Genome-Wide Analysis of the Apple (Malus domestica) Cysteine-Rich Receptor-Like Kinase (CRK) Family: Annotation, Genomic Organization, and Expression Profiles in Response to Fungal Infection

Zuo, Cunwu; He, Li; Lv, Qianqian; Chen, Zhongjian; Yuzhen, Tian; Mao, Juan; Chu, Ming-Yu; Ma, Zhiying; An, Zeshan; Chen, Baihong

doi:10.1007/s11105-019-01179-w

Cited by 23 publications

(14 citation statements)

References 43 publications

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“…The best studied of these is FLS2, which detects the bacterial flagellin protein and initiates an immune response cascade [ 53 ]. The 3 RLKs we identified show high sequence similarity to immune-related cysteine-rich RLKs in Arabidopsis and Oryza , and contain the “stress-antifungal domain” PF01657, which has been linked to salt stress as well as fungal responses when present in several proteins [ 54 , 55 ]. Arabidopsis CRK5 , for example, alters defense responses either through resistance to infection or programmed cell death, depending on how the gene is expressed [ 56 ], and CRK6 and CRK 14 are involved in the general non–self-response [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

Host genotype controls ecological change in the leaf fungal microbiome

et al. 2022

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Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

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Section: Discussionmentioning

confidence: 99%

Host genotype controls ecological change in the leaf fungal microbiome

et al. 2022

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“…Other stress‐responsive elements were also identified in the three gene families, including the DRE‐Core or DRE1 element, which is important for the responses to dehydration (Narusaka et al 2003, Sun et al 2008), the W‐box that is involved in biotic stress (Muthusamy et al 2017), and LTR and STRE elements that are crucial for responses to low temperature and osmotic and oxidative stress, respectively (Mittal et al 2009). Additionally, many cis ‐elements are involved in hormone responses, such as SA‐responsive elements (TCA‐element) and MeJA responsive elements (CGTCA‐motif and TGACG‐motif), which are associated with the response to pathogen stimulus (Cui et al 2020, Zuo et al 2020). Together, our findings suggest that diverse cis‐regulatory elements involved in various cellular processes are present in the promoter regions of MAP kinase gene family members, likely acting as diverse functions related to growth, development, and stress response.…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide analysis of mitogen‐activated protein (MAP) kinase gene family expression in response to biotic and abiotic stresses in sugarcane

Ali

Chu

et al. 2020

Physiologia Plantarum

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To systematically analyze mitogen-activated protein (MAP) kinase gene families and their expression profiles in sugarcane (Saccharum spp. hybrids; Sh) under diverse biotic and abiotic stresses, we identified 15 ShMAPKs, 6 ShMAPKKs and 16 ShMAPKKKs genes in the sugarcane cultivar R570 genome. These were also confirmed in one S. spontaneum genome and two transcriptome datasets of sugarcane trigged by Acidovorax avenae subsp. avenae (Aaa) and Xanthomonas albilineans (Xa) infections. Phylogenetic analysis revealed that four subgroups were present in each ShMAPK and ShMAPKK family and three sub-families (RAF, MEKK and ZIK) presented in the ShMAPKKK family. Conserved protein motif and gene structure analyses supported the evolutionary relationships of the three families inferred from the phylogenetic analysis. All of the ShMAPK, ShMAPKK and ShMAPKKK genes identified in Saccharum spp. R570 were distributed on chromosomes 1-7 and 9-10. RNA-seq and qRT-PCR analyses indicated that ShMAPK07 and ShMAPKKK02 were defense-responsive genes in sugarcane challenged by both Aaa and Xa stimuli, while some genes were upregulated specifically by Aaa and Xa infection. Additionally, ShMAPK05 acted as a negative regulator under drought and salinity stress, but served as a positive regulator under salicylic acid (SA) treatment. ShMAPK07 plays a positive role under drought stress, but a negative role under SA treatment. ShMAPKKK01 was negatively modulated by both salinity stress and SA treatment, whereas ShMAPKKK06 was positively regulated by both of the two stress stimuli. Our results suggest that members of MAPK cascade gene families regulate adverse stress responses through multiple signal transduction pathways in sugarcane.

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“…LRR is a domain frequently found in AGPs and HRGPs ( Figure 2 B,C) which may facilitate dimerization of the molecules that contain it [ 12 ]. CeKLA3 and its homologs from the A1 subcluster ( Figure 4 ) belong to the cysteine-rich receptor-like kinase (CRK) family [ 50 , 51 ], characterized by N-terminal salt stress response/antifungal PF01657 domains with conserved cysteines involved in disulfide bridges.…”

Section: Discussionmentioning

confidence: 99%

The Arabinogalactan Protein Family of Centaurium erythraea Rafn

Paunović

Ćuković

Bogdanović

et al. 2021

Plants

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Centaurium erythraea (centaury) is a medicinal plant with exceptional developmental plasticity in vitro and vigorous, often spontaneous, regeneration via shoot organogenesis and somatic embryogenesis, during which arabinogalactan proteins (AGPs) play an important role. AGPs are highly glycosylated proteins belonging to the super family of O-glycosylated plant cell surface hydroxyproline-rich glycoproteins (HRGPs). HRGPs/AGPs are intrinsically disordered and not well conserved, making their homology-based mining ineffective. We have applied a recently developed pipeline for HRGP/AGP mining, ragp, which is based on machine learning prediction of proline hydroxylation, to identify HRGP sequences in centaury transcriptome and to classify them into motif and amino acid bias (MAAB) classes. AGP sequences with low AG glycomotif representation were also identified. Six members of each of the three AGP subclasses, fasciclin-like AGPs, receptor kinase-like AGPs and AG peptides, were selected for phylogenetic and expression analyses. The expression of these 18 genes was recorded over 48 h following leaf mechanical wounding, as well as in 16 tissue samples representing plants from nature, plants cultivated in vitro, and developmental stages during shoot organogenesis and somatic embryogenesis. None of the selected genes were upregulated during both wounding recovery and regeneration. Possible functions of AGPs with the most interesting expression profiles are discussed.

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Genome-Wide Analysis of the Apple (Malus domestica) Cysteine-Rich Receptor-Like Kinase (CRK) Family: Annotation, Genomic Organization, and Expression Profiles in Response to Fungal Infection

Cited by 23 publications

References 43 publications

Host genotype controls ecological change in the leaf fungal microbiome

Host genotype controls ecological change in the leaf fungal microbiome

Genome‐wide analysis of mitogen‐activated protein (MAP) kinase gene family expression in response to biotic and abiotic stresses in sugarcane

The Arabinogalactan Protein Family of Centaurium erythraea Rafn

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