{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T04:31:35Z","timestamp":1786509095085,"version":"build-2736575974"},"reference-count":42,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T00:00:00Z","timestamp":1786320000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32341044"],"award-info":[{"award-number":["32341044"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32472751"],"award-info":[{"award-number":["32472751"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"award":["32341044"],"award-info":[{"award-number":["32341044"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"award":["32472751"],"award-info":[{"award-number":["32472751"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Zhejiang Provincial Major Agricultural Science and Technology Projects of New Varieties Breeding","award":["2021C02065"],"award-info":[{"award-number":["2021C02065"]}]},{"name":"the earmarked fund for CARS","award":["CARS-21"],"award-info":[{"award-number":["CARS-21"]}]},{"name":"National Key Research and Development Program of China","award":["2023YFD1201504"],"award-info":[{"award-number":["2023YFD1201504"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Nucleotide-binding site leucine-rich repeat (NLR, historically termed NBS-LRR) proteins are among the most rapidly evolving components of plant innate immunity, yet comparative analyses of NLR subfamily diversification between wild and cultivated accessions of tomato (Solanum lycopersicum) have remained limited. Here, we compared the NLR gene family across three representative tomato accessions\u2014the wild species S. chilense and the cultivated tomatoes S. lycopersicum Heinz1706 (large-fruited) and S. lycopersicum LA1464 (cherry tomato)\u2014by integrating genome-wide identification, phylogenetic reconstruction, motif analysis, orthologous clustering, selection-pressure assessment, and expression profiling. We identified 220, 223, and 245 candidate NLR genes in S. chilense, Heinz1706, and LA1464, respectively, and classified them into TIR-type (TNL) and coiled-coil-type (CNL) subfamilies at a consistent ratio of approximately 1:5 across all three accessions. Motif analysis revealed pronounced structural divergence between TNL and CNL proteins, most notably in the region corresponding to the second conserved motif of the NB-ARC domain. Orthologous clustering identified 67 gene clusters shared among the three accessions; within these, TNL genes showed greater sequence divergence (higher Ka and Ks values) than CNL genes but significantly lower Ka\/Ks ratios (\u03c9), indicating stronger purifying selection despite their greater raw divergence. Expression profiling further showed that CNL genes were more broadly expressed across tissues and were induced by multiple pathogen-associated molecular patterns, whereas TNL gene expression was more spatially restricted and preferentially induced by effector-related treatments. These results indicate that the TNL and CNL subfamilies of the tomato NLR repertoire have followed distinct evolutionary trajectories and regulatory strategies. As these conclusions are based on comparative genomic and transcriptomic evidence from three accessions rather than on functional validation, they should be regarded as hypotheses; nonetheless, they offer candidate genomic resources and a comparative framework that may inform future disease-resistance breeding in tomato.<\/jats:p>","DOI":"10.3390\/biology15161350","type":"journal-article","created":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T08:08:53Z","timestamp":1786349333000},"page":"1350","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Distinct Evolutionary Constraints Shape TNL and CNL Immune Receptors in Wild and Cultivated Tomato"],"prefix":"10.3390","volume":"15","author":[{"given":"Shibo","family":"Meng","sequence":"first","affiliation":[{"name":"College of Horticulture, Anhui Agricultural University, Hefei 230036, China"},{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiajun","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Horticulture, Anhui Agricultural University, Hefei 230036, China"},{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enmei","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4740-1843","authenticated-orcid":false,"given":"Yuan","family":"Cheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meiying","family":"Ruan","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenxu","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingjing","family":"Ye","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rongqing","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuping","family":"Yao","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8068-8574","authenticated-orcid":false,"given":"Zhimiao","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guozhi","family":"Zhou","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7426-498X","authenticated-orcid":false,"given":"Hongjian","family":"Wan","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yougen","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Horticulture, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Cao, Y., Mo, W., Li, Y., Xiong, Y., Wang, H., Zhang, Y., Lin, M., Zhang, L., and Li, X. (2024). Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt. BMC Biol., 22.","DOI":"10.1186\/s12915-024-01836-x"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"msaf015","DOI":"10.1093\/molbev\/msaf015","article-title":"Deciphering Plant NLR Genomic Evolution: Synteny-Informed Classification Unveils Insights into TNL Gene Loss","volume":"42","author":"Guo","year":"2025","journal-title":"Mol. Biol. Evol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Zhou, D., Chen, X., Chen, X., Xia, Y., Liu, J., and Zhou, G. (2023). Plant immune receptors interact with hemibiotrophic pathogens to activate plant immunity. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1252039"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Wang, W., Liu, N., Gao, C., Rui, L., and Tang, D. (2019). The Pseudomonas Syringae Effector AvrPtoB Associates With and Ubiquitinates Arabidopsis Exocyst Subunit EXO70B1. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.01027"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2100","DOI":"10.1111\/pbi.14116","article-title":"Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)","volume":"21","author":"Amas","year":"2023","journal-title":"Plant Biotechnol. J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1111\/pbi.13262","article-title":"Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation","volume":"18","author":"Dolatabadian","year":"2019","journal-title":"Plant Biotechnol. J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1534\/g3.117.040485","article-title":"Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species","volume":"7","author":"Qian","year":"2017","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_8","first-page":"5","article-title":"Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula","volume":"146","author":"Wang","year":"2007","journal-title":"Plant Physiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Jupe, F., Pritchard, L., Etherington, G.J., MacKenzie, K., Cock, P.J.A., Wright, F., Sharma, S.K., Bolser, D., Bryan, G.J., and Jones, J.D.G. (2012). Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genom., 13.","DOI":"10.1186\/1471-2164-13-75"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Lozano, R., Ponce, O., Ramirez, M., Mostajo, N., and Orjeda, G. (2012). Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group phureja. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0034775"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1104\/pp.111.181990","article-title":"Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis","volume":"157","author":"Guo","year":"2011","journal-title":"Plant Physiol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Kang, Y.J., Kim, K.H., Shim, S., Yoon, M.Y., Sun, S., Kim, M.Y., Van, K., and Lee, S.-H. (2012). Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol., 12.","DOI":"10.1186\/1471-2229-12-139"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Lozano, R., Hamblin, M.T., Prochnik, S., and Jannink, J.-L. (2015). Identification and distribution of the NBS-LRR gene family in the Cassava genome. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1554-9"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Nepal, M., Andersen, E., Neupane, S., and Benson, B. (2017). Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. Genes, 8.","DOI":"10.3390\/genes8100249"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"752","DOI":"10.4161\/viru.36329","article-title":"Proteomics of effector-triggered immunity (ETI) in plants","volume":"5","author":"Hurley","year":"2014","journal-title":"Virulence"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Tente, E., Ereful, N., Rodriguez, A.C., Grant, P., O\u2019Sullivan, D.M., Boyd, L.A., and Gordon, A. (2021). Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot. BMC Plant Biol., 21.","DOI":"10.1186\/s12870-021-03086-3"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1007\/s42994-023-00104-w","article-title":"TIR enzymatic functions: Signaling molecules and receptor mechanisms","volume":"4","author":"Wan","year":"2023","journal-title":"aBIOTECH"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"eabe3069","DOI":"10.1126\/science.abe3069","article-title":"Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme","volume":"370","author":"Ma","year":"2020","journal-title":"Science"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"eabd9993","DOI":"10.1126\/science.abd9993","article-title":"Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ","volume":"370","author":"Martin","year":"2020","journal-title":"Science"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1105\/tpc.009308","article-title":"Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis","volume":"15","author":"Meyers","year":"2003","journal-title":"Plant Cell"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1038\/s41586-022-05231-w","article-title":"A wheat resistosome defines common principles of immune receptor channels","volume":"610","author":"Li","year":"2022","journal-title":"Nature"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3528","DOI":"10.1016\/j.cell.2021.05.003","article-title":"The ZAR1 resistosome is a calcium-permeable channel triggering plant immune signaling","volume":"184","author":"Bi","year":"2021","journal-title":"Cell"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1126\/science.aav5870","article-title":"Reconstitution and structure of a plant NLR resistosome conferring immunity","volume":"364","author":"Wang","year":"2019","journal-title":"Science"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Zhang, B., Liu, M., Wang, Y., Yuan, W., and Zhang, H. (2022). Plant NLRs: Evolving with pathogen effectors and engineerable to improve resistance. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1018504"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1105\/tpc.10.8.1307","article-title":"The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes","volume":"10","author":"Milligan","year":"1998","journal-title":"Plant Cell"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1094\/MPMI.2000.13.10.1130","article-title":"The broad-spectrum tospovirus resistance gene Sw-5 of tomato is a homolog of the root-knot nematode resistance gene Mi","volume":"13","author":"Brommonschenkel","year":"2000","journal-title":"Mol. Plant-Microbe Interact."},{"key":"ref_27","first-page":"521","article-title":"The I2C family from the wilt disease resistance locus I2 belongs to the nucleotide binding, leucine-rich repeat superfamily of plant resistance genes","volume":"9","author":"Ori","year":"1997","journal-title":"Plant Cell"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Andolfo, G., D\u2019Agostino, N., Frusciante, L., and Ercolano, M.R. (2021). The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies. Genes, 12.","DOI":"10.3390\/genes12020184"},{"key":"ref_29","first-page":"1158","article-title":"Genome-wide identification and evaluation of NBS-LRR disease-resistant gene family in cultivated tomatoes and wild tomatoes","volume":"52","author":"Shi","year":"2021","journal-title":"J. South. Agric."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Song, X., Li, C., Liu, Z., Zhou, R., Shen, S., Yu, T., Jia, L., and Li, N. (2024). Genome-Wide Analysis of the NBS-LRR Gene Family and SSR Molecular Markers Development in Solanaceae. Horticulturae, 10.","DOI":"10.3390\/horticulturae10121293"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Bashir, S., Rehman, N., Fakhar Zaman, F., Naeem, M.K., Jamal, A., Tellier, A., Ilyas, M., Silva Arias, G.A., and Khan, M.R. (2022). Genome-wide characterization of the NLR gene family in tomato (Solanum lycopersicum) and their relatedness to disease resistance. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.931580"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: Interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","article-title":"TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data","volume":"13","author":"Chen","year":"2020","journal-title":"Mol. Plant"},{"key":"ref_36","first-page":"1718","article-title":"Patterns of presence\u2013absence variation of NLRs across populations of Solanum chilense are clade-dependent and mainly shaped by past demographic history","volume":"245","author":"Gagnon","year":"2024","journal-title":"New Phytol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Jim\u00e9nez-G\u00f3mez, J.M., and Maloof, J.N. (2009). Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol., 9.","DOI":"10.1186\/1471-2229-9-85"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1094\/PHYTO-09-24-0273-R","article-title":"Genome-Wide Identification and Expression Analysis of the Nucleotide-Binding Leucine-Rich Repeat Gene Families in Rubber Tree","volume":"115","author":"Liu","year":"2025","journal-title":"Phytopathology"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"504","DOI":"10.2174\/1389202921999200601142258","article-title":"Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance","volume":"21","author":"Ratnaparkhe","year":"2020","journal-title":"Curr. Genom."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1016\/j.cell.2019.07.038","article-title":"A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana","volume":"178","author":"Monteiro","year":"2019","journal-title":"Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1101\/gr.159402","article-title":"Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana","volume":"12","author":"Meyers","year":"2002","journal-title":"Genome Res."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Mondrag\u00f3n-Palomino, M., Stam, R., John-Arputharaj, A., and Dresselhaus, T. (2017). Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms. BMC Ecol. Evol., 17.","DOI":"10.1186\/s12862-017-1099-4"}],"container-title":["Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/16\/1350\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T04:18:32Z","timestamp":1786508312000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/16\/1350"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,10]]},"references-count":42,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["biology15161350"],"URL":"https:\/\/doi.org\/10.3390\/biology15161350","relation":{},"ISSN":["2079-7737"],"issn-type":[{"value":"2079-7737","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,10]]}}}