Genomic Organization, Rapid Evolution and Meiotic Instability of Nucleotide-Binding-Site-Encoding Genes in a New Fruit Crop, “Chestnut Rose”

Sweetpotato, Ipomoea batatas (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that IbNBS75, IbNBS219, and IbNBS256 respond to stem nematode infection; IbNBS240, IbNBS90, and IbNBS80 respond to cold stress, while IbNBS208, IbNBS71, and IbNBS159 respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.

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Dm3 Is One Member of a Large Constitutively Expressed Family of Nucleotide Binding Site—Leucine-Rich Repeat Encoding Genes

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2002.15.3.251 ◽

2002 ◽

Vol 15 (3) ◽

pp. 251-261 ◽

Cited By ~ 62

Author(s):

Katherine A. Shen ◽

Doris B. Chin ◽

Rosa Arroyo-Garcia ◽

Oswaldo E. Ochoa ◽

Dean O. Lavelle ◽

...

Keyword(s):

Binding Site ◽

Downy Mildew ◽

Point Mutations ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Leucine Rich Repeat ◽

Intron Splice ◽

Major Cluster ◽

Wide Range ◽

Encoding Genes

The major cluster of resistance genes in lettuce cv. Diana contains approximately 32 nucleotide binding site—leucine-rich repeat encoding genes. Previous molecular dissection of this complex region had identified a large gene, RGC2B, as a candidate for encoding the downy mildew resistance gene, Dm3. This article describes genetic and transgenic complementation data that demonstrated RGC2B is necessary and sufficient to confer resistance with Dm3 specificity. Ethylmethanesulphonate was used to induce mutations to downy mildew susceptibility in cv. Diana (Dm1, Dm3, Dm7, and Dm8). Nineteen families were identified with a complete loss of resistance in one of the four resistance specificities. Sequencing revealed a variety of point mutations in RGC2B in the six dm3 mutants. Losses of resistance were due to single changes in amino acid sequence or a change in an intron splice site. These mutations did not cluster in any particular region of RGC2B. A full-length ge-nomic copy of RGC2B was isolated from a lambdaphage library and introduced into two genotypes of lettuce. Trans-genics expressing RGC2B exhibited resistance to all isolates expressing Avr3 from a wide range of geographical origins. In a wildtype Dm3-expressing genotype, many of the RGC2 family members are expressed at low levels throughout the plant.

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Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

PLANT PHYSIOLOGY ◽

10.1104/pp.111.181990 ◽

2011 ◽

Vol 157 (2) ◽

pp. 757-769 ◽

Cited By ~ 122

Author(s):

Ya-Long Guo ◽

Joffrey Fitz ◽

Korbinian Schneeberger ◽

Stephan Ossowski ◽

Jun Cao ◽

...

Keyword(s):

Binding Site ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Leucine Rich Repeat ◽

Genome Wide ◽

Encoding Genes

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Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes inBrachypodium distachyon

Comparative and Functional Genomics ◽

10.1155/2012/418208 ◽

2012 ◽

Vol 2012 ◽

pp. 1-12 ◽

Cited By ~ 32

Author(s):

Shenglong Tan ◽

Song Wu

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Resistance Genes ◽

Brachypodium Distachyon ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Disease Resistance Genes ◽

Protein Motifs ◽

Wide Range ◽

Encoding Genes

Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Many R-genes have been identified in various plant species. However, little is known about the NBS-encoding genes inBrachypodium distachyon. In this study, using computational analysis of theB. distachyongenome, we identified 126 regular NBS-encoding genes and characterized them on the bases of structural diversity, conserved protein motifs, chromosomal locations, gene duplications, promoter region, and phylogenetic relationships. EST hits and full-length cDNA sequences (fromBrachypodiumdatabase) of 126 R-like candidates supported their existence. Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS. Further expression analysis of the regular NBS-encoding genes inBrachypodiumdatabase revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue.

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Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.)

