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Basic characteristic analysis of 429 LecRKs. (a) Typical domain architectures of C-, L-and G-type LecRKs. Protein number of each architecture was presented behind the sequence. Six main domains, including calcium-dependent lectin (C-lectin), legume-lectin (L-lectin), bulb-lectin (G-lectin), kinase, plasminogen/apple/nematode (PAN) and S-locus, were marked concurrently in different colors; (b) The number of amino acids predicted for three types of LecRKs. (c) Phylogenetic tree analysis of 314 LecRKs with complete kinase domains indicates three types of LecRK proteins segregated distinctly with independent evolutionary branches.
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Sugarcane is an important sugar and bioenergy ethanol crop, and the hyperploidy has led to stagnant progress in sugarcane genome decipherment, which also hindered the genome-wide analyses of versatile lectin receptor kinases (LecRKs). The published genome of Saccharum spontaneum, one of the two sugarcane ancestor species, enables us to study the ch...
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... typical domain architectures of three types of the LecRKs were mapped by domain analysis (Figure 1a). Only two domains of lectin and kinase existed in C-and L-type LecRKs. ...
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... existence of these atypical domains also enhances the diversity of the LecRK structure. Overall, the length of G-type proteins is longer than L-type, which corresponds to the number of typical domains they carry (Figure 1b). In order to verify whether the three types of LecRKs evolved independently, 314 LecRK proteins with complete kinase domains were selected as the research objects. ...
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... the kinase domains are more conservative than lectin domains [6], the sequence of kinase domains in each selected protein was extracted to construct the phylogenetic tree. An interesting result was presented in Figure 1c. Clearly, three types of LecRKs were distinctly segregated and have independent evolutionary branches with each other (C-, L-and G-type groups). ...
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... shown in Figure 1a, five typical domain architectures were displayed. However, detailed domain orientation and layout patterns of LecRKs on the plasma membrane, including TM, were unknown. ...
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... 158 representative non-allelic LecRKs (52 L-and 106 G-types) that contained both complete lectin and kinase domains were selected for motif architecture analysis ( Figure 3). Based on the 52 L-and 106 G-type LecRKs, respectively, the phylogenetic trees were constructed using their kinase sequences and a total of 15 highly conserved motifs were predicted ( Figure S1) in the L-and G-type LecRKs, respectively. According to the phylogenetic tree, all sequences carrying motifs were rearranged. ...
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... evolutionary relationship of three types (C-, L-and G-types) of genes was constructed using a complete kinase domain from 314 selected proteins. The fact indicates that the three types of genes evolved independently (Figure 1c), which was also found in the LecRK family of Populus [6]. Similarly, in S. lycopersicum, the unrooted neighborjoining distance tree demonstrates that the evolution of the three types of the LecRK family is also strictly independent [19]. ...
Citations
... The disease was reportedly epidemic in Taiwan of China in 1976 when over 10,000 hectares of sugarcane were infected [11]. The disease has been prevalent in the main sugarcane planting areas of China in recent years in Guangxi, Yunnan, Guangdong and Fujian provinces, resulting in severe yield loss [12]. Based on our field survey in Fusui County of Guangxi Province, yield loss could reach 20-30% in susceptible varieties. ...
... S. tainanensis was proposed to be the imperfect state of ascomycete Leptosphaeria taiwanensis when its sexual stage was observed [13]. Despite its relatively long history of discovery, the literature on this pathogen has been limited to descriptions of morphology and taxonomy [14], disease-resistance breeding [11], host resistance [12] and genome assembly [15]. Studies on the biology of the sugarcane leaf blight fungus have been scarce, making it difficult to study the pathogenic mechanism of this fungus on sugarcane. ...
