Abstract
Potato and its wild relatives are distributed mainly in the Mexican highlands and central Andes of South America. The South American A-genome species, including cultivated potatoes, are reproductively isolated from Mexican diploid species. Whole-genome sequencing has disclosed genome structure and similarity, mostly in cultivated potatoes and their closely related species. In this study, we generated a chromosome-scale assembly of the genome of a Mexican diploid species, Solanum bulbocastanum Dun., using PacBio long-read sequencing, optical mapping, and Hi-C scaffolding technologies. The final sequence assembly consisted of 737.9 Mb, among which 647.0 Mb were anchored to the 12 chromosomes. Compared with chromosome-scale assemblies of S. lycopersicum (tomato), S. etuberosum (non-tuber-bearing species with E-genome), S. verrucosum, S. chacoense, S. multidissectum, and S. phureja (all four are A-genome species), the S. bulbocastnum genome was the shortest. It contained fewer transposable elements (56.2%) than A-genome species. A cluster analysis was performed based on pairwise ratios of syntenic regions among the seven chromosome-scale assemblies, showing that the A-genome species were first clustered as a distinct group. Then, this group was clustered with S. bulbocastanum. Sequence similarity in 1,624 single-copy orthologous gene groups among 36 Solanum species and clones separated S. bulbocastanum as a specific group, including other Mexican diploid species, from the A-genome species. Therefore, the S. bulbocastanum genome differs in genome structure and gene sequences from the A-genome species. These findings provide important insights into understanding and utilizing the genetic diversity of S. bulbocastanum and the other Mexican diploid species in potato breeding.
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Claims 7
Claim · model-written summary
A chromosome-scale genome assembly of Solanum bulbocastanum was generated.
- Taxon
- Solanum bulbocastanum Dun.Solanum bulbocastanume0
- Outcome
- chromosome-scale assemblye0
Not reportedComparatorValue
Verbatim
e0“we generated a chromosome-scale assembly of the genome of a Mexican diploid species, Solanum bulbocastanum Dun.”
Claim · model-written summary
The assembly totalled 737.9 Mb.
- Taxon
- Solanum bulbocastanum Dun.Solanum bulbocastanumt0
- Outcome
- sequence assemblye0
- Value
- 737.9 Mbe0
Verbatim
e0“The final sequence assembly consisted of 737.9 Mb”
t0“Solanum bulbocastanum Dun.”
Claim · model-written summary
Of the assembly, 647.0 Mb was anchored to 12 chromosomes.
- Taxon
- Solanum bulbocastanum Dun.Solanum bulbocastanumt0
- Outcome
- anchored to the 12 chromosomese0
- Value
- 647.0 Mbe0
Verbatim
e0“among which 647.0 Mb were anchored to the 12 chromosomes”
t0“Solanum bulbocastanum Dun.”
Claim · model-written summary
The S. bulbocastnum genome was shortest among the compared assemblies.
Verbatim
e0“the S. bulbocastnum genome was the shortest”
Claim · model-written summary
The genome had fewer transposable elements than A-genome species, at 56.2%.
Verbatim
e0“It contained fewer transposable elements (56.2%) than A-genome species.”
t0“Solanum bulbocastanum Dun.”
Claim · model-written summary
Syntenic-region clustering first grouped A-genome species separately and then with S. bulbocastanum.
- Taxon
- S. bulbocastanumSolanum bulbocastanume0
- Outcome
- clustered with S. bulbocastanume0
Verbatim
e0“the A-genome species were first clustered as a distinct group. Then, this group was clustered with S. bulbocastanum.”
Claim · model-written summary
Single-copy ortholog similarity separated S. bulbocastanum and other Mexican diploids from A-genome species.
- Taxon
- S. bulbocastanumSolanum bulbocastanume0
- Outcome
- separated S. bulbocastanum as a specific groupe0
- Value
- 1,624 single-copy orthologous gene groupse0
- Comparator
- A-genome speciese0
Verbatim
e0“Sequence similarity in 1,624 single-copy orthologous gene groups among 36 Solanum species and clones separated S. bulbocastanum as a specific group, including other Mexican diploid species, from the A-genome species.”