Genes ◽

10.3390/genes9080384 ◽

2018 ◽

Vol 9 (8) ◽

pp. 384 ◽

Cited By ~ 9

Author(s):

Surendra Neupane ◽

Ethan J. Andersen ◽

Achal Neupane ◽

Madhav P. Nepal

Keyword(s):

Binding Site ◽

Functional Divergence ◽

Crop Improvement ◽

Functional Characterization ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Leucine Rich Repeat ◽

Genome Wide ◽

A Genome ◽

Encoding Genes

Nucleotide Binding Site—Leucine-Rich Repeat (NBS-LRR) genes encode disease resistance proteins involved in plants’ defense against their pathogens. Although sunflower is affected by many diseases, only a few molecular details have been uncovered regarding pathogenesis and resistance mechanisms. Recent availability of sunflower whole genome sequences in publicly accessible databases allowed us to accomplish a genome-wide identification of Toll-interleukin-1 receptor-like Nucleotide-binding site Leucine-rich repeat (TNL), Coiled Coil (CC)-NBS-LRR (CNL), Resistance to powdery mildew 8 (RPW8)-NBS-LRR (RNL) and NBS-LRR (NL) protein encoding genes. Hidden Markov Model (HMM) profiling of 52,243 putative protein sequences from sunflower resulted in 352 NBS-encoding genes, among which 100 genes belong to CNL group including 64 genes with RX_CC like domain, 77 to TNL, 13 to RNL, and 162 belong to NL group. We also identified signal peptides and nuclear localization signals present in the identified genes and their homologs. We found that NBS genes were located on all chromosomes and formed 75 gene clusters, one-third of which were located on chromosome 13. Phylogenetic analyses between sunflower and Arabidopsis NBS genes revealed a clade-specific nesting pattern in CNLs, with RNLs nested in the CNL-A clade, and species-specific nesting pattern for TNLs. Surprisingly, we found a moderate bootstrap support (BS = 50%) for CNL-A clade being nested within TNL clade making both the CNL and TNL clades paraphyletic. Arabidopsis and sunflower showed 87 syntenic blocks with 1049 high synteny hits between chromosome 5 of Arabidopsis and chromosome 6 of sunflower. Expression data revealed functional divergence of the NBS genes with basal level tissue-specific expression. This study represents the first genome-wide identification of NBS genes in sunflower paving avenues for functional characterization and potential crop improvement.

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Comparative Genetics of Nucleotide Binding Site-Leucine Rich Repeat Resistance Gene Homologues in the Genomes of Two Dicotyledons: Tomato and Arabidopsis

Genetics ◽

10.1093/genetics/155.1.309 ◽

2000 ◽

Vol 155 (1) ◽

pp. 309-322 ◽

Cited By ~ 6

Author(s):

Qilin Pan ◽

Yong-Sheng Liu ◽

Ofra Budai-Hadrian ◽

Marianne Sela ◽

Lea Carmel-Goren ◽

...

Keyword(s):

Binding Site ◽

Plant Disease Resistance ◽

Rapid Evolution ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Genetic Maps ◽

R Gene ◽

Leucine Rich Repeat ◽

Plant Families ◽

Plant Pathogen Interactions

Abstract The presence of a single resistance (R) gene allele can determine plant disease resistance. The protein products of such genes may act as receptors that specifically interact with pathogen-derived factors. Most functionally defined R-genes are of the nucleotide binding site-leucine rich repeat (NBS-LRR) supergene family and are present as large multigene families. The specificity of R-gene interactions together with the robustness of plant-pathogen interactions raises the question of their gene number and diversity in the genome. Genomic sequences from tomato showing significant homology to genes conferring race-specific resistance to pathogens were identified by systematically “scanning” the genome using a variety of primer pairs based on ubiquitous NBS motifs. Over 70 sequences were isolated and 10% are putative pseudogenes. Mapping of the amplified sequences on the tomato genetic map revealed their organization as mixed clusters of R-gene homologues that showed in many cases linkage to genetically characterized tomato resistance loci. Interspecific examination within Lycopersicon showed the existence of a null allele. Consideration of the tomato and potato comparative genetic maps unveiled conserved syntenic positions of R-gene homologues. Phylogenetic clustering of R-gene homologues within tomato and other Solanaceae family members was observed but not with R-gene homologues from Arabidopsis thaliana. Our data indicate remarkably rapid evolution of R-gene homologues during diversification of plant families.

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