Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family in Solanum pimpinellifolium and Arabidopsis thaliana

NBS-LRR (nucleotide-binding site and leucine-rich repeat) is one of the largest resistance gene families in plants. The completion of the genome sequencing of wild tomato Solanum pimpinellifolium provided an opportunity to conduct a comprehensive analysis of the NBS-LRR gene superfamily at the genome-wide level. In this study, gene identification, chromosome mapping, and phylogenetic analysis of the NBS-LRR gene family were analyzed using the bioinformatics methods. The results revealed 245 NBS-LRRs in total, similar to that in the cultivated tomato. These genes are unevenly distributed on 12 chromosomes, and ~59.6% of them form gene clusters, most of which are tandem duplications. Phylogenetic analysis divided the NBS-LRRs into 2 subfamilies (CNL-coiled-coil NBS-LRR and TNL-TIR NBS-LRR), and the expansion of the CNL subfamily was more extensive than the TNL subfamily. Novel conserved structures were identified through conserved motif analysis between the CNL and TNL subfamilies. Compared with the NBS-LRR sequences from the model plant Arabidopsis thaliana, wide genetic variation occurred after the divergence of S. pimpinellifolium and A thaliana. Species-specific expansion was also found in the CNL subfamily in S. pimpinellifolium. The results of this study provide the basis for the deeper analysis of NBS-LRR resistance genes and contribute to mapping and isolation of candidate resistance genes in S. pimpinellifolium.

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Genome-Level Evolution of Resistance Genes in Arabidopsis thaliana

Genetics ◽

10.1093/genetics/165.1.309 ◽

2003 ◽

Vol 165 (1) ◽

pp. 309-319

Author(s):

Andrew Baumgarten ◽

Steven Cannon ◽

Russ Spangler ◽

Georgiana May

Keyword(s):

Arabidopsis Thaliana ◽

Gene Family ◽

Resistance Genes ◽

Gene Diversity ◽

Chromosome Region ◽

Gene Families ◽

Evolutionary Mechanisms ◽

Chromosome Duplication ◽

Gene Copies ◽

Genome Level

Abstract Pathogen resistance genes represent some of the most abundant and diverse gene families found within plant genomes. However, evolutionary mechanisms generating resistance gene diversity at the genome level are not well understood. We used the complete Arabidopsis thaliana genome sequence to show that most duplication of individual NBS-LRR sequences occurs at close physical proximity to the parent sequence and generates clusters of closely related NBS-LRR sequences. Deploying the statistical strength of phylogeographic approaches and using chromosomal location as a proxy for spatial location, we show that apparent duplication of NBS-LRR genes to ectopic chromosomal locations is largely the consequence of segmental chromosome duplication and rearrangement, rather than the independent duplication of individual sequences. Although accounting for a smaller fraction of NBS-LRR gene duplications, segmental chromosome duplication and rearrangement events have a large impact on the evolution of this multi-gene family. Intergenic exchange is dramatically lower between NBS-LRR sequences located in different chromosome regions as compared to exchange between sequences within the same chromosome region. Consequently, once translocated to new chromosome locations, NBS-LRR gene copies have a greater likelihood of escaping intergenic exchange and adopting new functions than do gene copies located within the same chromosomal region. We propose an evolutionary model that relates processes of genome evolution to mechanisms of evolution for the large, diverse, NBS-LRR gene family.

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Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat

Genome ◽

10.1139/g97-087 ◽

1997 ◽

Vol 40 (5) ◽

pp. 659-665 ◽

Cited By ~ 87

Author(s):

Evans S. Lagudah ◽

Odile Moullet ◽

Rudi Appels

Keyword(s):

Disease Resistance ◽

Gene Family ◽

Binding Site ◽

Resistance Gene ◽

Resistance Genes ◽

Gene Sequence ◽

Nucleotide Binding ◽

Disease Resistance Gene ◽

Leucine Rich Repeat ◽

Rich Region

The Cre3 gene confers a high level of resistance to the root endoparasitic nematode Heterodera avenae in wheat. A DNA marker cosegregating with H. avenae resistance was used as an entry point for map-based cloning of a disease resistance gene family at the Cre3 locus. Two related gene sequences have been analysed at the Cre3 locus. One, identified as a cDNA clone, encodes a polypeptide with a nucleotide binding site (NBS) and a leucine-rich region; this member of the disease resistance gene family is expressed in roots. A second Cre3 gene sequence, cloned as genomic DNA, appears to be a pseudogene, with a frame shift caused by a deletion event. These two genes, related to members of the cytoplasmic NBS – leucine rich repeat class of plant disease resistance genes were physically mapped to the distal 0.06 fragment of the long arm of wheat chromosome 2D and cosegregated with nematode resistance.Key words: cereal cyst nematode, disease resistance genes, nucleotide-binding site, leucine-rich repeat.

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Resistance of Arabidopsis thaliana to the obligate biotrophic parasite Plasmodiophora brassicae

Plant Protection Science ◽

10.17221/10543-pps ◽

2017 ◽

Vol 38 (SI 2 - 6th Conf EFPP 2002) ◽

pp. 519-522 ◽

Cited By ~ 3

Author(s):

A. Arbeiter ◽

M. Fähling ◽

H. Graf ◽

M.D. Sacristán ◽

J. Siemens

Keyword(s):

Arabidopsis Thaliana ◽

Salicylic Acid ◽

Jasmonic Acid ◽

Resistance Gene ◽

Resistance Genes ◽

Plasmodiophora Brassicae ◽

Chromosome 1 ◽

Coding Sequences ◽

Resistance Phenotype ◽

Resistance Reaction

Two resistance phenotypes to P. brassicae have been found in A. thaliana. A first resistance phenotype has been detected to the isolate 'e<sub>2</sub>' and is polygenically inherited. The second resistance to isolate 'e<sub>3</sub>' is caused by the dominant resistance gene RPB1. By crossing no influence could be shown for salicylic acid, jasmonic acid and ethylene in the latter resistance reaction. The RPB1 locus was narrowed down to 71 kb on chromosome 1, where three pseudogenes and 13 coding sequences are located. Six of them showed cosegregation with RPB1. None of these sequences have similarities to identified resistance genes or other known genes. Ten coding sequences were expressed, but CDS9 was exclusively expressed in the resistant ecotype Tsu-0.

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Molecular Analysis of Antibiotic Resistance Gene Clusters in Vibrio cholerae O139 and O1 SXT Constins

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.45.11.2991-3000.2001 ◽

2001 ◽

Vol 45 (11) ◽

pp. 2991-3000 ◽

Cited By ~ 210

Author(s):

Bianca Hochhut ◽

Yasmin Lotfi ◽

Didier Mazel ◽

Shah M. Faruque ◽

Roger Woodgate ◽

...

Keyword(s):

Antibiotic Resistance ◽

Vibrio Cholerae ◽

Resistance Gene ◽

Resistance Genes ◽

Dna Sequences ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Gene Clusters ◽

Vibrio Cholerae O139 ◽

El Tor

ABSTRACT Many recent Asian clinical Vibrio cholerae E1 Tor O1 and O139 isolates are resistant to the antibiotics sulfamethoxazole (Su), trimethoprim (Tm), chloramphenicol (Cm), and streptomycin (Sm). The corresponding resistance genes are located on large conjugative elements (SXT constins) that are integrated into prfC on the V. cholerae chromosome. We determined the DNA sequences of the antibiotic resistance genes in the SXT constin in MO10, an O139 isolate. In SXTMO10, these genes are clustered within a composite transposon-like structure found near the element's 5′ end. The genes conferring resistance to Cm (floR), Su (sulII), and Sm (strA and strB) correspond to previously described genes, whereas the gene conferring resistance to Tm, designated dfr18, is novel. In some other O139 isolates the antibiotic resistance gene cluster was found to be deleted from the SXT-related constin. The El Tor O1 SXT constin, SXTET, does not contain the same resistance genes as SXTMO10. In this constin, the Tm resistance determinant was located nearly 70 kbp away from the other resistance genes and found in a novel type of integron that constitutes a fourth class of resistance integrons. These studies indicate that there is considerable flux in the antibiotic resistance genes found in the SXT family of constins and point to a model for the evolution of these related mobile elements.

