{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T02:30:55Z","timestamp":1785465055240,"version":"3.56.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2021,1,30]],"date-time":"2021-01-30T00:00:00Z","timestamp":1611964800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UK\u2019s Biotechnology and Biological Sciences Research Council"},{"name":"Indian Department of Biotechnology","award":["BB\/L011611\/1"],"award-info":[{"award-number":["BB\/L011611\/1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Solanum sitiens is a self-incompatible wild relative of tomato, characterized by salt and drought-resistance traits, with the potential to contribute through breeding programmes to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S.pennellii and S.chilense. Therefore, the availability of a reference genome for S.sitiens will facilitate the genetic and molecular understanding of salt and drought resistance.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n A high-quality de novo genome and transcriptome assembly for S.sitiens (Accession LA1974) has been developed. A hybrid assembly strategy was followed using Illumina short reads (\u223c159\u00d7 coverage) and PacBio long reads (\u223c44\u00d7 coverage), generating a total of \u223c262 Gbp of DNA sequence. A reference genome of 1245 Mbp, arranged in 1483 scaffolds with an N50 of 1.826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT). In addition, \u223c63 Gbp of RNA-Seq were generated to support the prediction of 31\u00a0164 genes from the assembly, and to perform a de novo transcriptome. Lastly, we identified three large inversions compared to S.lycopersicum, containing several drought-resistance-related genes, such as beta-amylase 1 and YUCCA7.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n S.sitiens (LA1974) raw sequencing, transcriptome and genome assembly have been deposited at the NCBI\u2019s Sequence Read Archive, under the BioProject number \u2018PRJNA633104\u2019. All the commands and scripts necessary to generate the assembly are available at the following github repository: https:\/\/github.com\/MCorentin\/Solanum_sitiens_assembly.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab048","type":"journal-article","created":{"date-parts":[[2021,1,23]],"date-time":"2021-01-23T10:58:04Z","timestamp":1611399484000},"page":"1941-1945","source":"Crossref","is-referenced-by-count":16,"title":["De novo<\/i>\n genome assembly of\n Solanum sitiens<\/i>\n reveals structural variation associated with drought and salinity tolerance"],"prefix":"10.1093","volume":"37","author":[{"given":"Corentin","family":"Molitor","sequence":"first","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasz J","family":"Kurowski","sequence":"additional","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro M","family":"Fidalgo de Almeida","sequence":"additional","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pramod","family":"Eerolla","sequence":"additional","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel J","family":"Spindlow","sequence":"additional","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarvesh P","family":"Kashyap","sequence":"additional","affiliation":[{"name":"Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research , Varanasi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bijendra","family":"Singh","sequence":"additional","affiliation":[{"name":"Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research , Varanasi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H C","family":"Prasanna","sequence":"additional","affiliation":[{"name":"Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research , Varanasi, India"},{"name":"Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research , Bangalore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew J","family":"Thompson","sequence":"additional","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7880-2519","authenticated-orcid":false,"given":"Fady R","family":"Mohareb","sequence":"additional","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,1,30]]},"reference":[{"key":"2023061310310385600_btab048-B1","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/j.tplants.2013.08.003","article-title":"Resolution by recombination: breaking up Solanum pennellii introgressions","volume":"18","author":"Alseekh","year":"2013","journal-title":"Trends Plant Sci"},{"key":"2023061310310385600_btab048-B2","author":"Atherton","year":"1986"},{"key":"2023061310310385600_btab048-B3","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1038\/ng.3046","article-title":"The genome of the stress-tolerant wild tomato species Solanum pennellii","volume":"46","author":"Bolger","year":"2014","journal-title":"Nat. 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