Lavin M, Herendeen PS, Wojciechowski MF. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst Biol. 2005;54(4):575–94.
Article
PubMed
Google Scholar
Lewis GP. Legumes of the world. Richmond, UK: Royal Botanic Gardens, Kew; 2005.
Google Scholar
Abbo S, Lev-Yadun S, Gopher A. Plant domestication and crop evolution in the near east: on events and processes. Crit Rev Plant Sci. 2012;31:241–57.
Article
Google Scholar
Smýkal P, Coyne CJ, Ambrose MJ, Maxted N, Schaefer H, Blair MW, Berger J, Greene SL, Nelson MN, Besharat N, et al. Legume crops phylogeny and genetic diversity for science and breeding. Crit Rev Plant Sci. 2015;34:43–104.
Article
Google Scholar
Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S, Deyholos MK, Peng Y, Joyce B, Stewart CN Jr, Rolf M, et al. Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. Mol Biol Evol. 2015;32(1):193–210.
Article
CAS
PubMed
Google Scholar
Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, et al. A gene expression atlas of the model legume Medicago truncatula. Plant J. 2008;55(3):504–13.
Article
CAS
PubMed
Google Scholar
Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S, Fan G, Whaley AM, et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol. 2012;30(1):83–9.
Article
CAS
Google Scholar
Kang YJ, Kim SK, Kim MY, Lestari P, Kim KH, Ha B-K, Jun TH, Hwang WJ, Lee T, Lee J, et al. Genome sequence of mungbean and insights into evolution within Vigna species. Nat Commun. 2014;5:5443.
Article
CAS
PubMed
Google Scholar
Ehlers JD, Hall AE. Cowpea (Vigna unguiculata L. Walp.). Field Crop Res. 1997;53(1–3):187–204.
Article
Google Scholar
Yang K, Tian Z, Chen C, Luo L, Zhao B, Wang Z, Yu L, Li Y, Sun Y, Li W, et al. Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication. Proc Natl Acad Sci U S A. 2015;112(43):13213–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet. 2014;46(7):707–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH. Synteny and collinearity in plant genomes. Science. 2008;320(5875):486–8.
Article
CAS
PubMed
Google Scholar
Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 2008;18(12):1944–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K. The flowering world: a tale of duplications. Trends Plant Sci. 2009;14(12):680–8.
Article
PubMed
CAS
Google Scholar
Severin AJ, Cannon SB, Graham MM, Grant D, Shoemaker RC. Changes in twelve homoeologous genomic regions in soybean following three rounds of polyploidy. Plant Cell. 2011;23(9):3129–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178–83.
Article
CAS
PubMed
Google Scholar
Zheng F, Wu H, Zhang R, Li S, He W, Wong FL, Li G, Zhao S, Lam HM. Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family. BMC Genomics. 2016;17:402.
Article
PubMed
PubMed Central
CAS
Google Scholar
Foyer CH, Lam HM, Nguyen HT, Siddique KH, Varshney RK, Colmer TD, Cowling W, Bramley H, Mori TA, Hodgson JM, et al. Neglecting legumes has compromised human health and sustainable food production. Nat Plants. 2016;2:16112.
Article
PubMed
Google Scholar
Fitch WM. Distinguishing homologous from analogous proteins. Syst Zool. 1970;19(2):99–113.
Article
CAS
PubMed
Google Scholar
Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC bioinformatics. 2011;12:124.
Article
PubMed
PubMed Central
Google Scholar
Wang Y, Coleman-Derr D, Chen G, Gu YQ. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 2015;43(W1):W78–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics. 2011;Chapter 6:Unit 6 12 11–19.
Google Scholar
Shi T, Huang H, Sanderson MJ, Tax FE. Evolutionary dynamics of leucine-rich repeat receptor-like kinases and related genes in plants: a phylogenomic approach. J Integr Plant Biol. 2014;56(7):648–62.
Article
CAS
Google Scholar
Liu J, Chen N, Grant JN, Cheng ZM, Stewart CN Jr, Hewezi T. Soybean kinome: functional classification and gene expression patterns. J Exp Bot. 2015;66(7):1919–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Song W, Wang B, Li X, Wei J, Chen L, Zhang D, Zhang W, Li R. Identification of Immune Related LRR-Containing Genes in Maize ( Zea mays L.) by Genome-Wide Sequence Analysis. Int J Genomics. 2015;2015:1–11.
