De Novo Genome Assembly Of Solanum Sitiens Reveals Structural Variation Associated With Drought And Salinity Tolerance.
De Novo Genome Assembly Of Solanum Sitiens Reveals Structural Variation Associated With Drought And Salinity Tolerance.
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DOI：
10.1093/bioinformatics/btab048
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发表时间：
2021-08-04
期刊：
影响因子：
--
通讯作者：
Mohareb FR
中科院分区：
文献类型：
--
作者：
Molitor C;Kurowski TJ;Fidalgo de Almeida PM;Eerolla P;Spindlow DJ;Kashyap SP;Singh B;Prasanna H;Thompson AJ;Mohareb FR
Solanum sitiens是番茄的自交不亲和野生近缘种，具有耐盐和抗旱特性，有潜力通过育种计划对栽培番茄的作物改良做出贡献。该物种与其他抗胁迫野生番茄亲缘植物如S.pennellii和S. chilense相比具有独特的形态、分类和生态型。因此，S.sitiens参考基因组的可用性将有助于对盐和干旱抗性的遗传和分子认识。已经开发了用于S.sitiens的高质量从头基因组和转录组组装（登录号LA 1974）。使用Illumina短读段（159×覆盖率）和PacBio长读段（144 ×覆盖率）遵循杂交组装策略，生成总计15262 Gbp的DNA序列。产生了1245 Mbp的参考基因组，其排列在1483个支架中，N50为1.826 Mbp。使用基准通用单拷贝直系同源物（BUSCO）和K-mer分析工具（KAT）估计基因组完整性为95%。此外，产生了1063 Gbp的RNA-Seq以支持来自组装的31164个基因的预测，并进行从头转录组。最后，我们确定了三个大倒位相比，番茄，含有几个抗旱相关的基因，如β-淀粉酶1和YUCCA 7。 S.sitiens（LA 1974）原始测序、转录组和基因组组装已经以BioProject编号“PRJNA 633104”保藏在NCBI的Sequence Read Archive。生成程序集所需的所有命令和脚本都可以在以下github存储库中找到：https://github.com/MCorentin/Solanum_sitiens_assembly。 补充数据可在Bioinformatics在线获得。
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. 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 (∼159× coverage) and PacBio long reads (∼44× coverage), generating a total of ∼262 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, ∼63 Gbp of RNA-Seq were generated to support the prediction of 31 164 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. S.sitiens (LA1974) raw sequencing, transcriptome and genome assembly have been deposited at the NCBI’s Sequence Read Archive, under the BioProject number ‘PRJNA633104’. All the commands and scripts necessary to generate the assembly are available at the following github repository: https://github.com/MCorentin/Solanum_sitiens_assembly. Supplementary data are available at Bioinformatics online.
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DOI：
10.1534/g3.120.401612
发表时间：
2020-11-05
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Scott AD;Zimin AV;Puiu D;Workman R;Britton M;Zaman S;Caballero M;Read AC;Bogdanove AJ;Burns E;Wegrzyn J;Timp W;Salzberg SL;Neale DB
通讯作者：
Neale DB
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影响因子：
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作者：
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通讯作者：
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影响因子：
11.6
作者：
Schmidt, Maximilian H. -W.;Vogel, Alexander;Usadel, Bjorn
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影响因子：
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作者：
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通讯作者：
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水通道活性以提高作物耐受性。
影响因子：
6
作者：
Shekoofa A;Sinclair TR
通讯作者：
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