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Apple Contains Receptor-like Genes Homologous to the Cladosporium fulvum Resistance Gene Family of Tomato with a Cluster of Genes Cosegregating with Vf Apple Scab Resistance

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2001.14.4.508 ◽

2001 ◽

Vol 14 (4) ◽

pp. 508-515 ◽

Cited By ~ 111

Author(s):

Boris A. Vinatzer ◽

Andrea Patocchi ◽

Luca Gianfranceschi ◽

Stefano Tartarini ◽

Hong-Bin Zhang ◽

...

Keyword(s):

Gene Family ◽

Resistance Gene ◽

Resistance Genes ◽

Transmembrane Domain ◽

Venturia Inaequalis ◽

Scab Resistance ◽

Common Disease ◽

Resistance Locus ◽

Cladosporium Fulvum ◽

High Quality

Scab caused by the fungal pathogen Venturia inaequalis is the most common disease of cultivated apple (Malus × domestica Borkh.). Monogenic resistance against scab is found in some small-fruited wild Malus species and has been used in apple breeding for scab resistance. Vf resistance of Malus floribunda 821 is the most widely used scab resistance source. Because breeding a high-quality cultivar in perennial fruit trees takes dozens of years, cloning disease resistance genes and using them in the transformation of high-quality apple varieties would be advantageous. We report the identification of a cluster of receptor-like genes with homology to the Cladosporium fulvum (Cf) resistance gene family of tomato on bacterial artificial chromosome clones derived from the Vf scab resistance locus. Three members of the cluster were sequenced completely. Similar to the Cf gene family of tomato, the deduced amino acid sequences coded by these genes contain an extracellular leucine-rich repeat domain and a transmembrane domain. The transcription of three members of the cluster was determined by reverse transcription-polymerase chain reaction to be constitutive, and the transcription and translation start of one member was verified by 5′ rapid amplification of cDNA ends. We discuss the parallels between Cf resistance of tomato and Vf resistance of apple and the possibility that one of the members of the gene cluster is the Vf gene. Cf homologs from other regions of the apple genome also were identified and are likely to present other scab resistance genes.

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Genome-wide Analysis of the Rice Mate Gene Family: Identification, Genomic Organization and Expression Profiles in Response to Abiotic Stresses

10.21203/rs.3.rs-62337/v1 ◽

2020 ◽

Author(s):

Zhixuan Du ◽

Qitao Su ◽

Zheng Wu ◽

Zhou Huang ◽

Jianzhong Bao ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Abiotic Stresses ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Chemical Properties ◽

Motif Analysis ◽

Functional Homology ◽

Exogenous Compounds

Abstract Background: Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice.Results: In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. In addition, physical and chemical properties of the encoded proteins, subcellular localization, chromosome localization, stress-related cis-elements in abiotic stresses were determined, and a phylogenetic analysis and conserved motif analysis were performed. The rice MATE family can be divided into four subfamilies. It is speculated that members of the rice MATE family have many potential functions, such as the transport and accumulation of flavonoids and alkaloids, the extrusion of plant or exogenous compounds, the regulation of disease resistance and the response to abiotic stress, based on the proteins and cis-acting elements with known functions in the same subfamily. Analysis of gene expression showed that most of the genes were constitutively expressed. Furthermore, eight MATE genes were chosen for qRT-PCR-based analysis and showed differential expression patterns in response to salt and drought stress. Conclusions: Phylogenetic analysis, element prediction, expression data and homology with other species provided strong evidence for functional homology of MATE gene in rice. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

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Phylogeny and Genomic Organization of the TIR and Non-TIR NBS-LRR Resistance Gene Family in Medicago truncatul

