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Not AvailableHere, we isolated and characterized peanut bacterial artificial chromosomes (BACs) containing a high density of R genes. Analysis of two genomic regions identified several TIR‐NBS‐LRR (Toll‐interleukin‐1 receptor, nucleotide‐binding site, leucine‐rich repeat) resistance gene analogs or gene fragments. We reconstructed their evolutionary history characterized by tandem duplications, possibly facilitated by transposon activities. We found evidence of both intergenic and intragenic gene conversions and unequal crossing‐over, which may be driving forces underlying the functional evolution of resistance.Not Availabl

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Lead ArticleMicroRNAs (miRNAs) are small regulatory RNAs that play a defining role in post-transcriptional gene silencing of eukaryotes by either mRNA cleavage or translational inhibition. Plant miRNAs have been implicated in innumerable growth and developmental processes that extend beyond their ability to respond to biotic and abiotic stresses. Active in an organism’s immune defence response, host miRNAs display a propensity to target viral genomes. During viral invasion, these virus-targeting miRNAs can be identified by their altered expression. All the while, pathogenic viruses, as a result of their long-term interaction with plants, have been evolving viral suppressors of RNA silencing (VSRs), as well as viral-encoded miRNAs as a counter-defence strategy. However, the gene silencing attribute of miRNAs has been ingeniously manipulated to down-regulate the expression of any gene of interest, including VSRs, in artificial miRNA (amiRNA)-based transgenics. Since we currently have a better understanding of the intricacies of miRNA-mediated gene regulation in plant–virus interactions, the majority of miRNAs manipulated to confer antiviral resistance to date are in plants. This review will share the insights gained from the studies of plant-virus combat and from the endeavour to manipulate miRNAs, including prospective challenges in the context of the evolutionary dynamics of the viral genome. Next generation sequencing technologies and bioinformatics analysis will further delineate the molecular details of host–virus interactions. The need for appropriate environmental risk assessment principles specific to amiRNA-based virus resistance is also discussed.Not Availabl

Vector Quantized Spectral Clustering Applied to Whole Genome Sequences of Plants

We develop a Vector Quantized Spectral Clustering (VQSC) algorithm that is a combination of spectral clustering (SC) and vector quantization (VQ) sampling for grouping genome sequences of plants. The inspiration here is to use SC for its accuracy and VQ to make the algorithm computationally cheap (the complexity of SC is cubic in terms of the input size). Although the combination of SC and VQ is not new, the novelty of our work is in developing the crucial similarity matrix in SC as well as use of k -medoids in VQ, both adapted for the plant genome data. For Soybean, we compare our approach with commonly used techniques like Un-weighted Pair Graph Method with Arithmetic mean (UPGMA) and Neighbor Joining (NJ). Experimental results show that our VQSC outperforms both these techniques significantly in terms of cluster quality (average improvement of 21% over UPGMA and 24% over NJ) as well as time complexity (order of magnitude faster than both UPGMA and NJ)

MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species

Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology regions at once. However, the applications are not fully convenient for biologists because some of them do not include the function of synteny determination but visualize the multiple synteny plots by allowing users to upload their synteny data by determining the synteny based only on BLAST similarity information, with some algorithms not designed for synteny determination. Here, we introduce a web application that determines and visualizes multiple synteny from two types of files, simplified browser extensible data and protein sequence file by MCScanX algorithm, which have been used in many synteny studies

Evolution of a Complex Disease Resistance Gene Cluster in Diploid Phaseolus and Tetraploid Glycine1[W][OA]

We used a comparative genomics approach to investigate the evolution of a complex nucleotide-binding (NB)-leucine-rich repeat (LRR) gene cluster found in soybean (Glycine max) and common bean (Phaseolus vulgaris) that is associated with several disease resistance (R) genes of known function, including Rpg1b (for Resistance to Pseudomonas glycinea1b), an R gene effective against specific races of bacterial blight. Analysis of domains revealed that the amino-terminal coiled-coil (CC) domain, central nucleotide-binding domain (NB-ARC [for APAF1, Resistance genes, and CED4]), and carboxyl-terminal LRR domain have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare. In contrast, interparalogue exchanges involving the CC and LRR domains were common, consistent with both of these regions coevolving with pathogens. Residues under positive selection were overrepresented within the predicted solvent-exposed face of the LRR domain, although several also were detected within the CC and NB-ARC domains. Superimposition of these latter residues onto predicted tertiary structures revealed that the majority are located on the surface, suggestive of a role in interactions with other domains or proteins. Following polyploidy in the Glycine lineage, NB-LRR genes have been preferentially lost from one of the duplicated chromosomes (homeologues found in soybean), and there has been partitioning of NB-LRR clades between the two homeologues. The single orthologous region in common bean contains approximately the same number of paralogues as found in the two soybean homeologues combined. We conclude that while polyploidization in Glycine has not driven a stable increase in family size for NB-LRR genes, it has generated two recombinationally isolated clusters, one of which appears to be in the process of decay

Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean1[W][OA]

The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues