Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/118050 |
| _version_ | 1855514575958441984 |
|---|---|
| author | Hoopes, G. Meng, X. Hamilton, J.P. Achakkagari, S.R. Brito Ribeiro, Mauro César Lambert de Bolger, M.E. Coombs, J.J. Esselink, D. Kaiser, N.R. Kodde, L. Kyriakidou, M. Lavrijssen, B. Lieshout, N. van Shereda, R. Tuttle, H.K. Vaillancourt, B. Wood, J.C. Boer, J.M de Bornowski, N. Bourke, P. Douches, D. Eck, H.J. van Ellis, David Feldman, M.J. Gardner, K.M. Hopman, J.C.P. Jiang, J. Jong, W.S. de Kuhl, J.C. Novy, R.G. Oome, S. Sathuvalli, V. Tan, E.H. Ursum, R.A. Vales, M.I. Vining, K. Visser, Richard G.F. Vossen, J. Yencho, George Craig Anglin, N.L Bachem, C.W.B. Endelman, J.B. Shannon, L.M. Stromvik, M.V. Tai, H.H. Usadel, B. Buell, C.R. Finkers, R. |
| author_browse | Achakkagari, S.R. Anglin, N.L Bachem, C.W.B. Boer, J.M de Bolger, M.E. Bornowski, N. Bourke, P. Brito Ribeiro, Mauro César Lambert de Buell, C.R. Coombs, J.J. Douches, D. Eck, H.J. van Ellis, David Endelman, J.B. Esselink, D. Feldman, M.J. Finkers, R. Gardner, K.M. Hamilton, J.P. Hoopes, G. Hopman, J.C.P. Jiang, J. Jong, W.S. de Kaiser, N.R. Kodde, L. Kuhl, J.C. Kyriakidou, M. Lavrijssen, B. Lieshout, N. van Meng, X. Novy, R.G. Oome, S. Sathuvalli, V. Shannon, L.M. Shereda, R. Stromvik, M.V. Tai, H.H. Tan, E.H. Tuttle, H.K. Ursum, R.A. Usadel, B. Vaillancourt, B. Vales, M.I. Vining, K. Visser, Richard G.F. Vossen, J. Wood, J.C. Yencho, George Craig |
| author_facet | Hoopes, G. Meng, X. Hamilton, J.P. Achakkagari, S.R. Brito Ribeiro, Mauro César Lambert de Bolger, M.E. Coombs, J.J. Esselink, D. Kaiser, N.R. Kodde, L. Kyriakidou, M. Lavrijssen, B. Lieshout, N. van Shereda, R. Tuttle, H.K. Vaillancourt, B. Wood, J.C. Boer, J.M de Bornowski, N. Bourke, P. Douches, D. Eck, H.J. van Ellis, David Feldman, M.J. Gardner, K.M. Hopman, J.C.P. Jiang, J. Jong, W.S. de Kuhl, J.C. Novy, R.G. Oome, S. Sathuvalli, V. Tan, E.H. Ursum, R.A. Vales, M.I. Vining, K. Visser, Richard G.F. Vossen, J. Yencho, George Craig Anglin, N.L Bachem, C.W.B. Endelman, J.B. Shannon, L.M. Stromvik, M.V. Tai, H.H. Usadel, B. Buell, C.R. Finkers, R. |
| author_sort | Hoopes, G. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations predicted to have a high negative impact on protein function, complicating breeder’s efforts to reduce genetic load. The StCDF1 locus controls maturity and analysis of six tetraploid genomes revealed 12 allelic variants correlated with maturity in a dosage dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids. |
| format | Journal Article |
| id | CGSpace118050 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1180502024-11-13T13:37:22Z Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity Hoopes, G. Meng, X. Hamilton, J.P. Achakkagari, S.R. Brito Ribeiro, Mauro César Lambert de Bolger, M.E. Coombs, J.J. Esselink, D. Kaiser, N.R. Kodde, L. Kyriakidou, M. Lavrijssen, B. Lieshout, N. van Shereda, R. Tuttle, H.K. Vaillancourt, B. Wood, J.C. Boer, J.M de Bornowski, N. Bourke, P. Douches, D. Eck, H.J. van Ellis, David Feldman, M.J. Gardner, K.M. Hopman, J.C.P. Jiang, J. Jong, W.S. de Kuhl, J.C. Novy, R.G. Oome, S. Sathuvalli, V. Tan, E.H. Ursum, R.A. Vales, M.I. Vining, K. Visser, Richard G.F. Vossen, J. Yencho, George Craig Anglin, N.L Bachem, C.W.B. Endelman, J.B. Shannon, L.M. Stromvik, M.V. Tai, H.H. Usadel, B. Buell, C.R. Finkers, R. potatoes polyploidy alleles genomes genetic variation molecular biology Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations predicted to have a high negative impact on protein function, complicating breeder’s efforts to reduce genetic load. The StCDF1 locus controls maturity and analysis of six tetraploid genomes revealed 12 allelic variants correlated with maturity in a dosage dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids. 2022-03 2022-02-11T05:01:52Z 2022-02-11T05:01:52Z Journal Article https://hdl.handle.net/10568/118050 en Open Access Elsevier Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de BoerJ.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A., Vales M.I., Vining K., Visser R.G.F., Vossen J., Yencho G.C., Anglin N.L., BachemC.W.B., Endelman J.B., Shannon L.M., Strömvik M.V., Tai H.H., Usadel B., Buell C.R., and FinkersR. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complexgenome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Molecular Plant. ISSN 1752-9867. 38 p. |
