Abstract
Disease resistance in Brassica juncea has been shown against several diseases including blackleg, white rust, hypocotyl rot, turnip mosaic virus, leaf blight, black rot, and Alternaria blight. The identification of disease resistance genes is important to develop elite cultivars, which can survive exposure to these diseases. The largest family of resistance genes are nucleotide-binding site leucine-rich repeat genes (NLRs) which are classified into two major subfamilies: toll/interleukin-1 receptor-NLR (TNL) and coiled-coil-NLR (CNL) proteins. Here we present the first study of the genomic organization and evolutionary history of the NLR gene family in B. juncea, with comparative analysis to the diploid progenitors B. rapa and B. nigra. A total of 289 NLR genes were identified in B. juncea, with a ratio of 0.61:1 of TNL to non-TNL genes. The distribution of NLR genes was random and uneven, with chromosome A04 containing no NLR genes. Domain structure analysis revealed that 24% of NLR genes are typical resistance genes containing all three domains (TIR/CC, NBS, LRR), whereas the remaining genes are partially deleted or truncated. A total of 45% NLR genes were found to be physically clustered in the B. juncea genome. The NLR genes were analysed with OrthoFinder which showed that most physical clusters (63%) in B. juncea came from the same orthogroup. This study provides a valuable resource for the identification and characterization of candidate NLR genes for Brassica crop improvement.
Similar content being viewed by others
References
Alamery S, Tirnaz S, Bayer P, Tollenaere R, Chaloub B, Edwards D, Batley J (2018) Genome-wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus. Crop Pasture Sci 69:72–93
Ameline-Torregrosa C et al (2008) Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol 146:5–21. https://doi.org/10.1104/pp.107.104588
Baggs E, Dagdas G, Krasileva KV (2017) NLR diversity, helpers and integrated domains: making sense of the NLR IDentity. Curr Opin Plant Biol 38:59–67. https://doi.org/10.1016/j.pbi.2017.04.012
Bateman A et al (2004) The Pfam protein families database. Nucleic Acids Res 32:D138–D141. https://doi.org/10.1093/nar/gkh121
Bayer PE, Edwards D, Batley J (2018a) Bias in resistance gene prediction due to repeat masking. Nat Plants 4:762
Bayer PE, Golicz AA, Tirnaz S, Chan CKK, Edwards D, Batley J (2018b) Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. Plant Biotechnol J 1–12
Chalhoub B et al (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed. Genome Sci 345:950–953. https://doi.org/10.1126/science.1253435
Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, Li P, Hua W, Wang X (2011) BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 11:136
Christie N, Tobias PA, Naidoo S, Külheim C (2016) The Eucalyptus grandis NBS-LRR gene family: physical clustering and expression hotspots. Front Plant Sci 6. https://doi.org/10.3389/fpls.2015.01238
Collier SM, Hamel L-P, Moffett P (2011) Cell death mediated by the N-terminal domains of a unique and highly conserved class of NB-LRR protein. Mol Plant-Microbe Interact 24:918–931. https://doi.org/10.1094/MPMI-03-11-0050
Dangl JL, Jones JDG (2001) Plant pathogens and integrated defence responses to infection. nature 411:826–833
DeYoung BJ, Innes RW (2006) Plant NBS-LRR proteins in pathogen sensing and host defense. Nat Immunol 7:1243–1249
Dodds PN, Lawrence GJ, Ellis JG (2001) Six amino acid changes confined to the leucine-rich repeat β-Strand/β-Turn motif determine the difference between the P and P2 rust resistance specificities in flax. Plant Cell 13:163–178. https://doi.org/10.1105/tpc.13.1.163
Emms DM, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16:157. https://doi.org/10.1186/s13059-015-0721-2
Golicz AA et al (2016) The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7:13390. https://doi.org/10.1038/ncomms13390http://www.nature.com/articles/ncomms13390#supplementary-information
Goodstein DM et al (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186. https://doi.org/10.1093/nar/gkr944
Gu L, Si W, Zhao L, Yang S, Zhang X (2015) Dynamic evolution of NBS–LRR genes in bread wheat and its progenitors. Mol Gen Genomics 290:727–738. https://doi.org/10.1007/s00438-014-0948-8
