Abstract
To elucidate the evolutionary history and basis of chromosomal, molecular and phenotypic differences between tomato and potato, genomic data from a key outgroup species is needed. Solanum etuberosum, a non-tuber-bearing species from Chile, fulfills this requirement: its ancestors diverged from the tomato-potato lineage shortly before the split of the tomato and potato clades. With the aim of investigating both genome and trait evolution, we sequenced and assembled the genome of S. etuberosum. The initial Illumina assembly consisted of 3666 scaffolds with the N50 statistic of 1.7Mb and captured 94% of the predicted 702 Mb genome size. The assembly was further scaffolded usingBioNano genome mapping, yielding a final genome assembly that surpassed an N50 of 5Mb.Hence, it is one of the most contiguous Solanum genome assemblies thus far, and with 97% coverage of the expected gene space, also one of the most complete ones. We subsequently annotated the genomesequence and reconstructed the evolution of genes crucial to potato and/or tomato phenotypes and specifically related to tuber formation, pathogen resistance, flower color and glycoalkaloid biosynthesis. The genome of S. etuberosum thus proved to be an invaluable resource for novel insights in the Solanum genus.
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Claims 8
Claim · model-written summary
The initial Illumina assembly of Solanum etuberosum had an N50 statistic of 1.7 Mb.
- Taxon
- Solanum etuberosum
.jpg?width=60)
Solanum etuberosume0 - Outcome
- N50 statistice1
- Value
- 1.7Mbe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e0“Solanum etuberosum, a non-tuber-bearing species from Chile”
e1“The initial Illumina assembly consisted of 3666 scaffolds with the N50 statistic of 1.7Mb and captured 94% of the predicted 702 Mb genome size”
Claim · model-written summary
The initial Illumina assembly of Solanum etuberosum consisted of 3666 scaffolds.
- Taxon
- Solanum etuberosumSolanum etuberosume0
- Outcome
- scaffoldse1
- Value
- 3666 scaffoldse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Solanum etuberosum, a non-tuber-bearing species from Chile”
e1“The initial Illumina assembly consisted of 3666 scaffolds with the N50 statistic of 1.7Mb and captured 94% of the predicted 702 Mb genome size”
Claim · model-written summary
The initial Illumina assembly captured 94% of the predicted 702 Mb genome size.
- Taxon
- Solanum etuberosumSolanum etuberosume0
- Outcome
- capturede1
- Value
- 94%e1
- Comparator
- the predicted 702 Mb genome sizee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Solanum etuberosum, a non-tuber-bearing species from Chile”
e1“The initial Illumina assembly consisted of 3666 scaffolds with the N50 statistic of 1.7Mb and captured 94% of the predicted 702 Mb genome size”
Claim · model-written summary
Scaffolding with BioNano genome mapping gave a final assembly with an N50 of 5 Mb or more.
- Taxon
- Solanum etuberosumSolanum etuberosume0
- Treatment
- BioNano genome mappinge2
- Outcome
- N50e2
- Value
- 5Mbe2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Solanum etuberosum, a non-tuber-bearing species from Chile”
e2“The assembly was further scaffolded usingBioNano genome mapping, yielding a final genome assembly that surpassed an N50 of 5Mb”
Claim · model-written summary
The S. etuberosum genome assembly is one of the most contiguous Solanum genome assemblies.
- Taxon
- Solanum etuberosumSolanum etuberosume0
- Outcome
- most contiguouse3
- Comparator
- Solanum genome assembliese3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Solanum etuberosum, a non-tuber-bearing species from Chile”
e3“one of the most contiguous Solanum genome assemblies thus far”
Claim · model-written summary
The S. etuberosum genome assembly covers 97% of the expected gene space.
- Taxon
- Solanum etuberosumSolanum etuberosume0
- Outcome
- coverage of the expected gene spacee4
- Value
- 97%e4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Solanum etuberosum, a non-tuber-bearing species from Chile”
e4“with 97% coverage of the expected gene space, also one of the most complete ones”
Claim · model-written summary
The S. etuberosum genome assembly is also one of the most complete Solanum genome assemblies.
- Taxon
- Solanum etuberosumSolanum etuberosume0
- Outcome
- most completee4
- Comparator
- Solanum genome assembliese3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Solanum etuberosum, a non-tuber-bearing species from Chile”
e3“one of the most contiguous Solanum genome assemblies thus far”
e4“with 97% coverage of the expected gene space, also one of the most complete ones”
Claim · model-written summary
Evolution of genes related to tuber formation, pathogen resistance, flower color and glycoalkaloid biosynthesis was reconstructed from the annotated S. etuberosum genome.
- Taxon
- Solanum etuberosumSolanum etuberosume0
- Outcome
- evolution of genese5
- Qualifier
- tuber formation, pathogen resistance, flower color and glycoalkaloid biosynthesise5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Solanum etuberosum, a non-tuber-bearing species from Chile”
e5“reconstructed the evolution of genes crucial to potato and/or tomato phenotypes and specifically related to tuber formation, pathogen resistance, flower color and glycoalkaloid biosynthesis”