Article
CAS
Google Scholar
Jones JD, Dangl JL. The plant immune system. Nature. 2006;444(7117):323–9.
Article
CAS
PubMed
Google Scholar
Thomma BP, Nurnberger T, Joosten MH. Of PAMPs and effectors: the blurred PTI-ETI dichotomy. Plant Cell. 2011;23(1):4–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nurnberger T, Jones JD, Felix G, Boller T. A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature. 2007;448(7152):497–500.
Article
CAS
PubMed
Google Scholar
Wang G, Ellendorff U, Kemp B, Mansfield JW, Forsyth A, Mitchell K, Bastas K, Liu C-M, Woods-Tör A, Zipfel C, et al. A genome-wide functional investigation into the roles of receptor-like proteins in Arabidopsis. Plant Physiol. 2008;147:503–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xi L, Wu XN, Gilbert M, Schulze WX. Classification and interactions of LRR receptors and co-receptors within the Arabidopsis plasma membrane - an overview. Front Plant Sci. 2019;10:472.
Article
PubMed
PubMed Central
Google Scholar
Lannoo N, Van Damme EJM. Lectin domains at the frontiers of plant defense. Front Plant Sci. 2014;5:1–16.
Article
Google Scholar
Tor M, Lotze MT, Holton N. Receptor-mediated signalling in plants: molecular patterns and programmes. J Exp Bot. 2009;60(13):3645–54.
Article
PubMed
PubMed Central
CAS
Google Scholar
Aslam SN, Erbs G, Morrissey KL, Newman MA, Chinchilla D, Boller T, Molinaro A, Jackson RW, Cooper RM. Microbe-associated molecular pattern (MAMP) signatures, synergy, size and charge: influences on perception or mobility and host defence responses. Mol Plant Pathol. 2009;10:375–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shiu S-H, Bleecker AB. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci. 2001;98:10763–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trdá L, Boutrot F, Claverie J, Brul e D, Dorey S, Poinssot B. Perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline. Front Plant Sci. 2015;6:219.
Sekhwal MK, Li P, Lam I, Wang X, Cloutier S, You FM. Disease resistance gene Analogs (RGAs) in plants. Int J Mol Sci. 2015;16:19248–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
McClean PE, Mamidi S, McConnell M, Chikara S, Lee R. Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genomics. 2010;11:184.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ghiurcuta CG, Moret BM. Evaluating synteny for improved comparative studies. Bioinformatics. 2014;30(12):i9–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L. Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends in genetics : TIG. 2005;21(12):673–82.
Article
CAS
PubMed
Google Scholar
Kevei Z, Seres A, Kereszt A, Kalo P, Kiss P, Toth G, Endre G, Kiss GB. Significant microsynteny with new evolutionary highlights is detected between Arabidopsis and legume model plants despite the lack of macrosynteny. Mol Gen Genomics. 2005;274(6):644–57.
Article
CAS
Google Scholar
Pearson WR. An introduction to sequence similarity ("homology") searching. Curr Protoc Bioinformatics. 2013;Chapter 3:Unit3 1.
PubMed
Google Scholar
Tekaia F. Inferring Orthologs: open questions and perspectives. Genomics Insights. 2016;9:17–28.
Article
PubMed
PubMed Central
Google Scholar
Liu D, Hunt M, Tsai IJ. Inferring synteny between genome assemblies: a systematic evaluation. BMC Bioinformatics. 2018;19(1):26.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li J, Dai X, Zhuang Z, Zhao PX. LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. Nucleic Acids Res. 2016;44(D1):D1189–94.
Article
CAS
PubMed
Google Scholar
Young N, Debellé F, Oldroyd G et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011;480:520–24.
Vasconcelos EV, de Andrade Fonseca AF, Pedrosa-Harand A, de Andrade Bortoleti KC, Benko-Iseppon AM, da Costa AF, Brasileiro-Vidal AC. Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH. Chromosom Res. 2015;23(2):253–66.
Article
CAS
Google Scholar
Munoz-Amatriain M, Mirebrahim H, Xu P, Wanamaker SI, Luo M, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, et al. Genome resources for climate-resilient cowpea, an essential crop for food security. Plant J. 2017;89(5):1042–54.
