Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization

Aono, Alexandre Hild; Pimenta, Ricardo José Gonzaga; Silva, Caroline Marcela da; Costa, Francisco Cleilson Lopes; Kuroshu, Reginaldo Massanobu; Souza, Anete Pereira de; Pereira, Welison Andrade

doi:10.1016/j.gene.2022.147127

Cited by 4 publications

(12 citation statements)

References 93 publications

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“…In our study, wide set of proteins motifs and domains were detected, highlighting that their functioning in phosphorylating targets is much more than a formidable task. The maximum number of introns corroborated with those observed in cowpea (Ferreira-Neto et al, 2021b), soybean (Jinyi Liu et al, 2015) and common bean (Aono et al, 2023). Introns are unique components of eukaryotic organisms, and it is assumed that they participate in complex and specific characteristics, so they are not eliminated from the gene structure (Chorev and Carmel, 2012; Lynch, 2007; Wahl et al, 2009).…”

Section: Discussionsupporting

confidence: 79%

“…The blast-based approach could be used to determine such proteins in genome-wide analysis studies (Abbas et al, 2022). However, the profile-HMM-based approach seems to be the most frequente approach in such studies (Aono et al, 2023(Aono et al, , 2021bFerreira-Neto et al, 2021b;Liu et al, 2020b;Jinyi Liu et al, 2015;Lv et al, 2020;Singh et al, 2014b;Wei et al, 2014b;Yan et al, 2018bYan et al, , 2017bZhu et al, 2021bZhu et al, , 2018dZhu et al, , 2018bZulawski et al, 2014b).…”

Section: Discussionmentioning

confidence: 99%

“…Notably, the PKs of the RLK group stood out in the differential expression studies, with 49 subfamilies, in 13.5% of the cases occurring PKs of the RLK-Pelle_DLSV subfamily, 8.9% PKs of the RLK-Pelle_LRR-XI-1 subfamily, and 7.2% PKs of the subfamily RLK-Pelle_LRR-I-1. Like the Phaseolus kinome differential gene expression (Aono et al, 2023), the first two subfamilies also stood out. However, the groups with the highest correlations between Aurora kinase subfamily means and a UNKNOWN subfamily (R = 0.99, Supplementary file S15).…”

Section: Discussionmentioning

confidence: 99%

“…The protein kinases are core regulators of the plant metabolism and are considered important modulators of biotic stress. The number of protein kinases among plant species is a quite variable information, in average 4.0% for the species common bean (3.25%), maize (3.8%), Arabidopsis (3.4%), grapevine (3.7%), cowpea (4.3%), soybean (4.7%) and rubber tree (4.9%) (Aono et al, 2023; Ferreira-Neto et al, 2021b; Jinyi Liu et al, 2015; Wei et al, 2014b; Zhu et al, 2018d; Zulawski et al, 2014b). In cucumber, 831 PK were found and classified into 20 different groups and 125 subfamilies.…”

Section: Discussionmentioning

confidence: 99%

“…The Csa kinome is a set of 831 protein kinases, that were retrieved from Csa proteome (CuGenDBv2: Gy14). The first plant kinome was defined in Arabidopsis in 2004 (Champion et al, 2004;Zulawski et al, 2014a), after that many others plant kinomes have been investigated in several plant species, such as, in rice (Dardick et al, 2007), maize (Wei et al, 2014a), tomato (Singh et al, 2014a), soybean (J Liu et al, 2015), wheat (Yan et al, 2017a), Brassica napus (Gill et al, 2017), Gossypium (Yan et al, 2018a), grapevine (Zhu et al, 2018c), pineapple (Zhu et al, 2018a), strawberry (Liu et al, 2020a), pecan (Zhu et al, 2021a), sugarcane and sorgum (Aono et al, 2021a), cowpea (Ferreira-Neto et al, 2021a), common bean (Aono et al, 2023), rubber tree (Santos et al, 2023). Some genome-wide analyses have been done in some sub-families of protein kinases (Wei et al, 2019) and dirigent gene family (Yadav et al, 2021) in the cucurbits species, there is no evidence of of comparative studies comprising all the protein kinase loci of Csa.…”

Section: Introductionmentioning

confidence: 99%

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TheCucumis sativuskinome: Identification, annotation, and expression patterns in response to powdery mildew infection

Costa

Aono

Silva

et al. 2023

Preprint

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Protein kinases make up a family of enzymes that play a key role in regulating metabolism. In the cucumber species (Cucumis sativus), this family has not yet been fully characterized. Considering its importance in studies of the botanical family Cucurbitaceae, we identified and characterized the complete set of cucumber kinases, including phylogenetic and classification analyses, their genome positions, chemical characterization, and expression through RNA-seq data in response to powdery mildew and Alternaria leaf spot. The cucumber kinome is made up of 831 proteins, widely distributed across the species's seven chromosomes, with the majority located on chromosome three. The kinases were classified into 21 (9 +11 grupos named Others) groups and 125 subfamilies, with the RLK-Pelle group being the most abundant. There was no evidence of gene duplication and it has a smaller genome compared to other species in the botanical family Cucurbitaceae. Our study provides more information to support the understanding about the function PKs and shows how similar PK subfamilies are in composition, their properties and how they are expressed in disease related scenarios.

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Section: Discussionsupporting

confidence: 79%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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TheCucumis sativuskinome: Identification, annotation, and expression patterns in response to powdery mildew infection

Costa

Aono

Silva

et al. 2023

Preprint

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Mapping yield and yield-related traits using diverse common bean germplasm

Reinprecht,

Schram,

Perry

et al. 2024

Front. Genet.

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Common bean (bean) is one of the most important legume crops, and mapping genes for yield and yield-related traits is essential for its improvement. However, yield is a complex trait that is typically controlled by many loci in crop genomes. The objective of this research was to identify regions in the bean genome associated with yield and a number of yield-related traits using a collection of 121 diverse bean genotypes with different yields. The beans were evaluated in replicated trials at two locations, over two years. Significant variation among genotypes was identified for all traits analyzed in the four environments. The collection was genotyped with the BARCBean6K_3 chip (5,398 SNPs), two yield/antiyield gene-based markers, and seven markers previously associated with resistance to common bacterial blight (CBB), including a Niemann–Pick polymorphism (NPP) gene-based marker. Over 90% of the single-nucleotide polymorphisms (SNPs) were polymorphic and separated the panel into two main groups of small-seeded and large-seeded beans, reflecting their Mesoamerican and Andean origins. Thirty-nine significant marker-trait associations (MTAs) were identified between 31 SNPs and 15 analyzed traits on all 11 bean chromosomes. Some of these MTAs confirmed genome regions previously associated with the yield and yield-related traits in bean, but a number of associations were not reported previously, especially those with derived traits. Over 600 candidate genes with different functional annotations were identified for the analyzed traits in the 200-Kb region centered on significant SNPs. Fourteen SNPs were identified within the gene model sequences, and five additional SNPs significantly associated with five different traits were located at less than 0.6 Kb from the candidate genes. The work confirmed associations between two yield/antiyield gene-based markers (AYD1m and AYD2m) on chromosome Pv09 with yield and identified their association with a number of yield-related traits, including seed weight. The results also confirmed the usefulness of the NPP marker in screening for CBB resistance. Since disease resistance and yield measurements are environmentally dependent and labor-intensive, the three gene-based markers (CBB- and two yield-related) and quantitative trait loci (QTL) that were validated in this work may be useful tools for simplifying and accelerating the selection of high-yielding and CBB-resistant bean cultivars.

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Genome-wide characterization of the sunflower kinome: classification, evolutionary analysis and expression patterns under different stresses

Yan,

Yang,

Chao

et al. 2024

Front. Plant Sci.

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Protein kinases play a significant role in plant responses to biotic and abiotic stresses, as well as in growth and development. While the kinome has been extensively investigated in crops such as Arabidopsis thaliana, soybean, common bean, and cotton, studies on protein kinases in sunflower remain limited. Our objective is to explore protein kinases in sunflower to bridge the research gap and enhance the understanding of their functions. We identified a total of 2,583 protein kinases from sunflower, which were classified into 22 families and 121 subfamilies. By comparing the subfamily members between sunflower and other species, we found that three subfamilies in sunflower—RLK-Pelle_CrRLK1L-1, RLK-Pelle_SD-2b, and RLK-Pelle_WAK—had undergone significant expansion. We then investigated the chromosomal distribution, molecular weight, isoelectric point, transmembrane domain, signal peptide, and structural and evolutionary diversity of the protein kinases. Through these studies, we have obtained a basic understanding of protein kinases in sunflower. To investigate the role of protein kinases in sunflower’s response to biotic and abiotic stresses, we obtained 534 transcriptome datasets from various research groups, covering eight types of abiotic stress and two types of biotic stress. For the first time, we overcame the batch effects in the data and utilized a gene scoring system developed by our lab to perform a comprehensive analysis of multiple transcriptome datasets from different research groups. Ultimately, 73 key protein kinases were identified from numerous candidates, and functional annotation revealed that they are key members of signaling pathways such as ABA, MAPK, and SOS, actively participating in sunflower’s response to biotic and abiotic stresses. In summary, through the exploration of protein kinases in sunflower, we have filled the gap in protein kinase research and provided a substantial amount of foundational data. By using the new scoring method to eliminate batch effects between transcriptome datasets, we achieved the first comprehensive analysis of large-scale transcriptome data. This method allows for a more thorough and detailed identification of key protein kinases that are widely regulated under various stress conditions, providing numerous candidate genes for sunflower stress resistance research.

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Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization

Cited by 4 publications

References 93 publications

TheCucumis sativuskinome: Identification, annotation, and expression patterns in response to powdery mildew infection

TheCucumis sativuskinome: Identification, annotation, and expression patterns in response to powdery mildew infection

Mapping yield and yield-related traits using diverse common bean germplasm

Genome-wide characterization of the sunflower kinome: classification, evolutionary analysis and expression patterns under different stresses

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