The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
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
Open accessAbstract
Summary: 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‐LRR s 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‐LRR s 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 S olanum species S. berthaultii (Rpi‐ber2) and S. ruiz‐ceballosii (Rpi‐rzc1), we were able to apply R en S eq successfully to identify markers that co‐segregate with resistance towards the late blight pathogen P hytophthora infestans. These SNP identification workflows were designed as easy‐to‐adapt Galaxy pipelines.
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Jones, J. D. G., & Dangl, J. L. (2006) · Nature · doi:10.1038/nature05286 · Cited by 13,177
Self-citationVelvet: Algorithms for de novo short read assembly using de Bruijn graphs
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,491
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Ashburner, M. (1989) · Cold Spring Harbor Laboratory eBooks · Cited by 6,756
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080
Self-citationVersatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,982
Plant pathogens and integrated defence responses to infection
Dangl, J. L., & Jones, J. D. G. (2001) · Nature · doi:10.1038/35081161 · Cited by 3,949
Self-citationGoecks, J., Nekrutenko, A., Taylor, J., & The Galaxy Team (2010) · Genome Biology · doi:10.1186/gb-2010-11-8-r86 · Cited by 3,453
The tomato genome sequence provides insights into fleshy fruit evolution
The Tomato Genome Consortium (2012) · Nature · doi:10.1038/nature11119 · Cited by 3,289
Genome sequence and analysis of the tuber crop potato
The Potato Genome Sequencing Consortium (2011) · Nature · doi:10.1038/nature10158 · Cited by 2,065
Galaxy: A platform for interactive large-scale genome analysis
Giardine, B., Riemer, C., Hardison, R. C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., et al. (2005) · Genome Research · doi:10.1101/gr.4086505 · Cited by 2,026
Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
Blankenberg, D., Kuster, G. V., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., & Taylor, J. (2010) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb1910s89 · Cited by 1,427
Diversity Arrays: a solid state technology for sequence information independent genotyping
Jaccoud, D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.4.e25 · Cited by 971
Zwenger, S., & Basu, C. (2010) · Principles and Practices of Plant Genomics, Volume 3 · doi:10.1201/9781439845523-14 · Cited by 951
Meyers, B. C., Dickerman, A. W., Michelmore, R. W., Sivaramakrishnan, S., Sobral, B., & Young, N. D. (1999) · The Plant Journal · doi:10.1046/j.1365-313x.1999.00606.x · Cited by 838
Milligan, S. B., Bodeau, J., Yaghoobi, J., Kaloshian, I., Zabel, P., & Williamson, V. M. (1998) · The Plant Cell · doi:10.1105/tpc.10.8.1307 · Cited by 803
Direct selection of human genomic loci by microarray hybridization
Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., Song, X., Richmond, T. A., Middle, C. M., Rodesch, M. J., Packard, C. J., et al. (2007) · Nature Methods · doi:10.1038/nmeth1111 · Cited by 681
Genome-wide in situ exon capture for selective resequencing
Hodges, E., Xuan, Z., Balija, V., Kramer, M., Molla, M. N., Smith, S. W., Middle, C. M., Rodesch, M. J., Albert, T. J., Hannon, G. J., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.42 · Cited by 677
A beginner’s guide to eukaryotic genome annotation
Yandell, M., & Ence, D. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3174 · Cited by 588
Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato
Tai, T. H., Dahlbeck, D., Clark, E. T., Gajiwala, P., Pasion, R., Whalen, M. C., Stall, R. E., & Staskawicz, B. J. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.24.14153 · Cited by 479
Schulze-Lefert, P., & Panstruga, R. (2011) · Trends in Plant Science · doi:10.1016/j.tplants.2011.01.001 · Cited by 415
Identification and localisation of the NB-LRR gene family within the potato genome
Jupe, F., Pritchard, L., Etherington, G. J., MacKenzie, K., Cock, P. J., Wright, F., Sharma, S. K., Bolser, D., Bryan, G. J., Jones, J. D., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-75 · Cited by 310
Self-citationTargeted enrichment strategies for next‐generation plant biology
Cronn, R., Knaus, B. J., Liston, A., Maughan, P. J., Parks, M., Syring, J. V., & Udall, J. (2012) · American Journal of Botany · doi:10.3732/ajb.1100356 · Cited by 217
Schornack, S., Ballvora, A., Gürlebeck, D., Peart, J., Ganal, M., Baker, B., Bonas, U., & Lahaye, T. (2004) · The Plant Journal · doi:10.1046/j.1365-313x.2003.01937.x · Cited by 208
Ernst, K., Kumar, A., Kriseleit, D., Kloos, D., Phillips, M. S., & Ganal, M. W. (2002) · The Plant Journal · doi:10.1046/j.1365-313x.2002.01341.x · Cited by 202
A comparative analysis of exome capture
Parla, J. S., Iossifov, I. H., Grabill, I., Spector, M. S., Kramer, M., & McCombie, W. R. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r97 · Cited by 146
Lozano, R. D., Ponce, O., Ramirez, M., Mostajo, N., & Orjeda, G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034775 · Cited by 120
Andolfo, G., Sanseverino, W., Rombauts, S., de Peer, Y. V., Bradeen, J. M., Carputo, D., Frusciante, L., & Ercolano, M. R. (2012) · New Phytologist · doi:10.1111/j.1469-8137.2012.04380.x · Cited by 99
Saintenac, C., Faure, S., Remay, A., Choulet, F., Ravel, C., Paux, E., Balfourier, F., Feuillet, C., & Sourdille, P. (2010) · Chromosoma · doi:10.1007/s00412-010-0302-9 · Cited by 71
Śliwka, J., Jakuczun, H., Chmielarz, M., Hara-Skrzypiec, A., Tomczyńska, I., Kilian, A., & Zimnoch‐Guzowska, E. (2012) · BMC Genetics · doi:10.1186/1471-2156-13-11 · Cited by 62
Self-citationSavant Genome Browser 2: visualization and analysis for population-scale genomics
Fiume, M., Smith, E., Brook, A., Strbenac, D., Turner, B., Mezlini, A. M., Robinson, M. D., Wodak, S. J., & Brudno, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks427 · Cited by 54
Community gene annotation in practice
Loveland, J. E., Gilbert, J. G. R., Griffiths, E., & Harrow, J. (2012) · Database · doi:10.1093/database/bas009 · Cited by 26
Metadata
- Authors
- Jupe, F., Witek, K., Verweij, W., Śliwka, J., Pritchard, L., Etherington, G. J., Maclean, D., Cock, P. J., Leggett, R. M., Bryan, G. J., Cardle, L., Hein, I., & Jones, J. D. G.
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2013-10-08
- Volume
- 76
- Issue
- 3
- Pages
- 530-544
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- OpenAlex
- W1970697531
- Cited by
- 393
- References
- 36
- FWCI
- 21.32
- Type
- journal article
- Language
- en
- Open access
- hybrid
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