Sugarcane leaf blight (SLB), a major fungal leaf disease of sugarcane (Saccharum spp.), has been attributed to Stagonospora tainanensis. In December 2020 and May 2021, signs of leaf blight were observed on sugarcane in the fields of Chongzuo City, in the Guangxi Province of China. Lesions on the leaves were characterized by yellow or dark red spots in the center. Fungal species were isolated, purified and subjected to pathogenicity evaluation on the sugarcane plants. An isolate that caused symptoms the same as those observed in the field was initially identified as S. tainanensis (Leptosphaeria taiwanensis, perfect state) based on its morphological characteristics both of asexual and sexual stages. Dark brown and nearly spherical pycnidia with conidia of long ellipsoidal, hyaline, one to four cells and 29.27 to 54.39 μm long and 9.03 to 16.12 μm wide were found on corn meal agar medium. Ascomata with asci of cylindrical to clavate, a short stipe and eight spores slightly constricted at the septum, with the size of the spore ranging from 36 to 44 μm long and 8.5 to 12 μm wide, were formed on the sugarcane-leaf-decoction saccharose agar medium. The identity of the species was further confirmed by rDNA ITS and TEF-1α sequencing. The optimal temperature for mycelial growth was 25 °C and the optimal pH was 6.0. The pathogen grew well in a medium with oats as the carbon source and yeast extract as the nitrogen source, but poorly in a medium with urea as the nitrogen source. This study is the first to identify the sugarcane leaf blight pathogen in Guangxi, and the first publication describing the biological characterization of S. tainanensis. The occurrence of sugarcane leaf blight should alert sugarcane breeders and plant pathologists to consider integrating control of this potentially important disease into the agenda of their breeding and disease control programs.
... Most of the new sugarcane varieties have been developed from the interspecific hybridization of Saccharum offici-narum and Saccharum spontaneum. The resulting varieties tend to be polyploids and aneuploids with chromosome counts ranging from 80 to 120 [8][9][10]. ...
... Thus, using this morphogenetic regulator rather than hormones might lead to significant improvement in the transformation efficiency of monocotyledonous plant species such as sugarcane. Thus, despite the challenges, targeted base gene editing without induction of a foreign DNA donor [9,[101][102][103][104][105][106][107] or cleavage of double-stranded DNA [108][109][110][111] in sugarcane hold bright perspectives to accelerate genome modification ( Table 2 and 3) and breeding for boosting its productivity and sugar recovery on sustainable basis. ...
Sugarcane crop constitutes one of the most vital sources of sugar and bioenergy globally; however, higher level of polyploidy makes its genome editing an intricate task. Recently, genome editing has become easier with CRISPR/Cas9 system that uses Cas9 to target sequence-specific regions and introduce double-strand breaks into the target region. This technique has been successfully employed to develop new varieties of sugarcane having desired phenotypic and physiological traits. Several genes can be fused with the CRISPR/Cas9 system leading to successful metabolic engineering and biological improvement for ensuring sustainable enhancement in sugarcane production. This simple RNA-guided genome editing technique has become a revolutionary tool and innovative application in biology that might be effectively employed for inducing specified genomic modifications in plant tissues. This review attempts to synthesize fundamentals of ge-nome editing techniques with an ultimate aim to find out opportunities and challenges of sugar-cane genome editing. It also tends to summarize the advances and achievements of gene editing via CRISPR-based genome editing technique for numerous field crops. Lastly, the enormous potential of CRISPR/Cas9 for gene editing in sugarcane, major challenges and future perspectives have been objectively elaborated.
... Most of the new sugarcane varieties have been developed from the interspecific hybridization of Saccharum officinarum and Saccharum spontaneum. The resulting varieties tend to be polyploids and aneuploids with chromosome counts ranging from 80 to 120 [8][9][10]. ...
... Thus, using this morphogenetic regulator rather than hormones might lead to significant improvement in the transformation efficiency of monocotyledonous plant species such as sugarcane. Thus, despite the challenges, targeted base gene editing without induction of a foreign DNA donor [9,[101][102][103][104][105][106][107] or cleavage of double-stranded DNA [108][109][110][111] in sugarcane hold bright perspectives to accelerate genome modification (Tables 2 and 3) and breeding for boosting its productivity and sugar recovery on sustainable basis. ...
