Journal Article•
Molecular cloning, characterization and transcriptional variability study of resistance gene candidates from wild Curcuma spp. for resistance against Pythium aphanidermatum.
TL;DR: A PCR mediated approach has been made using degenerate primers designed on conserved region (P-loop and GLPL) of the NBS domain from R-genes that provides the source for cloning analogous sequences called resistance gene candidates (RGCs) from three wild turmeric plants resistant or susceptible to Pythium aphanidermatum.
Abstract: The genetic base of preferred turmeric (Curcuma longa L.) genotypes has eroded due to their continuous domestication through exclusive vegetative routes thus making them highly susceptible to various pests and pathogens. Molecular cloning of resistance related sequences from wild genotypes can result in efficient turmeric improvement by evolving more effective resistance specificities compared to cultigens. In this study, a PCR mediated approach has been made using degenerate primers designed on conserved region (P-loop and GLPL) of the NBS domain from R-genes that provides the source for cloning analogous sequences called resistance gene candidates (RGCs) from three wild turmeric- Curcuma aromatica, Curcuma angustifolia and Curcuma zedoaria. Twenty-one wild turmeric RGCs were isolated and grouped into four phenetic classes. A strong amino acid identity ranging from 41 to 53% together with presence of internal conserved motifs provided evidence that the isolated RGCs belong to the non-toll interleukin receptor (non-TIR) NBS-LRR R-gene sub-family. Southern hybridization showed a high copy representation of turmeric RGCs. Expression variability of wild turmeric RGCs was analyzed through reverse transcription PCR in root tissues of the three wild turmeric plants resistant or susceptible to Pythium aphanidermatum. Cap12 and Can12 showed a constitutive expression in both resistant and susceptible plants of Curcuma aromatica and Curcuma angustifolia respectively while Czp11 expression was realized only in Pythium aphanidermatum resistant lines of Curcuma zedoaria as well as Curcuma longa L. This result can pave way towards the identification and characterization of a potential Pythium aphanidermatum resistance gene in turmeric.
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TL;DR: Structural and phylogenetic analyses grouped CzR1 within the non-TIR (homology to Toll/interleukin-1 receptors) subclass of NBS-LRR R-genes and semi quantitative RT-PCR analysis showed constitutive expression of CZR1 which gets significantly upregulated in response to infection by different strains of P. aphanidermatum.
18 citations
TL;DR: In this article , degenerate primers were used for cloning and characterization of NBS-LRR type resistant gene from betelvine against anthracnose disease, and a strong amino acid identity ranging from 90.38 to 97.75% and the presence of internal conserved motifs, provided evidence that the identified resistance gene analogs (RGAs) belong to the non-TIR NBS LRR class of R genes.
References
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TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
57,055 citations
"Molecular cloning, characterization..." refers methods in this paper
...The phylogenetic tree was constructed by the neighbor-joining method (Saitou and Nei, 1987) using the NJ algorithm implemented in the Molecular Evolutionary Genetics Analysis (MEGA) software package version 2....
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...The phylogenetic tree was constructed by the neighbor-joining method (Saitou and Nei, 1987) using the NJ algorithm implemented in the Molecular Evolutionary Genetics Analysis (MEGA) software package version 2.1 with the Poisson correction (Kumar et al. 2001)....
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TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.
38,522 citations
TL;DR: MEGA2 vastly extends the capabilities of MEGA version 1 by facilitating analyses of large datasets, enabling creation and analyses of groups of sequences, and expanding the repertoire of statistical methods for molecular evolutionary studies.
Abstract: Summary: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. Availability: http://www.megasoftware.net.
6,184 citations
"Molecular cloning, characterization..." refers methods in this paper
...The phylogenetic tree was constructed by the neighbor-joining method (Saitou and Nei, 1987) using the NJ algorithm implemented in the Molecular Evolutionary Genetics Analysis (MEGA) software package version 2.1 with the Poisson correction (Kumar et al. 2001)....
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TL;DR: The current knowledge of recognition-dependent disease resistance in plants is reviewed, and a few crucial concepts are included to compare and contrast plant innate immunity with that more commonly associated with animals.
Abstract: Plants cannot move to escape environmental challenges. Biotic stresses result from a battery of potential pathogens: fungi, bacteria, nematodes and insects intercept the photosynthate produced by plants, and viruses use replication machinery at the host's expense. Plants, in turn, have evolved sophisticated mechanisms to perceive such attacks, and to translate that perception into an adaptive response. Here, we review the current knowledge of recognition-dependent disease resistance in plants. We include a few crucial concepts to compare and contrast plant innate immunity with that more commonly associated with animals. There are appreciable differences, but also surprising parallels.
3,814 citations
"Molecular cloning, characterization..." refers background in this paper
...About 75% of plant R-genes encode proteins with a nucleotide-binding site and leucine-rich repeat (NBS-LRR) domains that confer resistance to various pests and pathogens including bacteria, fungi, viruses, insects and nematodes (Dangl and Jones, 2001)....
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TL;DR: The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges.
Abstract: The Arabidopsis genome contains ∼200 genes that encode proteins with similarity to the nucleotide binding site and other domains characteristic of plant resistance proteins. Through a reiterative process of sequence analysis and reannotation, we identified 149 NBS-LRR–encoding genes in the Arabidopsis (ecotype Columbia) genomic sequence. Fifty-six of these genes were corrected from earlier annotations. At least 12 are predicted to be pseudogenes. As described previously, two distinct groups of sequences were identified: those that encoded an N-terminal domain with Toll/Interleukin-1 Receptor homology (TIR-NBS-LRR, or TNL), and those that encoded an N-terminal coiled-coil motif (CC-NBS-LRR, or CNL). The encoded proteins are distinct from the 58 predicted adapter proteins in the previously described TIR-X, TIR-NBS, and CC-NBS groups. Classification based on protein domains, intron positions, sequence conservation, and genome distribution defined four subgroups of CNL proteins, eight subgroups of TNL proteins, and a pair of divergent NL proteins that lack a defined N-terminal motif. CNL proteins generally were encoded in single exons, although two subclasses were identified that contained introns in unique positions. TNL proteins were encoded in modular exons, with conserved intron positions separating distinct protein domains. Conserved motifs were identified in the LRRs of both CNL and TNL proteins. In contrast to CNL proteins, TNL proteins contained large and variable C-terminal domains. The extant distribution and diversity of the NBS-LRR sequences has been generated by extensive duplication and ectopic rearrangements that involved segmental duplications as well as microscale events. The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges.
1,503 citations
"Molecular cloning, characterization..." refers background in this paper
...Thus, the RGCs can not only act as useful tools for the isolation of full-length resistance genes conferring both qualitative and quantitative resistance to different pathogens but also provide vital information about the organization, expression and evolution of R-genes (Pan et al., 2000; Bai et al., 2002; Meyers et al., 2003; Deng et al., 2003; He et al., 2004)....
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...…full-length resistance genes conferring both qualitative and quantitative resistance to different pathogens but also provide vital information about the organization, expression and evolution of R-genes (Pan et al., 2000; Bai et al., 2002; Meyers et al., 2003; Deng et al., 2003; He et al., 2004)....
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...The NBS-LRR R-genes are abundant in plant genomes with approximately 150 and 600 isolated from Arabidopsis and rice respectively (Meyers et al., 2003; Zhou et al., 2004)....
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