NBS-Encoding Genes in Brassica napus Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci

Fu, Ying; Zhang, Yaofeng; Mason, Annaliese S.; Lin, Baogang; Zhang, Dongqing; Yu, Han‐Qing; Fu, Donghui

doi:10.3389/fpls.2019.00026

Cited by 30 publications

(46 citation statements)

References 101 publications

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“…This was higher than the numbers reported by Chalhoub et al (2014) who identified 425, 211 and 274 NLR genes from B. napus B. rapa and B. oleracea respectively using the MAST approach, but with a more stringent E-value. Using HMMER and Pfam based on functional NLR coding domains as search queries and excluding pseudogenes, Fu et al (2019) found 464, 202 and 146 NLR genes respectively resulting in much fewer NLR genes than identified by Alamery et al (2018). Similarly using HMMER and Pfam approaches, Yu et al (2014) identified 206 NLRs from B. rapa and 157 from B. oleracea and Zhang et al (2016) identified 204 from B. rapa.…”

Section: Genome-wide Identification Of Nlr Genes In Brassica Speciesmentioning

confidence: 99%

Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding

2020

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The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome duplications (WGDs) generate abundant gene copies, most of which are lost during genome fractionation. At sub‐genomic levels, some retained copies undergo duplication forming clusters which facilitate rapid evolution through recombination. The number, distribution and genetic variations of the NLR genes vary among Brassica species and within populations suggesting differential selection pressure exerted by pathogen populations throughout the evolutionary history. A study of the evolution of disease resistance genes in agriculturally important plants such as Brassicas helps gain insights into their function and inform the identification of resistance genes for breeding of resistant lines.

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Section: Genome-wide Identification Of Nlr Genes In Brassica Speciesmentioning

confidence: 99%

Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding

2020

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“…Expression analysis in eight tissues, a measurement of the activity and function of genes, showed that NBS genes were highly or preferentially expressed in the root (Fig. 5c), resulting from the greater pressure on the root than the other tissues 43 . Among these NBS genes, the tandem duplication did not show lower expression levels, which was inconsistent with the overall result.…”

Section: Tandem Gene Duplicationmentioning

confidence: 99%

The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant

Chen

Zheng

et al. 2020

Hortic Res

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Tea is one of the most popular nonalcoholic beverages due to its characteristic secondary metabolites with numerous health benefits. Although two draft genomes of tea plant (Camellia sinensis) have been published recently, the lack of chromosome-scale assembly hampers the understanding of the fundamental genomic architecture of tea plant and potential improvement. Here, we performed a genome-wide chromosome conformation capture technique (Hi-C) to obtain a chromosome-scale assembly based on the draft genome of C. sinensis var. sinensis and successfully ordered 2984.7 Mb (94.7%) scaffolds into 15 chromosomes. The scaffold N50 of the improved genome was 218.1 Mb,~157-fold higher than that of the draft genome. Collinearity comparison of genome sequences and two genetic maps validated the high contiguity and accuracy of the chromosome-scale assembly. We clarified that only one Camellia recent tetraploidization event (CRT, 58.9-61.7 million years ago (Mya)) occurred after the core-eudicot common hexaploidization event (146.6-152.7 Mya). Meanwhile, 9243 genes (28.6%) occurred in tandem duplication, and most of these expanded after the CRT event. These gene duplicates increased functionally divergent genes that play important roles in tea-specific biosynthesis or stress response. Sixty-four catechin-and caffeine-related quantitative trait loci (QTLs) were anchored to chromosome assembly. Of these, two catechin-related QTL hotspots were derived from the CRT event, which illustrated that polyploidy has played a dramatic role in the diversification of tea germplasms. The availability of a chromosome-scale genome of tea plant holds great promise for the understanding of genome evolution and the discovery of novel genes contributing to agronomically beneficial traits in future breeding programs.

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“…Focusing on the NLR genes, comparative genomics and transcriptomics analyses supplemented with a database query on B. napus and its progenitors, B. rapa and B. oleracea, revealed many more NBS (also known as NLR) genes in the C sub-genome of B. napus. A number of these genes underly the QTL regions for resistance against Blackleg, Sclerotinia and Clubroot, supporting the concept that the diversification of the R genes likely happened after interspecific hybridisation between B. rapa and B. oleracea [ 90 ].…”

Section: Application Of Omics Technologies In Brassica mentioning

confidence: 72%

“…capitata ) [ 88 ] and the in silico exploration of 641 NBS-LRR-type disease resistance genes in B. napus , together highlighting the genomic distribution and structural variation of these genes in B. napus [ 89 ]. Other examples include the in silico evolutionary study of NBS genes in B. napus , where comparative genomic analysis highlighted the NBS gene’s distribution from its progenitors B. rapa and B. oleracea in relation to the three main Brassica diseases—Blackleg, Clubroot and Sclerotinia [ 90 ]. Coupled with modern bioinformatics tools and the integration of multi-omics data sets, in silico methods are powerful tools that rapidly provide accurate and detailed models to answer various research questions ranging from candidate gene identification to evolutionary pathways of resistance mechanisms in both the Brassica host and the fungal pathogens [ 91 ].…”

Section: Application Of Omics Technologies In Brassica mentioning

confidence: 99%

Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era

Neik

Amas

Barbetti

et al. 2020

Plants

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Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host–pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.

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NBS-Encoding Genes in Brassica napus Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci

Cited by 30 publications

References 101 publications

Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding

Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding

The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant

Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era

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