Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

Zhang, Yanmei; Chen, Min; Sun, Ling; Wang, Yue; Yin, Jianmei; Liu, Jia; Sun, Xiaoqin; Hang, Yue‐Yu

doi:10.3389/fgene.2020.00484

Cited by 35 publications

(32 citation statements)

References 49 publications

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“…Sequence alignment and phylogenetic analysis were performed as described by Shao et al (2014) ; Zhang Y. M. et al (2020) . Briefly, amino acid sequences of the conserved NBS domain encoded by barley NLR genes were retrieved and aligned using ClustalW with default options, and then manually corrected in MEGA 7.0 ( Kumar et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

Jiang

Shao

2021

Front. Genet.

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Barley is one of the top 10 crop plants in the world. During its whole lifespan, barley is frequently infected by various pathogens. In this study, we performed genome-wide analysis of the largest group of plant disease resistance (R) genes, the nucleotide binding site–leucine-rich repeat receptor (NLR) gene, in an updated barley genome. A total of 468 NLR genes were identified from the improved barley genome, including one RNL subclass and 467 CNL subclass genes. Proteins of 43 barley CNL genes were shown to contain 25 different integrated domains, including WRKY and BED. The NLR gene number identified in this study is much larger than previously reported results in earlier versions of barley genomes, and only slightly fewer than that in the diploid wheat Triticum urartu. Barley Chromosome 7 contains the largest number of 112 NLR genes, which equals to seven times of the number of NLR genes on Chromosome 4. The majority of NLR genes (68%) are located in multigene clusters. Phylogenetic analysis revealed that at least 18 ancestral CNL lineages were presented in the common ancestor of barley, T. urartu and Arabidopsis thaliana. Among them fifteen lineages expanded to 533 sub-lineages prior to the divergence of barley and T. urartu. The barley genome inherited 356 of these sub-lineages and duplicated to the 467 CNL genes detected in this study. Overall, our study provides an updated profile of barley NLR genes, which should serve as a fundamental resource for functional gene mining and molecular breeding of barley.

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Section: Methodsmentioning

confidence: 99%

Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

Jiang

Shao

2021

Front. Genet.

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“…A typical NBS-encoding gene consists of a variable domain at the N-terminal, a highly conserved NBS domain in the middle, and a diverse leucine-rich repeat (LRR) domain at the C-terminal. Therefore, according to the structure of N-terminal domains that possess a coiled-coil (CC), Drosophila toll and mammalian interleukin-1 receptor-like (TIR), or resistance to powdery mildew8 (RPW8) domain, NBS-encoding genes can be classified into three subclasses: CC-NBS-LRR (CNL), TIR-NBS-LRR (TNL), and RPW8-NBS-LRR (RNL) ( Meyers et al, 2003 ; Shao et al, 2014 , 2016 , 2019 ; Zhang et al, 2016 , 2020 ; Qian et al, 2017 ; Xue et al, 2020 ). As an example of function, the CNL gene, RPP8 , in Arabidopsis thaliana provides resistance against downy mildew after Peronospora parasiticia infection ( Mcdowell et al, 1998 ).…”

Section: Introductionmentioning

confidence: 99%

Distinct Evolutionary Patterns of NBS-Encoding Genes in Three Soapberry Family (Sapindaceae) Species

et al. 2020

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Nucleotide-binding site (NBS)-type disease resistance genes (R genes) play key roles in plant immune responses and have co-evolved with pathogens over the course of plant lifecycles. Comparative genomic studies tracing the dynamic evolution of NBS-encoding genes have been conducted using many important plant lineages. However, studies on Sapindaceae species have not been performed. In this study, a discrepant number of NBS-encoding genes were identified in the genomes of Xanthoceras sorbifolium (180), Dinnocarpus longan (568), and Acer yangbiense (252). These genes were unevenly distributed and usually clustered as tandem arrays on chromosomes, with few existed as singletons. The phylogenetic analysis revealed that NBS-encoding genes formed three monophyletic clades, RPW8-NBS-LRR (RNL), TIR-NBS-LRR (TNL), and CC-NBS-LRR (CNL), which were distinguished by amino acid motifs. The NBS-encoding genes of the X. sorbifolium, D. longan, and A. yangbiense genomes were derived from 181 ancestral genes (three RNL, 23 TNL, and 155 CNL), which exhibited dynamic and distinct evolutionary patterns due to independent gene duplication/loss events. Specifically, X. sorbifolium exhibited a "first expansion and then contraction" evolutionary pattern, while A. yangbiense and D. longan exhibited a "first expansion followed by contraction and further expansion" evolutionary pattern. However, further expansion in D. longan was stronger than in A. yangbiense after divergence, suggesting that D. longan gained more genes in response to various pathogens. Additionally, the ancient and recent expansion of CNL genes generated the dominance of this subclass in terms of gene numbers, while the low copy number status of RNL genes was attributed to their conserved functions.

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“…Furthermore, the expression of the FtsZ2-1 gene under various stresses was researched. Tubulin genes were screened from the cassava genome, along with six other species, for instance, Arabidopsis thaliana [ 52 ], Dioscorea rotundata [ 53 ], Hevea brasiliensis [ 54 ], Oryza sativa [ 55 ], and Vitis vinifera [ 56 ]. In this study, 23 cassava tubulins were found and renamed as MeTubulin1 to MeTubulin23 in the order of screening, lower than Hevea brasiliensis (31), but higher than Arabidopsis thaliana (16), Dioscorea rotundata (11), Oryza sativa (16), and Vitis vinifera (18); according to amino acid sequences, motif composition, intron structure, phylogenetic feature, and tubulin type of cassava, the 23 cassava tubulin genes can be divided into four main groups.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of Tubulin Gene Family in Cassava and Expression of Family Member FtsZ2-1 during Various Stress

Cao

Wang

et al. 2021

Plants

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Filamentous temperature-sensitive protein Z (Tubulin/FtsZ) family is a group of conserved GTP-binding (guanine nucleotide-binding) proteins, which are closely related to plant tissue development and organ formation as the major component of the cytoskeleton. According to the published genome sequence information of cassava (Manihot esculenta Crantz), 23 tubulin genes (MeTubulins) were identified, which were divided into four main groups based on their type and phylogenetic characteristics. The same grouping generally has the same or similar motif composition and exon–intron structure. Collinear analysis showed that fragment repetition event is the main factor in amplification of cassava tubulin superfamily gene. The expression profiles of MeTubulin genes in various tissue were analyzed, and it was found that MeTubulins were mainly expressed in leaf, petiole, and stem, while FtsZ2-1 was highly expressed in storage root. The qRT-PCR results of the FtsZ2-1 gene under hormone and abiotic stresses showed that indole-3-acetic acid (IAA) and gibberellin A3 (GA3) stresses could significantly increase the expression of the FtsZ2-1 gene, thereby revealing the potential role of FtsZ2-1 in IAA and GA3 stress-induced responses.

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Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

Cited by 35 publications

References 49 publications

Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

Distinct Evolutionary Patterns of NBS-Encoding Genes in Three Soapberry Family (Sapindaceae) Species

Genome-Wide Analysis of Tubulin Gene Family in Cassava and Expression of Family Member FtsZ2-1 during Various Stress

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