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2002.15.6.529 ◽

2002 ◽

Vol 15 (6) ◽

pp. 529-539 ◽

Cited By ~ 75

Author(s):

Hongyan Zhu ◽

Steven B. Cannon ◽

Nevin D. Young ◽

Douglas R. Cook

Keyword(s):

Phylogenetic Analysis ◽

Resistance Gene ◽

Resistance Genes ◽

Physical Mapping ◽

Genomic Organization ◽

Interleukin 1 ◽

Legume Species ◽

Leucine Rich Repeat ◽

Model Legume ◽

Physical Clusters

Sequences homologous to the nucleotide binding site (NBS) domain of NBS-leucine-rich repeat (LRR) resistance genes were retrieved from the model legume M. truncatula through several methods. Phylogenetic analysis classified these sequences into TIR (toll and interleukin-1 receptor) and non-TIR NBS subfamilies and further subclassified them into several well-defined clades within each subfamily. Comparison of M. truncatula NBS sequences with those from several closely related legumes, including members of the tribes Trifoleae, Viceae, and Phaseoleae, reveals that most clades contain sequences from multiple legume species. Moreover, sequences from species within the closely related Trifoleae and Viceae tribes (e.g., Medicago and Pisum spp.) tended to be cophyletic and distinct from sequences of Phaseoleae species (e.g., soybean and bean). These results suggest that the origin of major clades within the NBS-LRR family predate radiation of these Papilionoid legumes, while continued diversification of these sequences mirrors speciation within this legume subfamily. Detailed genetic and physical mapping of both TIR and non-TIR NBS sequences in M. truncatula reveals that most NBS sequences are organized into clusters, and few, if any, clusters contain both TIR and non-TIR sequences. Examples were found, however, of physical clusters that contain sequences from distinct phylogenetic clades within the TIR or non-TIR subfamilies. Comparative mapping reveals several blocks of resistance gene loci that are syntenic between M. truncatula and soybean and between M. truncatula and pea.

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Intron Loss and Gain During Evolution of the Catalase Gene Family in Angiosperms

Genetics ◽

10.1093/genetics/149.1.355 ◽

1998 ◽

Vol 149 (1) ◽

pp. 355-365

Author(s):

Julia A Frugoli ◽

Mark A McPeek ◽

Terry L Thomas ◽

C Robertson McClung

Keyword(s):

Arabidopsis Thaliana ◽

Gene Family ◽

Gene Families ◽

Intron Loss ◽

Flowering Plants ◽

Chromosome 1 ◽

Chromosome 4 ◽

Splice Sites ◽

Catalase Gene ◽

Sequence Of Events

Abstract Angiosperms (flowering plants), including both monocots and dicots, contain small catalase gene families. In the dicot, Arabidopsis thaliana, two catalase (CAT) genes, CAT1 and CAT3, are tightly linked on chromosome 1 and a third, CAT2, which is more similar to CAT1 than to CAT3, is unlinked on chromosome 4. Comparison of positions and numbers of introns among 13 angiosperm catalase genomic sequences indicates that intron positions are conserved, and suggests that an ancestral catalase gene common to monocots and dicots contained seven introns. Arabidopsis CAT2 has seven introns; both CAT1 and CAT3 have six introns in positions conserved with CAT2, but each has lost a different intron. We suggest the following sequence of events during the evolution of the Arabidopsis catalase gene family. An initial duplication of an ancestral catalase gene gave rise to CAT3 and CAT1. CAT1 then served as the template for a second duplication, yielding CAT2. Intron losses from CAT1 and CAT3 followed these duplications. One subclade of monocot catalases has lost all but the 5′-most and 3′-most introns, which is consistent with a mechanism of intron loss by replacement of an ancestral intron-containing gene with a reverse-transcribed DNA copy of a fully spliced mRNA. Following this event of concerted intron loss, the Oryza sativa (rice, a monocot) CAT1 lineage acquired an intron in a novel position, consistent with a mechanism of intron gain at proto-splice sites.