Inturrisi FC, Bayer PE, Yang H, Chan CKK, Edwards D, Batley J (2018) Genome-wide analysis of NBS-LRR genes in Indian mustard (Brassica juncea) and prediction of candidate disease resistance genes. Phytopathology 108(10):111
Jones P et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236–1240. https://doi.org/10.1093/bioinformatics/btu031
Jupe F et al (2012) Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics 13:75
Kang YJ et al (2012) Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol 12:1–13. https://doi.org/10.1186/1471-2229-12-139
Kohler A et al (2008) Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Mol Biol 66:619–636. https://doi.org/10.1007/s11103-008-9293-9
Kroj T, Chanclud E, Michel-Romiti C, Grand X, Morel J-B (2016) Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. New Phytol 210:618–626. https://doi.org/10.1111/nph.13869
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Lozano R, Ponce O, Ramirez M, Mostajo N, Orjeda G (2012) Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group Phureja. PLoS One 7:e34775. https://doi.org/10.1371/journal.pone.0034775
Lozano R, Hamblin MT, Prochnik S, Jannink J-L (2015) Identification and distribution of the NBS-LRR gene family in the Cassava genome. BMC Genomics 16:360
Lupas A, Van Dyke M, Stock J (1991) Predicting coiled coils from protein sequences. Science 252:1162–1164
Lv S, Changwei Z, Tang J, Li Y, Wang Z, Jiang D, Hou X (2015) Genome-wide analysis and identification of TIR-NBS-LRR genes in Chinese cabbage (Brassica rapa ssp. pekinensis) reveal expression patterns to TuMV infection. Physiol Mol Plant Pathol 90:89–97. https://doi.org/10.1016/j.pmpp.2015.04.001
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 39(Database issue):D225–D229. https://doi.org/10.1093/nar/gkq1189
Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20:317–332. https://doi.org/10.1046/j.1365-313X.1999.00606.x
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Genome-wide analysis of NBS-LRR–encoding genes in Arabidopsis. Plant Cell 15:809–834. https://doi.org/10.1105/tpc.009308
Moser BR, Evangelista RL, Jham G (2015) Fuel properties of Brassica juncea oil methyl esters blended with ultra-low sulfur diesel fuel. Renew Energy 78:82–88. https://doi.org/10.1016/j.renene.2015.01.016
Mun J-H, Yu H-J, Park S, Park B-S (2009) Genome-wide identification of NBS-encoding resistance genes in Brassica rapa. Mol Gen Genomics 282:617–631. https://doi.org/10.1007/s00438-009-0492-0
Nandety RS, Caplan JL, Cavanaugh K, Perroud B, Wroblewski T, Michelmore RW, Meyers BC (2013) The Role of TIR-NBS and TIR-X proteins in plant basal defense responses. Plant Physiol 162:1459–1472. https://doi.org/10.1104/pp.113.219162
Paterson AH et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556 http://www.nature.com/nature/journal/v457/n7229/suppinfo/nature07723_S1.html
Perazzolli M et al (2014) Characterization of resistance gene analogues (RGAs) in apple (Malus × domestica Borkh.) and their evolutionary history of the Rosaceae Family. PLoS One 9:e83844. https://doi.org/10.1371/journal.pone.0083844
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:W116–W120. https://doi.org/10.1093/nar/gki442
Sarris PF, Cevik V, Dagdas G, Jones JDG, Krasileva KV (2016) Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens. BMC Biol 14:8. https://doi.org/10.1186/s12915-016-0228-7
Seo E, Kim S, Yeom S-I, Choi D (2016) Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae. Plants Front Plant Sci 7. https://doi.org/10.3389/fpls.2016.01205
Shao Z-Q et al (2016) Large-scale analyses of angiosperm nucleotide-binding site-leucine-rich repeat genes reveal three anciently diverged classes with distinct evolutionary patterns. Plant Physiol 170:2095–2109. https://doi.org/10.1104/pp.15.01487
Singh S, Chand S, Singh NK, Sharma TR (2015) Genome-wide distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species. PLoS One 10:e0125964. https://doi.org/10.1371/journal.pone.0125964
Skrypetz S (2007) Mustard seed: situation and outlook. Bi-Weekly Bulletin 20(11). Available: http://publications.gc.ca/collections/collection_2007/agr/A27-18-20-11E.pdf
Takken FLW, Tameling WIL (2009) To Nibble at Plant Resistance Proteins. Science 324:744–746. https://doi.org/10.1126/science.1171666
