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Reanalysis of genome sequences of tomato accessions and its wild relatives: development of Tomato Genomic Variation (TGV) database integrating SNPs and INDELs polymorphisms.
Bioinformatics ( IF 4.4 ) Pub Date : 2020-07-06 , DOI: 10.1093/bioinformatics/btaa617
Prateek Gupta 1 , Pankaj Singh Dholaniya 2 , Sameera Devulapalli 1 , Nilesh Ramesh Tawari 3 , Yellamaraju Sreelakshmi 1 , Rameshwar Sharma 1
Affiliation  

Facilitated by technological advances and expeditious decrease in the sequencing costs, whole-genome sequencing (WGS) is increasingly implemented to uncover variations in cultivars/accessions of many crop plants. In tomato (Solanum lycopersicum), the availability of the genome sequence, followed by the resequencing of tomato cultivars and its wild relatives, has provided a prodigious resource for the improvement of traits. A high-quality genome resequencing of 84 tomato accessions and wild relatives generated a dataset that can be used as a resource to identify agronomically important alleles across the genome. Converting this dataset into a searchable database, including information about the influence of SNPs on protein function, provides valuable information about the genetic variations. The database will assist in searching for functional variants of a gene for introgression into tomato cultivars.

中文翻译:

重新分析番茄种质及其野生近缘种的基因组序列:整合了SNP和INDEL多态性的番茄基因组变异(TGV)数据库的开发。

在技​​术进步和测序成本的迅速降低的推动下,全基因组测序(WGS)越来越多地用于发现许多农作物的栽培品种/品种的变异。在番茄(番茄),基因组序列的可用性以及随后对番茄品种及其野生近缘种进行重测序,为改善性状提供了巨大的资源。对84个番茄种质和野生亲缘种进行高质量的基因组重测序,生成了一个数据集,可用作识别整个基因组中具有农学意义的等位基因的资源。将此数据集转换为可搜索的数据库,包括有关SNP对蛋白质功能影响的信息,可提供有关遗传变异的有价值的信息。该数据库将有助于搜索基因渗入番茄品种的功能变体。
更新日期:2020-07-06
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