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NLR Diversity and Candidate Fusiform Rust Resistance Genes in Loblolly Pine

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab421 ◽

2021 ◽

Author(s):

Daniel Ence ◽

Katherine E Smith ◽

Shenghua Fan ◽

Leandro Gomide Neves ◽

Robin Paul ◽

...

Keyword(s):

Gene Family ◽

Resistance Gene ◽

Loblolly Pine ◽

Resistance Genes ◽

Rust Resistance ◽

De Novo ◽

Gene Diversity ◽

Gene Family Evolution ◽

Fusiform Rust ◽

Geographic Diversity

Abstract Resistance to fusiform rust disease in loblolly pine (Pinus taeda) is a classic gene-for-gene system. Early resistance gene mapping in the P. taeda family 10-5 identified RAPD markers for a major fusiform rust resistance gene, Fr1. More recently SNP markers associated with resistance were mapped to a full-length gene model in the loblolly pine genome encoding for an NLR protein. NLR genes are one of the most abundant gene families in plant genomes and are involved in effector-triggered immunity. Inter- and intraspecies studies of NLR gene diversity and expression have resulted in improved disease resistance. To characterize NLR gene diversity and discover potential resistance genes, we assembled de novo transcriptomes from 92 loblolly genotypes from across the natural range of the species. In these transcriptomes, we identified novel NLR transcripts that are not present in the loblolly pine reference genome and found significant geographic diversity of NLR genes providing evidence of gene family-evolution. We designed capture probes for these NLRs to identify and map SNPs that stably cosegregate with resistance to the SC20-21 isolate of Cronartium quercuum f.sp. fusiforme (Cqf) in half-sib progeny of the 10-5 family. We identified ten SNPs and two QTL associated with resistance to SC20-21 Cqf. The geographic diversity of NLR genes provides evidence of NLR gene family-evolution in loblolly pine. The SNPs associated with rust resistance provide a resource to enhance breeding and deployment of resistant pine seedlings.

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Cloning, Characterization, and Evolution of the NBS-LRR-Encoding Resistance Gene Analogue Family in Polyploid Cotton (Gossypium hirsutum L.)

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2004.17.11.1234 ◽

2004 ◽

Vol 17 (11) ◽

pp. 1234-1241 ◽

Cited By ~ 44

Author(s):

Limei He ◽

Chunguang Du ◽

Lina Covaleda ◽

Zhanyou Xu ◽

A. Forest Robinson ◽

...

Keyword(s):

Gene Family ◽

Resistance Gene ◽

Resistance Genes ◽

Plant Disease Resistance ◽

Index Analysis ◽

Polymerase Chain ◽

Encoding Gene ◽

Plant Disease Resistance Genes ◽

Encoding Genes ◽

Selection Of

The nucleotide-binding site-leucine-rich repeat (NBS-LRR)-encoding gene family has attracted much research interest because approximately 75% of the plant disease resistance genes that have been cloned to date are from this gene family. We cloned the NBS-LRR-encoding genes from polyploid cotton by a polymerase chain reaction-based approach. A sample of 150 clones was selected from the NBS-LRR gene sequence library and was sequenced, and 61 resistance gene analogs (RGA) were identified. Sequence analysis revealed that RGA are abundant and highly diverged in the cotton genome and could be categorized into 10 distinct subfamilies based on the similarities of their nucleotide sequences. The numbers of members vary many fold among different subfamilies, and gene index analysis showed that each of the subfamilies is at a different stage of RGA family evolution. Genetic mapping of a selection of RGA indicates that the RGA reside on a limited number of the cotton chromosomes, with those from a single subfamily tending to cluster and two of the RGA loci being colocalized with the cotton bacterial blight resistance genes. The distribution of RGA between the two subgenomes A and D of cotton is uneven, with RGA being more abundant in the A subgenome than in the D subgenome. The data provide new insights into the organization and evolution of the NBS-LRR-encoding RGA family in polyploid plants.

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