Sugarcane crop constitutes one of the most vital sources of sugar and bioenergy globally; however, higher level of polyploidy makes its genome editing an intricate task. Recently, genome editing has become easier with CRISPR/Cas9 system that uses Cas9 to target sequence-specific regions and introduce double-strand breaks into the target region. This technique has been successfully employed to develop new varieties of sugarcane having desired phenotypic and physiological traits. Several genes can be fused with the CRISPR/Cas9 system leading to successful metabolic engineering and biological improvement for ensuring sustainable enhancement in sugarcane production. This simple RNA-guided genome editing technique has become a revolutionary tool and innovative application in biology that might be effectively employed for inducing specified genomic modifications in plant tissues. This review attempts to synthesize fundamentals of genome editing techniques with an ultimate aim to find out opportunities and challenges of sugarcane genome editing. It also tends to summarize the advances and achievements of gene editing via CRISPR-based genome editing technique for numerous field crops. Lastly, the enormous potential of CRISPR/Cas9 for gene editing in sugarcane, major challenges and future perspectives have been objectively elaborated.
... Additionally, we have also discussed the probable roles of LecRLKs in plants that will bring new directions for crop improvement in future studies. The LecRLKs have been identified in several monocots, for example, O. sativa (Vaid et al., 2012), T. aestivum (Shumayla, Sharma, Pandey, et al., 2016), Setaria italica L. (Zhao et al., 2016), Saccharum spontaneum L., Brachypodium distachyon, Sorghum bicolor, Zea mays (Wang et al., 2021), etc ( In 2006, using a map-based cloning strategy, a gene Pi-d2 was isolated from O. sativa, which encodes LecRLK (B-lectin). One of the devastating diseases, rice blast, is caused by Magnaporthe grisea, which affects rice plants worldwide. ...
... The promoter studies indicated the occurrence of 115 putative cis-regulatory elements which were related to abiotic stress, hormone, light, and plant growth, and development. Besides, the cis-regulatory elements, 263 microsatellites were found in 141 LecLRK genes (Wang et al., 2021). p0090 The diverse expression pattern of LecRLKs in both susceptible and resistant varieties after Stagonospora tainanensis infestation demonstrated their involvement in plant protection from sugarcane leaf blight disease. ...
Lectin receptor-like kinase (LecRLK) is considered the second largest class of very influential cell surface receptor proteins referred to as receptor-like kinases (RLKs). The LecRLK consists of a lectin and serine/threonine kinase domain at its amino-terminus and carboxyl-terminus, respectively. In addition to these domains, LecRLK is endowed with a transmembrane domain. The LecRLKs were further grouped as L-LecRLKs, G-LecRLKs, and C-LecRLKs, attributable to the binding relevancy of the lectin domain. According to many research articles, the LecRLKs are present in numerous plant species such as Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Pisum sativum, Populus trichocarpa, Solanum lycopersicon, Solanum tuberosum, Triticum aestivum, Setaria italica L., etc. Various expression studies and cis-regulatory element analysis suggested the association of LecRLKs with several plant developmental processes, hormone responses, and stress-related signaling cascades. The Gene ontology studies pointed towards the connection of LecRLKs with molecular, biological, and cellular processes of plants. Moreover, overexpression and knockout development unveil the functioning of LecRLKs in stress resistance to both abiotic and biotic concerns. In this current chapter, we have emphasized the number and types of LecRLKs in both monocotyledonous and dicotyledonous plants and summarized their functions in plant development and stress resistance.
... The truncation of some domains from this classic structure can also be found, such as LRR (CN or TN), TIR or CC (NL), and in both C and N terminal domains (N) (Monteiro and Nishimura, 2018). Additionally, atypical or non-canonical integrated domains (IDs) that act as decoys and play roles in oligomerization or downstream signaling may be present, demonstrating the structural diversity of this NLR family (Kroj et al., 2016;Wang et al., 2021). The number of NLRs in plant genomes varies greatly and is often organized in tandem, which facilitates duplication, contraction, and transposition and provides a reservoir of genetic variation that allows plant evolutionary dynamics to respond to changes phytopathogen populations (Barragan and Weigel, 2021). ...
... The knowledge of how NLRs are distributed throughout the genome and their diversity is of great interest as it may reveal new sources of resistance that may be used to develop new cultivars (Monteiro and Nishimura, 2018). The growing number of sequenced plant genomes facilitates the search for novel NLR and has led to the genome-wide analysis of NLR genes (Denoeud et al., 2014;Song et al., 2015;Scott et al., 2020;Wang et al., 2021). However, its large number, frequently clustered genomic distribution, and low expression in uninfected tissues make cataloging NLR genes challenging and often underestimates the number of NLRs in genomes (Jupe et al., 2013;Steuernagel et al., 2015Steuernagel et al., , 2020. ...
