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Genes 2017, 8(10), 249; doi:10.3390/genes8100249

Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species

1
Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
2
Sanford PROMISE, Sanford Research, Sioux Falls, SD 57104, USA
*
Author to whom correspondence should be addressed.
Received: 12 July 2017 / Revised: 14 September 2017 / Accepted: 20 September 2017 / Published: 30 September 2017
(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)
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Abstract

Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence. View Full-Text
Keywords: nucleotide-binding site, leucine-rich repeat; NBS-LRR; evolutionary divergence; gene clustering; gene duplication; R genes; plant defense nucleotide-binding site, leucine-rich repeat; NBS-LRR; evolutionary divergence; gene clustering; gene duplication; R genes; plant defense
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Nepal, M.P.; Andersen, E.J.; Neupane, S.; Benson, B.V. Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. Genes 2017, 8, 249.

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