Characterization of Nucleotide Binding Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses

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

Genetics ◽

10.1534/genetics.107.086421 ◽

2008 ◽

Vol 178 (4) ◽

pp. 2081-2091 ◽

Cited By ~ 8

Author(s):

Qiang Xu ◽

Xiaopeng Wen ◽

Xiuxin Deng

Keyword(s):

Binding Site ◽

Genomic Organization ◽

Rapid Evolution ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Fruit Crop ◽

Chestnut Rose ◽

Encoding Genes ◽

Meiotic Instability

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Identification and characterization of six peroxiredoxin transcripts from mud crab Scylla paramamosain : The first evidence of peroxiredoxin gene family in crustacean and their expression profiles under biotic and abiotic stresses

Molecular Immunology ◽

10.1016/j.molimm.2017.11.029 ◽

2018 ◽

Vol 93 ◽

pp. 223-235 ◽

Cited By ~ 10

Author(s):

Dan-Dan Tu ◽

Yi-Lian Zhou ◽

Wen-Bin Gu ◽

Qi-Hui Zhu ◽

Bin-Peng Xu ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Expression Profiles ◽

Scylla Paramamosain ◽

Mud Crab ◽

Biotic And Abiotic Stresses ◽

Identification And Characterization

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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 characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

10.21203/rs.3.rs-17430/v2 ◽

2020 ◽

Author(s):

Chong Yang ◽

Juanjuan Li ◽

Faisal Islam ◽

Luyang Hu ◽

Jiansu Wang ◽

...

Keyword(s):

Helianthus Annuus ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Crop Improvement ◽

Plant Tolerance ◽

Biotic And Abiotic Stresses

Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes. Therefore, these functional genes related to increasing the plant tolerance or improving the crop quality, could be applied for the crop improvement..

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Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

10.1101/2020.02.08.939736 ◽

2020 ◽

Author(s):

Darlon V. Lantican ◽

Cris Q. Cortaga ◽

Anand Noel C. Manohar ◽

Fe M. dela Cueva ◽

Maria Luz J. Sison

Keyword(s):

Binding Site ◽

Resistance Gene ◽

De Novo ◽

Insect Pests ◽

Expression Profiles ◽

Interleukin 1 ◽

Coiled Coil ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Resistance Gene Analogs

AbstractMango is an economically important fruit crop largely cultivated in the (sub)tropics and thus, is constantly challenged by a myriad of insect pests and diseases. Here, we identified and characterized the resistance gene analogs (RGAs) of mango from de novo assembly of transcriptomic sequences. A core RGA database of mango with 747 protein models was established and classified based on conserved domains and motifs: 53 nucleotide binding site proteins (NBS); 27 nucleotide binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein (TM-CC), and 6 NBS-encoding proteins with other domains. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also determined. Phylogenetic analysis broadly clustered the core RGAs into 6 major clades based on their domain classification, while TM-CC proteins formed subclades all across the tree. The phylogenetic results suggest highly divergent functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms race. From the mango RGA transcripts, 134 unique EST-SSR loci were identified, and primers were designed targeting these potential markers. To date, this is the most comprehensive analysis of mango RGAs which offer a trove of markers for utilization in resistance breeding of mango.

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