You say tomato, I say potato: high-quality genome assembly of the sister-group species Solanum etuberosum provides insights into genome and trait evolution

Lidija Berke, Laurie Grandont, S.A. Aflitos, C.W.B. Bachem, F.F.M. Becker, K. Bouwmeester, H.C. van de Geest, F. Govers, Hans de Jong, S.A. Peters, G.F. Sanchez Perez, E.G.W.M. Schijlen, Ronald van den Berg, M.E. Schranz

Research output: Contribution to conferenceAbstractAcademic

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 using
BioNano 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 genome
sequence 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.
Original languageEnglish
Pages28-29
Publication statusPublished - 2016
Event13th Solanaceae Conference: SolGenomics: From Advances to Applications - Davis, California , United States
Duration: 12 Sep 201616 Sep 2016

Conference

Conference13th Solanaceae Conference
CountryUnited States
CityDavis, California
Period12/09/1616/09/16

Fingerprint

Solanum etuberosum
genome assembly
tomatoes
potatoes
genome
Solanum
glycoalkaloids
chromosome mapping
Chile
tubers
ancestry
genes
statistics
biosynthesis
flowers
genomics
phenotype
history
color
pathogens

Cite this

Berke, Lidija ; Grandont, Laurie ; Aflitos, S.A. ; Bachem, C.W.B. ; Becker, F.F.M. ; Bouwmeester, K. ; van de Geest, H.C. ; Govers, F. ; de Jong, Hans ; Peters, S.A. ; Sanchez Perez, G.F. ; Schijlen, E.G.W.M. ; van den Berg, Ronald ; Schranz, M.E. / You say tomato, I say potato: high-quality genome assembly of the sister-group species Solanum etuberosum provides insights into genome and trait evolution. Abstract from 13th Solanaceae Conference, Davis, California , United States.
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title = "You say tomato, I say potato: high-quality genome assembly of the sister-group species Solanum etuberosum provides insights into genome and trait evolution",
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.",
author = "Lidija Berke and Laurie Grandont and S.A. Aflitos and C.W.B. Bachem and F.F.M. Becker and K. Bouwmeester and {van de Geest}, H.C. and F. Govers and {de Jong}, Hans and S.A. Peters and {Sanchez Perez}, G.F. and E.G.W.M. Schijlen and {van den Berg}, Ronald and M.E. Schranz",
year = "2016",
language = "English",
pages = "28--29",
note = "13th Solanaceae Conference : SolGenomics: From Advances to Applications ; Conference date: 12-09-2016 Through 16-09-2016",

}

Berke, L, Grandont, L, Aflitos, SA, Bachem, CWB, Becker, FFM, Bouwmeester, K, van de Geest, HC, Govers, F, de Jong, H, Peters, SA, Sanchez Perez, GF, Schijlen, EGWM, van den Berg, R & Schranz, ME 2016, 'You say tomato, I say potato: high-quality genome assembly of the sister-group species Solanum etuberosum provides insights into genome and trait evolution' 13th Solanaceae Conference, Davis, California , United States, 12/09/16 - 16/09/16, pp. 28-29.

You say tomato, I say potato: high-quality genome assembly of the sister-group species Solanum etuberosum provides insights into genome and trait evolution. / Berke, Lidija; Grandont, Laurie; Aflitos, S.A.; Bachem, C.W.B.; Becker, F.F.M.; Bouwmeester, K.; van de Geest, H.C.; Govers, F.; de Jong, Hans; Peters, S.A.; Sanchez Perez, G.F.; Schijlen, E.G.W.M.; van den Berg, Ronald; Schranz, M.E.

2016. 28-29 Abstract from 13th Solanaceae Conference, Davis, California , United States.

Research output: Contribution to conferenceAbstractAcademic

TY - CONF

T1 - You say tomato, I say potato: high-quality genome assembly of the sister-group species Solanum etuberosum provides insights into genome and trait evolution

AU - Berke, Lidija

AU - Grandont, Laurie

AU - Aflitos, S.A.

AU - Bachem, C.W.B.

AU - Becker, F.F.M.

AU - Bouwmeester, K.

AU - van de Geest, H.C.

AU - Govers, F.

AU - de Jong, Hans

AU - Peters, S.A.

AU - Sanchez Perez, G.F.

AU - Schijlen, E.G.W.M.

AU - van den Berg, Ronald

AU - Schranz, M.E.

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

M3 - Abstract

SP - 28

EP - 29

ER -