| spellingShingle | potatoes polyploidy alleles genomes genetic variation molecular biology Hoopes, G. Meng, X. Hamilton, J.P. Achakkagari, S.R. Brito Ribeiro, Mauro César Lambert de Bolger, M.E. Coombs, J.J. Esselink, D. Kaiser, N.R. Kodde, L. Kyriakidou, M. Lavrijssen, B. Lieshout, N. van Shereda, R. Tuttle, H.K. Vaillancourt, B. Wood, J.C. Boer, J.M de Bornowski, N. Bourke, P. Douches, D. Eck, H.J. van Ellis, David Feldman, M.J. Gardner, K.M. Hopman, J.C.P. Jiang, J. Jong, W.S. de Kuhl, J.C. Novy, R.G. Oome, S. Sathuvalli, V. Tan, E.H. Ursum, R.A. Vales, M.I. Vining, K. Visser, Richard G.F. Vossen, J. Yencho, George Craig Anglin, N.L Bachem, C.W.B. Endelman, J.B. Shannon, L.M. Stromvik, M.V. Tai, H.H. Usadel, B. Buell, C.R. Finkers, R. Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity |
| title | Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity |
| title_full | Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity |
| title_fullStr | Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity |
| title_full_unstemmed | Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity |
| title_short | Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity |
| title_sort | phased chromosome scale genome assemblies of tetraploid potato reveals a complex genome transcriptome and predicted proteome landscape underpinning genetic diversity |
| topic | potatoes polyploidy alleles genomes genetic variation molecular biology |
| url | https://hdl.handle.net/10568/118050 |
| work_keys_str_mv | AT hoopesg phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT mengx phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT hamiltonjp phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT achakkagarisr phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT britoribeiromaurocesarlambertde phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT bolgerme phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT coombsjj phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT esselinkd phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT kaisernr phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT koddel phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT kyriakidoum phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT lavrijssenb phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT lieshoutnvan phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT sheredar phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT tuttlehk phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT vaillancourtb phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT woodjc phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT boerjmde phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT bornowskin phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT bourkep phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT douchesd phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT eckhjvan phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT ellisdavid phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT feldmanmj phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT gardnerkm phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT hopmanjcp phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT jiangj phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT jongwsde phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT kuhljc phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT novyrg phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT oomes phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT sathuvalliv phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT taneh phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT ursumra phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT valesmi phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT viningk phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT visserrichardgf phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT vossenj phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT yenchogeorgecraig phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT anglinnl phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT bachemcwb phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT endelmanjb phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT shannonlm phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT stromvikmv phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT taihh phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT usadelb phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT buellcr phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity AT finkersr phasedchromosomescalegenomeassembliesoftetraploidpotatorevealsacomplexgenometranscriptomeandpredictedproteomelandscapeunderpinninggeneticdiversity |