NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification

被引：23

作者：

Toda, Nicholas ^{[1
]}

Rustenholz, Camille ^{[2
]}

Baud, Agnes ^{[3
]}

Le Paslier, Marie-Christine ^{[1
]}

Amselem, Joelle ^{[3
]}

Merdinoglu, Didier ^{[2
]}

Faivre-Rampant, Patricia ^{[1
]}

机构：

[1] Univ Paris Saclay, INRAE, EPGV, F-91000 Evry, France

[2] Univ Strasbourg, INRAE, SVQV UMR A 1131, F-68000 Colmar, France

[3] Univ Paris Saclay, INRAE, URGI, F-78026 Versailles, France

来源：

GENES | 2020年 / 11卷 / 03期

关键词：

NLR disease resistance genes; NLR-Parser; functional annotation; PREDICTION; PLATFORM; FAMILY;

D O I：

10.3390/genes11030333

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Although there are a number of bioinformatic tools to identify plant nucleotide-binding leucine-rich repeat (NLR) disease resistance genes based on conserved protein sequences, only a few of these tools have attempted to identify disease resistance genes that have not been annotated in the genome. The overall goal of the NLGenomeSweeper pipeline is to annotate NLR disease resistance genes, including RPW8, in the genome assembly with high specificity and a focus on complete functional genes. This is based on the identification of the complete NB-ARC domain, the most conserved domain of NLR genes, using the BLAST suite. In this way, the tool has a high specificity for complete genes and relatively intact pseudogenes. The tool returns all candidate NLR gene locations as well as InterProScan ORF and domain annotations for manual curation of the gene structure.

引用

页数：5

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