Genome-wide identification, characterization, and expression profile ofNBS-LRRgene family in sweet orange (Citrussinensis)

Yin, Tuo; Han, Peichen; Xi, Dengxian; Yu, Wencai; Zhu, Ling; Du, Chaojin; Yang, Na; Liu, Xiaozhen; Zhang, Hanyao

doi:10.1016/j.gene.2022.147117

Cited by 23 publications

(14 citation statements)

References 85 publications

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“…The Ka/Ks analysis of the NLR gene family in Lagneria siceraria ( Wang et al, 2022 ) revealed that among 14 duplicated gene pairs, two gene pairs were segmentally duplicated, and the remaining were tandemly duplicated indicating that the tandem duplication was more favorable and all the duplicated gene pairs were products of negative selection. Ka/Ks analysis of the NLR gene family in C. sinensis ( Yin et al, 2023 ) demonstrated that 16 duplicated gene pairs were tandemly duplicated and were a product of negative selection. The segmental and tandem duplications are equally contributing to the expansion of CNL gene family across the different plants.…”

Section: Discussionmentioning

confidence: 99%

“… Liu et al, 2021 ) , 361 in Solanum tuberosum ( Jupe et al, 2012 ) , 78 in Solanum pimpinellifolium ( Wei et al, 2020 ) , 14 in Lagenaria siceraria, 146 in Triticum urartu ( Qian et al, 2021 ) , 166 in Discorea rotundata, 103 in Glycine max ( Afzal et al, 2022 ), 467 in Hordeum vulgare ( Liu et al, 2017 ), 54 in Broussonetia papyrifera (X. Zhang et al, 2023 ), 95 in Elaeis guineensis ( Rosli et al, 2018 ) , 10 in Citrus sinensis ( Yin et al, 2023 ), 47 in Alphonso , 27 in Hong Xiang Ya , and 36 in Tommy atkins ( ul Qamar et al, 2023 ). Machine learning approaches have also been applied in studies reported previously for the elucidation of candidate genes implicated in multi-stress responsiveness in Oryza sativa and Sorghum bicolor ( Woldesemayat et al, 2018 ; Ramkumar et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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Comparative genomics and bioinformatics approaches revealed the role of CC-NBS-LRR genes under multiple stresses in passion fruit

Zia,

Sadaqat,

Ding

et al. 2024

Front. Genet.

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Passion fruit is widely cultivated in tropical, subtropical regions of the world. The attack of bacterial and fungal diseases, and environmental factors heavily affect the yield and productivity of the passion fruit. The CC-NBS-LRR (CNL) gene family being a subclass of R-genes protects the plant against the attack of pathogens and plays a major role in effector-triggered immunity (ETI). However, no information is available regarding this gene family in passion fruit. To address the underlying problem a total of 25 and 21 CNL genes have been identified in the genome of purple (Passiflora edulis Sims.) and yellow (Passiflora edulis f. flavicarpa) passion fruit respectively. Phylogenetic tree was divided into four groups with PeCNLs present in 3 groups only. Gene structure analysis revealed that number of exons ranged from 1 to 9 with 1 being most common. Most of the PeCNL genes were clustered at the chromosome 3 and underwent strong purifying selection, expanded through segmental (17 gene pairs) and tandem duplications (17 gene pairs). PeCNL genes contained cis-elements involved in plant growth, hormones, and stress response. Transcriptome data indicated that PeCNL3, PeCNL13, and PeCNL14 were found to be differentially expressed under Cucumber mosaic virus and cold stress. Three genes were validated to be multi-stress responsive by applying Random Forest model of machine learning. To comprehend the biological functions of PeCNL proteins, their 3D structure and gene ontology (GO) enrichment analysis were done. Our research analyzed the CNL gene family in passion fruit to understand stress regulation and improve resilience. This study lays the groundwork for future investigations aimed at enhancing the genetic composition of passion fruit to ensure robust growth and productivity in challenging environments.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative genomics and bioinformatics approaches revealed the role of CC-NBS-LRR genes under multiple stresses in passion fruit

Zia,

Sadaqat,

Ding

et al. 2024

Front. Genet.

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“…The TIFY HMMER file was used as the reference sequence to filter out the E-value < 1 × 10 −5 from the results of protein sequence numbers [ 56 ], followed by the downloading of protein sequences of A. thaliana TIFY gene family members from the A. thaliana genome database TAIR ( https://www.arabidopsis.org/index.jsp ). Then, the BLASTP program was used to compare the homology of the E. japonica genome with the TIFY protein sequences of A. thaliana as a reference to screen out the protein sequences with E-value > 1e −5 , and then the HUMMER search program was subsequently used to compare the protein sequences of the TIFY gene family members [ 57 ]. Finally, the Conserved Domain Database (CDD) tool of the NCBI database ( https://www.ncbi.nlm.nih.gov/cdd ) and the online software Pfam ( http://pfam.xfam.org/ ) were used to confirm the presence of the TIFY structural domain [ 58 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions

Li,

Wen,

Zhu

et al. 2024

BMC Genomics

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Background Plant-specific TIFY proteins are widely found in terrestrial plants and play important roles in plant adversity responses. Although the genome of loquat at the chromosome level has been published, studies on the TIFY family in loquat are lacking. Therefore, the EjTIFY gene family was bioinformatically analyzed by constructing a phylogenetic tree, chromosomal localization, gene structure, and adversity expression profiling in this study. Results Twenty-six EjTIFY genes were identified and categorized into four subfamilies (ZML, JAZ, PPD, and TIFY) based on their structural domains. Twenty-four EjTIFY genes were irregularly distributed on 11 of the 17 chromosomes, and the remaining two genes were distributed in fragments. We identified 15 covariate TIFY gene pairs in the loquat genome, 13 of which were involved in large-scale interchromosomal segmental duplication events, and two of which were involved in tandem duplication events. Many abiotic stress cis-elements were widely present in the promoter region. Analysis of the Ka/Ks ratio showed that the paralogous homologs of the EjTIFY family were mainly subjected to purifying selection. Analysis of the RNA-seq data revealed that a total of five differentially expressed genes (DEGs) were expressed in the shoots under gibberellin treatment, whereas only one gene was significantly differentially expressed in the leaves; under both low-temperature and high-temperature stresses, there were significantly differentially expressed genes, and the EjJAZ15 gene was significantly upregulated under both low- and high-temperature stress. RNA-seq and qRT-PCR expression analysis under salt stress conditions revealed that EjJAZ2, EjJAZ4, and EjJAZ9 responded to salt stress in loquat plants, which promoted resistance to salt stress through the JA pathway. The response model of the TIFY genes in the jasmonic acid pathway under salt stress in loquat was systematically summarized. Conclusions These results provide a theoretical basis for exploring the characteristics and functions of additional EjTIFY genes in the future. This study also provides a theoretical basis for further research on breeding for salt stress resistance in loquat. RT-qPCR analysis revealed that the expression of one of the three EjTIFY genes increased and the expression of two decreased under salt stress conditions, suggesting that EjTIFY exhibited different expression patterns under salt stress conditions.

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“…Catalase (PF00199) and catalase-related (PF06628) Hidden Markov Model (HMM) files were obtained from the Pfam protein structural domain database (http://pfam.xfam.org/, accessed on 16 November 2021) [61]. The hmmsearch program of HMMER 3.0 software (http://www.eddylab.org/software/hmmer3/3.0/, accessed on 16 November 2021) [62] was used to scan the rubber tree protein data [63,64]. Protein sequences of three known CAT genes in A. thaliana (AtCAT1/AT1G20630, AtCAT2/AT4G35090, and AtCAT3/AT1G20620) were downloaded from the Arabidopsis genome database (https://www.arabidopsis.org/, accessed on 10 December 2021) [65] and used as reference sequences to blast the rubber tree protein data using the BLASTP method (version 2.2.6) [63,64].…”

Section: Identification Of Hbcat Genes In Rubber Treementioning

confidence: 99%

“…The hmmsearch program of HMMER 3.0 software (http://www.eddylab.org/software/hmmer3/3.0/, accessed on 16 November 2021) [62] was used to scan the rubber tree protein data [63,64]. Protein sequences of three known CAT genes in A. thaliana (AtCAT1/AT1G20630, AtCAT2/AT4G35090, and AtCAT3/AT1G20620) were downloaded from the Arabidopsis genome database (https://www.arabidopsis.org/, accessed on 10 December 2021) [65] and used as reference sequences to blast the rubber tree protein data using the BLASTP method (version 2.2.6) [63,64]. We combined the results of the HMMER-and BlASTP-based searches and removed redundant sequences.…”

Section: Identification Of Hbcat Genes In Rubber Treementioning

confidence: 99%

Comprehensive Analysis of the Catalase (CAT) Gene Family and Expression Patterns in Rubber Tree (Hevea brasiliensis) under Various Abiotic Stresses and Multiple Hormone Treatments

Yu,

Kong,

et al. 2023

IJMS

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Catalase (CAT) is one of the key enzymes involved in antioxidant defense systems and mainly scavenges H2O2 and plays a vital role in plant growth, development, and various adverse stresses. To date, a systematic study of the CAT gene family in rubber tree has not been reported. In this study, five HbCAT gene family members were identified from the rubber tree genome, and these were mainly clustered into two subfamilies. Gene structure and motif analysis showed that exon-intron and motif patterns were conserved across different plant species. Sequence analysis revealed that HbCAT proteins contain one active catalytic site, one heme-ligand signature sequence, three conserved amino acid residues (His, Tyr, and Asn), and one peroxisome-targeting signal 1 (PTS1) sequence. Fragment duplication is a selection pressure for the evolution of the HbCAT family based on Ka/Ks values. Analysis of cis-acting elements in the promoters indicated that HbCAT gene expression might be regulated by abscisic acid (ABA), salicylic acid (SA), and MYB transcription factors; furthermore, these genes might be involved in plant growth, development, and abiotic stress responses. A tissue-specific expression analysis showed that HbCATs gradually increased with leaf development and were highly expressed in mature leaves. Gene expression profiling exhibited the differential expression of the HbCATs under cold, heat, drought, and NaCl stresses. Our results provide comprehensive information about the HbCAT gene family, laying the foundation for further research on its function in rubber tree.

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Genome-wide identification, characterization, and expression profile ofNBS-LRRgene family in sweet orange (Citrussinensis)

Cited by 23 publications

References 85 publications

Comparative genomics and bioinformatics approaches revealed the role of CC-NBS-LRR genes under multiple stresses in passion fruit

Comparative genomics and bioinformatics approaches revealed the role of CC-NBS-LRR genes under multiple stresses in passion fruit

Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions

Comprehensive Analysis of the Catalase (CAT) Gene Family and Expression Patterns in Rubber Tree (Hevea brasiliensis) under Various Abiotic Stresses and Multiple Hormone Treatments

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