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A chromosome-level genome assembly of Solanum chilense , a tomato wild relative associated with resistance to salinity and drought.

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العنوان: A chromosome-level genome assembly of Solanum chilense , a tomato wild relative associated with resistance to salinity and drought.
المؤلفون: Molitor C; The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom., Kurowski TJ; The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom., Fidalgo de Almeida PM; Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom., Kevei Z; Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom., Spindlow DJ; The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom., Chacko Kaitholil SR; The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom., Iheanyichi JU; The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom., Prasanna HC; Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bangalore, India., Thompson AJ; Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom., Mohareb FR; The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom.
المصدر: Frontiers in plant science [Front Plant Sci] 2024 Mar 08; Vol. 15, pp. 1342739. Date of Electronic Publication: 2024 Mar 08 (Print Publication: 2024).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Frontiers Research Foundation Country of Publication: Switzerland NLM ID: 101568200 Publication Model: eCollection Cited Medium: Print ISSN: 1664-462X (Print) Linking ISSN: 1664462X NLM ISO Abbreviation: Front Plant Sci Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: Lausanne : Frontiers Research Foundation, 2010-
مستخلص: Introduction: Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources.
Methods: In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads.
Results: The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production.
Discussion: Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2 . These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2024 Molitor, Kurowski, Fidalgo de Almeida, Kevei, Spindlow, Chacko Kaitholil, Iheanyichi, Prasanna, Thompson and Mohareb.)
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فهرسة مساهمة: Keywords: BUSCO; Genome assembly; S. chilense; drought; salt; transcriptome
تواريخ الأحداث: Date Created: 20240325 Latest Revision: 20240326
رمز التحديث: 20240326
مُعرف محوري في PubMed: PMC10957597
DOI: 10.3389/fpls.2024.1342739
PMID: 38525148
قاعدة البيانات: MEDLINE
الوصف
تدمد:1664-462X
DOI:10.3389/fpls.2024.1342739