed a divergent repeat profile.”
Claim · model-written summary
Larger tomato-clade genomes had a higher fraction of unclassified elements.
- Taxon
- tomato
Solanum lycopersicume0 - Outcome
- proportion of unclassified elementse0
- Direction
- highere0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the larger genomes of species in the tomato clade were found to contain a higher proportion of unclassified elements.”
Claim · model-written summary
Repeat families and lineages were mostly conserved between the clades.
Verbatim
e0“Families and lineages of repetitive elements were largely conserved between the clades”
t0“potato and the tomato clades”
Claim · model-written summary
Relative proportions of repeat families differed between the clades.
Verbatim
e0“but their relative proportions differed.”
t0“potato and the tomato clades”
Claim · model-written summary
Ty3/Gypsy elements were the most abundant repeats.
Verbatim
e0“The most abundant repeats were Ty3/Gypsy elements.”
t0“potato and the tomato clades”
Claim · model-written summary
Ty3/Gypsy Chromoviruses differed strongly in abundance between clades.
Verbatim
e0“Striking differences in abundance were found in the highly dynamic Ty3/Gypsy Chromoviruses and Ty1/Copia Tork elements.”
t0“potato and the tomato clades”
Claim · model-written summary
Ty1/Copia Tork elements differed strongly in abundance between clades.
Verbatim
e0“Striking differences in abundance were found in the highly dynamic Ty3/Gypsy Chromoviruses and Ty1/Copia Tork elements.”
t0“potato and the tomato clades”
Claim · model-written summary
Solanum cardiophyllum had a divergent repeat profile within the potato clade.
- Taxon
- Solanum cardiophyllumSolanum cardiophyllume0
- Outcome
- repeat profilee0
- Direction
- divergente0
Verbatim
e0“Within the potato clade, early branching Solanum cardiophyllum showed a divergent repeat profile.”
Claim · model-written summary
Cultivated and wild potatoes differed mainly through satellite amplification in cultivated potatoes.
- Taxon
- potatoes
Solanum tuberosume0 - Material
- cultivated and wild potatoese0
- Outcome
- satellite amplificatione0
- Direction
- contrastse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“There were also contrasts between cultivated and wild potatoes, mostly due to satellite amplification in the cultivated species.”
Claim · model-written summary
Interspersed repeat profiles were very similar among potatoes.
- Taxon
- potatoesSolanum tuberosume0
- Outcome
- Interspersed repeat profilese0
- Qualifier
- very similare0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Interspersed repeat profiles were very similar among potatoes.”
Claim · model-written summary
Solanum etuberosum had a repeat profile more similar to the potato clade.
- Taxon
- Solanum etuberosum
.jpg?width=60)
Solanum etuberosume0 - Outcome
- repeat profilee0
- Direction
- more similare0
- Comparator
- potato cladee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e0“The repeat profile of Solanum etuberosum was more similar to that of the potato clade.”
Claim · model-written summary
Solanum repeat profiles were similar despite collinearity-level genome differences.
- Outcome
- repeat profilese0
- Qualifier
- very similar despite genome differentiation at the level of collinearitye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The repeat profiles in Solanum seem to be very similar despite genome differentiation at the level of collinearity.”
Claim · model-written summary
Unequal recombination may have removed transposable elements and produced structural rearrangements in the tomato clade.
- Taxon
- tomatoSolanum lycopersicume0
- Outcome
- structural rearrangementse0
- Qualifier
- Removal of transposable elements by unequal recombinatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Removal of transposable elements by unequal recombination may have been responsible for structural rearrangements across the tomato clade.”
Claim · model-written summary
Tomato-clade sequence variation fit clade-specific repeat amplification after divergence.
- Taxon
- tomatoSolanum lycopersicume0
- Outcome
- Sequence variabilitye0
- Comparator
- clade-specific amplification of repeatse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Sequence variability in the tomato clade is congruent with clade-specific amplification of repeats after its divergence from S. etuberosum and potatoes.”
Claim · model-written summary
Low interspersed-repeat differentiation may explain difficulty discriminating potato genomes by genomic in situ hybridization.
- Taxon
- potatoSolanum tuberosume0
- Outcome
- difficulty in discriminating their genomes by genomic in situ hybridization techniquese0
- Qualifier
- low differentiation among potato and its wild relatives at the level of interspersed repeatse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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.”