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van Lieshout N, van der Burgt A, de Vries ME, Ter Maat M, Eickholt D, Esselink D, van Kaauwen MPW, Kodde LP, Visser RGF, Lindhout P, Finkers R. Solyntus, the New Highly Contiguous Reference Genome for Potato ( Solanum tuberosum). G3 (BETHESDA, MD.) 2020; 10:3489-3495. [PMID: 32759330 PMCID: PMC7534448 DOI: 10.1534/g3.120.401550] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/28/2020] [Indexed: 11/18/2022]
Abstract
With the rapid expansion of the application of genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), the third largest food crop in the world, the related species S. phureja, designated "DM", has been used as the most popular reference genome for the last 10 years. Here, we introduce the de novo sequenced genome of Solyntus as the next standard reference in potato genome studies. A true Solanum tuberosum made up of 116 contigs that is also highly homozygous, diploid, vigorous and self-compatible, Solyntus provides a more direct and contiguous reference then ever before available. It was constructed by sequencing with state-of-the-art long and short read technology and assembled with Canu. The 116 contigs were assembled into scaffolds to form each pseudochromosome, with three contigs to 17 contigs per chromosome. This assembly contains 93.7% of the single-copy gene orthologs from the Solanaceae set and has an N50 of 63.7 Mbp. The genome and related files can be found at https://www.plantbreeding.wur.nl/Solyntus/ With the release of this research line and its draft genome we anticipate many exciting developments in (diploid) potato research.
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Affiliation(s)
- Natascha van Lieshout
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | | | | | | | - David Eickholt
- PepsiCo R&D, University of Minnesota, St. Paul, Minnesota 55108
| | - Danny Esselink
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | | | - Linda P Kodde
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | | | - Richard Finkers
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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Xu F, Lyu Y, Tong C, Wu W, Zhu X, Yin D, Yan Q, Zhang J, Pang X, Tobias CM, Wu R. A statistical model for QTL mapping in polysomic autotetraploids underlying double reduction. Brief Bioinform 2013; 15:1044-56. [DOI: 10.1093/bib/bbt073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Aversano R, Ercolano MR, Caruso I, Fasano C, Rosellini D, Carputo D. Molecular tools for exploring polyploid genomes in plants. Int J Mol Sci 2012; 13:10316-10335. [PMID: 22949863 PMCID: PMC3431861 DOI: 10.3390/ijms130810316] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/03/2012] [Accepted: 08/06/2012] [Indexed: 11/16/2022] Open
Abstract
Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.
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Affiliation(s)
- Riccardo Aversano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
| | - Maria Raffaella Ercolano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
| | - Immacolata Caruso
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
| | - Carlo Fasano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
| | - Daniele Rosellini
- Department of Applied Biology, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy; E-Mail:
| | - Domenico Carputo
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
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