Article
CAS
PubMed
Google Scholar
Restrepo-Montoya D, Brueggeman R, McClean PE, Osorno JM. Computational identification of receptor-like kinases “RLK” and receptor-like proteins “RLP” in legumes. BMC Genomics. 2020;21(1):459.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, et al. The Arabidopsis information resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012;40(Database issue):D1202–10.
Article
CAS
PubMed
Google Scholar
Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K, et al. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485(7400):635–41.
Article
CAS
Google Scholar
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007;449(7161):463–7.
Article
CAS
PubMed
Google Scholar
Tirnaz S, Zhang Y, Batley J. Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains. In: Jain M, Garg R, editors. Legume Genomics: Methods and Protocols. New York, NY: Springer US; 2020. p. 365–75.
Chapter
Google Scholar
Li P, Quan X, Jia G, Xiao J, Cloutier S, You FM. RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants. BMC Genomics. 2016;17(1):852.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lonardi S, Muñoz‐Amatriaín M, Liang Q, Shu S, Wanamaker SI, Lo S, Tanskanen, J, Schulman AH, Zhu T, Luo MC, Alhakami H, Ounit R, Hasan AM, Verdier J, Roberts PA, Santos JR, Ndeve A, Doležel J, Vrána J, Hokin SA, Farmer AD, Cannon SB, Close TJ. The genome of cowpea (Vigna unguiculata [L.] Walp.). Plant J. 2019;98:767–82.
McClean PE, Lavin M, Gepts P, Jackson SA. Phaseolus vulgaris : a diploid model for soybean. Plant Genetics and Genomics: Crops and Models. 2008;2:55–76.
Google Scholar
Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H, et al. An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics. 2014;15:312.
Article
PubMed
PubMed Central
CAS
Google Scholar
Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P. Identifying single copy orthologs in Metazoa. PLoS Comput Biol. 2011;7(12):e1002269.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu C, Nadon BD, Kim KD, Jackson SA. Genetic and epigenetic divergence of duplicate genes in two legume species. Plant, Cell and Environment. 2018;41:2033–44.
Fang G, Bhardwaj N, Robilotto R, Gerstein MB. Getting started in gene orthology and functional analysis. PLoS Comput Biol. 2010;6(3):e1000703.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jordan IK, Wolf YI, Koonin EV. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol. 2004;4:22.
Article
PubMed
PubMed Central
CAS
Google Scholar
Panchy N, Lehti-Shiu M, Shiu SH. Evolution of gene duplication in plants. Plant Physiol. 2016;171(4):2294–316.
Article
CAS
PubMed
PubMed Central
Google Scholar
Afzal AJ, Wood AJ, Lightfoot DA. Plant receptor-like serine threonine kinases: roles in signaling and plant defense. Mol Plant Microbe Interactions. 2008;21(5):507–17.
Article
CAS
Google Scholar
Shiu SH, Li WH. Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes. Mol Biol Evol. 2004;21(5):828–40.
Article
CAS
PubMed
Google Scholar
Lehti-Shiu MD, Zou C, Shiu S-H. Origin, Diversity, Expansion History, and Functional Evolution of the Plant Receptor-Like Kinase/Pelle Family. In: Tax F, Kemmerling B, editors. Receptor-like Kinases in Plants: From Development to Defense. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012. p. 1–22.
Google Scholar
De Smet R, Adams KL, Vandepoele K, Van Montagu MC, Maere S, Van de Peer Y. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci U S A. 2013;110(8):2898–903.
Article
PubMed
PubMed Central
Google Scholar
Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, dePamphilis CW. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol Biol. 2010;10:61.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li Z, De La Torre AR, Sterck L, Cánovas FM, Avila C, Merino I, Cabezas JA, Cervera MT, Ingvarsson PK, Van De Peer Y. Single-copy genes as molecularmarkers for phylogenomic studies in seed plants. Genome Biol Evol. 2017;9(5):1130–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng F, Wu J, Fang L, Wang X. Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Front Plant Sci. 2012;3(August):1–6.
CAS
Google Scholar
Dardick C, Schwessinger B, Ronald P. Non-arginine-aspartate (non-RD) kinases are associated with innate immune receptors that recognize conserved microbial signatures. Curr Opin Plant Biol. 2012;15:358–66.
Article
CAS
PubMed
Google Scholar
Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13(9):2178–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(Database issue):D1178–86.
Article
CAS
PubMed
Google Scholar
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–9.
Article
CAS
PubMed
Google Scholar