An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion

Liu, Yang; Zeng, Zhen; Zhang, Yanmei; Li, Qian; Jiang, Xing-Mei; Jiang, Zhen; Tang, Jihong; Chen, Dijun; Wang, Qiang; Chen, Jian-Qun; Shao, Zhu‐Qing

doi:10.1016/j.molp.2021.08.001

Cited by 90 publications

(124 citation statements)

References 76 publications

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“…The results showed that 581 of the 582 S. cereale NBS-LRR genes belong to the CNL subclass, whereas only one gene was classified to the ADR1-lineage of the RNL subclass. This is consistent with the studies on H. vulgare and T. urartu, which also identified only one RNL gene in each of the two genomes Liu et al, 2021), mirroring the conserved function of RNL genes. No TNL gene was detected in the S. cereale genome as have been observed in H. vulgare and T. urartu, supporting the theory that TNL genes were lost in the common ancestor of monocots (Liu et al, 2021).…”

Section: Identification Of Nbs-lrr Genes In the S Cereale Genomesupporting

confidence: 91%

“…We identified 582 NBS-LRR genes (Supplementary Table S1) in the S. cereale genome accounting for more than 0.6% of the 86,991 annotated protein coding genes. The number of NBS-LRR genes in S. cereale is greater than that in the H. vulgare genome (467 genes) and slightly more than that in the diploid wheat T. urartu genome (537 genes) Liu et al, 2021). This suggests that it is an important resource for Triticeae R gene mining.…”

Section: Identification Of Nbs-lrr Genes In the S Cereale Genomementioning

confidence: 96%

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Genome-wide Identification and Evolutionary Analysis of NBS-LRR Genes From Secale cereale

et al. 2021

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Secale cereale is an important crop in the Triticeae tribe of the Poaceae family, and it has unique agronomic characteristics and genome properties. It possesses resistance to many diseases and serves as an important resource for the breeding of other Triticeae crops. We performed a genome-wide study on S. cereale to identify the largest group of plant disease resistance genes (R genes), the nucleotide-binding site-leucine-rich repeat receptor (NBS-LRR) genes. In its genome, 582 NBS-LRR genes were identified, including one from the RNL subclass and 581 from the CNL subclass. The NBS-LRR gene number in the S. cereale genome is greater than that in barley and the diploid wheat genomes. S. cereale chromosome 4 contains the largest number of NBS-LRR genes among the seven chromosomes, which is different from the pattern in barley and the genomes B and D of wheat but similar to that in the genome A of wheat. Further synteny analysis suggests that more NBS-LRR genes on chromosome 4 have been inherited from a common ancestor by S. cereale and the wheat genome A than the wheat genomes B and D. Phylogenetic analysis revealed that at least 740 NBS-LRR lineages are present in the common ancestor of S. cereale, Hordeum vulgare and Triticum urartu. However, most of them have only been inherited by one or two species, with only 65 of them preserved in all three species. The S. cereale genome inherited 382 of these ancestral NBS-LRR lineages, but 120 of them have been lost in both H. vulgare and T. urartu. This study provides the full NBS-LRR profile of the S. cereale genome, which is a resource for S. cereale breeding and indicates that S. cereale can be an important material for the molecular breeding of other Triticeae crops.

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Section: Identification Of Nbs-lrr Genes In the S Cereale Genomesupporting

confidence: 91%

Section: Identification Of Nbs-lrr Genes In the S Cereale Genomementioning

confidence: 96%

Genome-wide Identification and Evolutionary Analysis of NBS-LRR Genes From Secale cereale

et al. 2021

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“…Genome sequences and annotation files of S. cereale, T. aestivum and H. vulgare were downloaded from https://bigd.big.ac.cn/, https://ftp.ensemblgenomes.org/pub/plants/release-51/fasta/ triticum_aestivum/dna/, and http://doi.org/10.5447/ipk/2021/ 3, respectively. The NBS-LRR genes of T. aestivum, T. urartu and H. vulgare were retrieved from previous studies Liu et al, 2021).…”

Section: Data Used In This Studymentioning

confidence: 99%

“…Chromosomes 1, 3, 5, 6 and 7 have 77, 74, 71, 104 and 61 NBS-LRR genes, respectively. We also compared the chromosome distribution pattern of NBS-LRR genes in the S. cereale genome with that in the barley and wheat genomes Liu et al, 2021), because the three species have the same number of chromosomes and have only diverged from each other for about 10 myr. Since the diploid wheat T. urartu with AA genome does not have a chromosomal level gff annotation file, we used the data of the hexaploid wheat T. aestivum, which contain information of all three sets of chromosomes (AABBDD) of wheat (Liu et al, 2021).…”

Section: Chromosomal Distribution Of Nbs-lrr Genes In the S Cereale Genomementioning

confidence: 99%

“…We also compared the chromosome distribution pattern of NBS-LRR genes in the S. cereale genome with that in the barley and wheat genomes Liu et al, 2021), because the three species have the same number of chromosomes and have only diverged from each other for about 10 myr. Since the diploid wheat T. urartu with AA genome does not have a chromosomal level gff annotation file, we used the data of the hexaploid wheat T. aestivum, which contain information of all three sets of chromosomes (AABBDD) of wheat (Liu et al, 2021). The results showed that chromosome 4, which has the largest number of NBS-LRR genes among all chromosomes in S. cereale, only has 16, 23 and 26 NBS-LRR genes in barley and the B and D genomes of wheat, representing the chromosome with the fewest NBS-LRR genes in these genomes.…”

Section: Chromosomal Distribution Of Nbs-lrr Genes In the S Cereale Genomementioning

confidence: 99%

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Co-expression network analysis and identification of core genes in the interaction between wheat and Puccinia striiformis f. sp. tritici

Wang,

Zhang,

Chen

et al. 2024

Arch Microbiol

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The epidemic of stripe rust, caused by the pathogen Puccinia Striiformis f. sp. tritici (Pst), would reduce wheat (Triticum aestivum) yields seriously. Traditional experimental methods are di cult to discover the interaction between wheat and Pst. Multi-omics data analysis provides a new idea for e ciently mining the interactions between host and pathogen. We used 140 wheat-Pst RNA-Seq data to screen for differentially expressed genes (DEGs) between disease-resistant and disease-susceptible samples, and carried out Gene Ontology (GO) enrichment analysis. Based on this, we constructed a gene coexpression network, identi ed the core genes and interacted gene pairs from the conservative modules. Finally, we checked the distribution of Nucleotide-binding and leucine-rich repeat (NLR) genes in the coexpression network and drew the wheat NLR gene co-expression network. In order to provide accessible information for related researchers, we built a web-based visualization platform to display the data. Based on the analysis, we found that various heat shock proteins (HSPs), protein kinases, and glycosidases frequently appeared in the network. They were likely to be involved in the biological processes of Pst infecting wheat. We also found that HSPs was signi cantly co-expressed in wheat and Pst, suggesting that there might be direct or indirect interactions between them. This study can assist scholars in conducting studies on the pathogenesis and help to advance the investigation of wheat-Pst interaction patterns.

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An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion

Cited by 90 publications

References 76 publications

Genome-wide Identification and Evolutionary Analysis of NBS-LRR Genes From Secale cereale

Genome-wide Identification and Evolutionary Analysis of NBS-LRR Genes From Secale cereale

DataSheet1.PDF

Co-expression network analysis and identification of core genes in the interaction between wheat and Puccinia striiformis f. sp. tritici

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