... Recent discoveries show that NLRs can be multi domain receptors, that is they present domains integrated to the canonical form NLR or TNL/CNL (Bailey et al., 2018;Wang et al., 2021). Knowing regions of the genome that have this canonical form can facilitate the description of noncanonical integrated domains that are upstream or downstream from the more conserved region (Monteiro and Nishimura, 2018). ...
The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (Coffea canephora, Coffea eugenioides and their interspecific hybrid Coffea arabica). A total of 1311 non-redundant NLR loci were identified in C. arabica, 927 in C. canephora, and 1079 in C. eugenioides, of which 809, 562, and 695 are complete loci, respectively. The NLR-Annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. The C. arabica genome presented a smaller number of NLR loci when compared to the sum of the parental genomes (C. canephora, and C. eugenioides). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared between C. arabica and the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars.
... A highly susceptible hybrid line 47 (FN12-047, score = 4), together with its resistant male parent ROC22, were selected for transcriptional expression analysis [28]. They were grown at Fujian Agriculture and Forestry University, Fuzhou, China. ...
... For each sugarcane line, two plants with similar growth vigor were selected for sampling and leaves located at the same position were pooled for each sample. The process of RNA isolation and sequencing is described in our previous report [28]. Quality control for the RNA-seq data was performed with fastqc 0.11.9 (Babraham Bioinformatics), and the quality-checked data was processed for trimming with fastp 0.20 [29]. ...
Sugarcane leaf blight (SLB), caused by Stagonospora tainanensis, is one of the most harmful fungal diseases, threatening the sugarcane industry and causing high losses of cane yield and sugar in susceptible cultivars. Using a two-way pseudo-testcross mapping strategy in combination with array genotyping, two high-density genetic maps were constructed for sugarcane cultivars YT93-159 and ROC22 with mean densities of respectively 3.0 and 3.5 cM per marker, and covering respectively 4485 and 2720 cM of genetic distance. The maps showed highly conserved colinearity with the genome of the ancestral species Saccharum officinarum, supporting the reliability of the linkage configurations of the maps. Quantitative trait locus (QTL) analysis of SLB resistance revealed six QTL (qSLB-1–qSLB-6). The major QTL qSLB-1 explaining 16.4% of phenotypic variance was assigned as the main QTL, and the total percentages of phenotypic variance explained in YT93-159 and ROC22 were 37.9% and 17.6%, respectively. Nine transcription factor and seven pathogen receptor genes lying in the qSLB-1 interval were highly expressed and are proposed as candidate causal genes for SLB resistance.
... In this study, we selected the sugarcane maturity stage for sampling. The field was watched throughout the plant life cycle, especially after appearance of sugarcane leaf blight disease (SLB) symptoms, and five different disease development stages were defined according to the previous report [54]. The leaf samples that had no visible sign of the SLB symptom and without pathogenic spores or hyphae observed under the microscope were represented as control [54]; Supplementary Material S5 shows the details. ...
... The field was watched throughout the plant life cycle, especially after appearance of sugarcane leaf blight disease (SLB) symptoms, and five different disease development stages were defined according to the previous report [54]. The leaf samples that had no visible sign of the SLB symptom and without pathogenic spores or hyphae observed under the microscope were represented as control [54]; Supplementary Material S5 shows the details. Three biological replicates were performed for each infection stage and for control (healthy), and a total of 18 samples were obtained. ...
... Three biological replicates were performed for each infection stage and for control (healthy), and a total of 18 samples were obtained. For each sugarcane accession, three plants with similar growth vigor and disease severity were selected for sampling, and the leaf located at the same leaf position was collected [54]. The collected samples were immediately put into liquid nitrogen and stored at −80 • C for later use. ...
The leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family is the largest family of the receptor-like protein kinases (RLKs) superfamily in higher plants, which is involved in regulating the plant growth and development, stress responses, signal transduction and so on. However, no comprehensive analyses of LRR-RLKs have been reported in sugarcane. Here, we performed a comprehensive analysis of the LRR-RLK gene family in sugarcane ancestor species Saccharum spontaneum. A total of 437 LRR-RLK genes were identified and categorized into 14 groups based on a maximum likelihood phylogenetic tree. The chromosome location showed an uneven distribution on all 32 chromosomes in sugarcane. Subsequently, the exon-intron organization structure and conserved motif arrangement were relatively conserved among the same groups or subgroups and between Arabidopsis and S. spontaneum genomes. Furthermore, the promoter sequences analyses showed that sugarcane LRR-RLK genes (SsLRR-RLKs) were strongly regulated by various environmental stimuli, phytohormonal factors and transcription factors (TFs). Eventually, the expression profiles of SsLRR-RLK genes at different stresses were analyzed based on RNA-seq data, suggesting their potential roles in the regulation of sugarcane responses to diverse abiotic and biotic stress. Overall, the findings provide insight into the potential functional roles and lay the foundation for further functional study.
Lectin receptor-like kinases (LecRKs) locate on the cell membrane and play diverse roles in perceiving environmental factors in higher plants. Studies have demonstrated that LecRKs are involved in plant development and response to abiotic and biotic stresses. In this review, we summarize the identified ligands of LecRKs in Arabidopsis, including extracellular purine (eATP), extracellular pyridine (eNAD⁺), extracellular NAD⁺ phosphate (eNADP⁺) and extracellular fatty acids (such as 3-hydroxydecanoic acid). We also discussed the posttranslational modification of these receptors in plant innate immunity and the perspectives of future research on plant LecRKs.
Plant cells recognize microbial patterns with the plasma‐membrane‐localized pattern‐recognition receptors consisting mainly of receptor kinases (RKs) and receptor‐like proteins (RLPs). RKs, such as bacterial flagellin receptor FLS2, and their downstream signaling components have been studied extensively. However, newly discovered regulatory components of RLP‐mediated immune signaling, such as the nlp20 receptor RLP23, await identification. Unlike RKs, RLPs lack a cytoplasmic kinase domain, instead recruiting the receptor‐like kinases (RLKs) BAK1 and SOBIR1. SOBIR1 specifically works as an adapter for RLP‐mediated immunity. To identify new regulators of RLP‐mediated signaling, we looked for SOBIR1‐binding proteins (SBPs) in Arabidopsis thaliana using protein immunoprecipitation and mass spectrometry, identifying two G‐type lectin RLKs, SBP1 and SBP2, that physically interacted with SOBIR1. SBP1 and SBP2 showed high sequence similarity, were tandemly repeated on chromosome 4, and also interacted with both RLP23 and BAK1. sbp1 sbp2 double mutants obtained via CRISPR‐Cas9 gene editing showed severely impaired nlp20‐induced reactive oxygen species burst, mitogen‐activated protein kinase (MAPK) activation, and defense gene expression, but normal flg22‐induced immune responses. We showed that SBP1 regulated nlp20‐induced immunity in a kinase activity‐independent manner. Furthermore, the nlp20‐induced the RLP23–BAK1 interaction, although not the flg22‐induced FLS2–BAK1 interaction, was significantly reduced in sbp1 sbp2. This study identified SBPs as new regulatory components in RLP23 receptor complex that may specifically modulate RLP23‐mediated immunity by positively regulating the interaction between the RLP23 receptor and the BAK1 co‐receptor.
Plant Nucleotide binding-Leucine rich repeat (NLR) proteins play a significant role in pathogen detection and the activation of effector-triggered immunity. NLR regulation has mainly been studied at a protein level, with large knowledge gaps remaining regarding the transcriptional control of NLR genes. The mis-regulation of NLR gene expression may lead to the inability of plants to recognize pathogen infection, lower levels of immune response activation, and ultimately plant susceptibility. This highlights the importance of understanding all aspects of NLR regulation. Three main mechanisms have been shown to control NLR expression: epigenetic modifications, cis elements which bind transcription factors, and post-transcriptional modifications. In this review, we aim to provide an overview of these mechanisms known to control NLR expression, and those which contribute toward successful immune responses. Furthermore, we discuss how pathogens can interfere with NLR expression to increase pathogen virulence. Understanding how these molecular mechanisms control NLR expression would contribute significantly toward building a complete picture of how plant immune responses are activated during pathogen infection—knowledge which can be applied during crop breeding programs aimed to increase resistance toward numerous plant pathogens.
