Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.
Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.
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DOI：
10.1111/tpj.12307
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发表时间：
2013-11
期刊：
影响因子：
--
通讯作者：
Jones JD
中科院分区：
文献类型：
--
作者：
Jupe F;Witek K;Verweij W;Sliwka J;Pritchard L;Etherington GJ;Maclean D;Cock PJ;Leggett RM;Bryan GJ;Cardle L;Hein I;Jones JD
RenSeq是一种以NB-LRR（核苷酸结合位点富亮氨酸重复序列）基因为靶点的抗性基因富集和测序方法，能够在植物基因组序列中发现和标注病原体抗性基因家族成员。我们成功地将RenSeq应用于马铃薯龙茄（Solanum tuberosum）克隆DM，并将鉴定到的nb - lrr数量从438个增加到755个。这些已鉴定的R基因位点大多数位于基因组中较差或以前未注释的区域。704个nb - lrr的12条染色体的序列和位置细节已经建立，可以通过我们提供的基因组浏览器访问。我们比较了这些NB-LRR基因和相应的寡核苷酸诱饵的最高序列相似性，并证明了~ 80%的序列一致性足以进行富集。对测序的番茄S. lycopersicum ‘ Heinz 1706 ’进行分析，将NB-LRR补体扩增到394个位点。我们进一步描述了一种应用RenSeq快速识别与感兴趣的病原体抗性性状共分离的分子标记的方法。在涉及野生茄种S. berthaultii （Rpi-ber2）和S. ruiz-ceballosii （Rpi-rzc1）的两个独立分离群体中，我们能够成功地利用RenSeq技术鉴定出对晚疫病病原菌疫霉（Phytophthora infestans）抗性的共分离标记。这些SNP鉴定工作流程被设计为易于适应的Galaxy管道。
RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ∼80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum ‘Heinz 1706’ extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.
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Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
3
作者：
Cronn, Richard;Knaus, Brian J.;Udall, Joshua
通讯作者：
Udall, Joshua
影响因子：
3.7
作者：
Lozano R;Ponce O;Ramirez M;Mostajo N;Orjeda G
通讯作者：
Orjeda G
影响因子：
11.6
作者：
Milligan, SB;Bodeau, J;Williamson, VM
通讯作者：
Williamson, VM
影响因子：
5.4
作者：
Bakker, Erin;Borm, Theo;Prins, Pjotr;van der Vossen, Edwin;Uenk, Gerda;Arens, Marjon;de Boer, Jan;van Eck, Herman;Muskens, Marielle;Vossen, Jack;van der Linden, Gerard;van Ham, Roeland;Klein-Lankhorst, Rene;Visser, Richard;Smant, Geert;Bakker, Jaap;Goverse, Aska
通讯作者：
Goverse, Aska