U N (1935) Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot 7:389–452
Urbach JM, Ausubel FM (2017) The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events. Proc Natl Acad Sci 114:1063–1068. https://doi.org/10.1073/pnas.1619730114
van Ooijen G, Mayr G, Kasiem MMA, Albrecht M, Cornelissen BJC, Takken FLW (2008) Structure–function analysis of the NB-ARC domain of plant disease resistance proteins. J Exp Bot 59:1383–1397. https://doi.org/10.1093/jxb/ern045
Voorrips RE (2002) MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs. J Hered 93:77–78. https://doi.org/10.1093/jhered/93.1.77
Wan H, Yuan W, Bo K, Shen J, Pang X, Chen J (2013) Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops. BMC Genomics 14:109. https://doi.org/10.1186/1471-2164-14-109
Wang X et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039 http://www.nature.com/ng/journal/v43/n10/abs/ng.919.html#supplementary-information
Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40(7):e49
Warren RF, Henk A, Mowery P, Holub E, Innes RW (1998) A mutation within the leucine-rich repeat domain of the Arabidopsis disease resistance Gene RPS5 partially suppresses multiple bacterial and downy mildew resistance genes. Plant Cell 10:1439–1452. https://doi.org/10.1105/tpc.10.9.1439
Wei H, Li W, Sun X, Zhu S, Zhu J (2013) Systematic analysis and comparison of nucleotide-binding site disease resistance genes in a diploid cotton Gossypium raimondii. PLoS One 8:1–13. https://doi.org/10.1371/journal.pone.0068435
Wilkes MA, Takei I, Caldwell RA, Trethowan RM (2013) The effect of genotype and environment on biodiesel quality prepared from Indian mustard (Brassica juncea) grown in Australia. Ind Crop Prod 48:124–132. https://doi.org/10.1016/j.indcrop.2013.04.016
Wu P et al (2014) Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapa. Gene 540:54–61. https://doi.org/10.1016/j.gene.2014.01.082
Xiao S, Ellwood S, Calis O, Patrick E, Li T, Coleman M, Turner JG (2001) Broad-Spectrum Mildew Resistance in Arabidopsis thaliana Mediated by RPW8. Science 291:118–120. https://doi.org/10.1126/science.291.5501.118
Yang S, Zhang X, Yue J-X, Tian D, Chen J-Q (2008) Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Gen Genomics 280:187–198. https://doi.org/10.1007/s00438-008-0355-0
Yang J et al (2016) The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet 48:1225–1232. https://doi.org/10.1038/ng.3657http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.3657.html#supplementary-information
Yu J et al (2014) Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana. BMC Genomics 15:3
Zhang Y-M, Shao Z-Q, Wang Q, Hang Y-Y, Xue J-Y, Wang B, Chen J-Q (2016a) Uncovering the dynamic evolution of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in Brassicaceae. J Integr Plant Biol 58:165–177. https://doi.org/10.1111/jipb.12365
Zhang Y, Xia R, Kuang H, Meyers BC (2016b) The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them. Mol Biol Evol 33:2692–2705. https://doi.org/10.1093/molbev/msw154
Zheng F et al (2016) Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family. BMC Genomics 17:1–13. https://doi.org/10.1186/s12864-016-2736-9
Zhou T et al (2004) Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Gen Genomics 271:402–415. https://doi.org/10.1007/s00438-004-0990-z
Acknowledgments
The authors acknowledge funding support from the Australian Research Council (ARC) (Projects FT130100604, DP1601004497, LP140100537, LP160100030). F.I. and S.T. acknowledge the support of University of Western Australia and Grains Research and Development Corporation. P.E.B. acknowledges support of the Forrest Research Foundation.
Author information
Authors and Affiliations
Contributions
F.I, P.E.B., D.E. and J.B. conceived the study. F.I and P.E.B. performed data analysis. H.Y. and S.T. assisted with the identification of resistance genes. F.I. wrote the manuscript. S.T. assisted with the manuscript writing. All authors approved the final version.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Inturrisi, F., Bayer, P.E., Yang, H. et al. Genome-wide identification and comparative analysis of resistance genes in Brassica juncea. Mol Breeding 40, 78 (2020). https://doi.org/10.1007/s11032-020-01159-z
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11032-020-01159-z