Dataset Information

Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome.

ABSTRACT: GRAS genes belong to the plant-specific transcription factors (TF's) family that are known to be involved in plant growth and development. In this study, we have identified 37 genes from the bottle gourd genome that encodes for GRAS TF's. Except for the SCLA, we were able to identify at least one gene from each of the 17 subfamilies. Gene structure and chromosomal analysis showed that maximum seven genes are present on Chr7 followed by six genes on Chr1. The subcellular location analysis revealed that most of the genes were localized in the nucleus, except for a few in chloroplast and mitochondria. Additionally, we have identified one tandem gene duplication event on Chr7 and three major motifs that were present in all the GRAS genes. Furthermore, the protein-protein interaction prediction and gene expression analysis showed five candidate hub-genes interact with various other genes and thus probably control the expression of interacting partners in different plant tissues. Overall, this study provides a comprehensive analysis of GRAS transcription factors in bottle gourd genome which could be further extended to other vegetable crops.

SUBMITTER: Sidhu NS

PROVIDER: S-EPMC7459283 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome.

Sidhu Navjot Singh NS Pruthi Gomsie G Singh Sahildeep S Bishnoi Ritika R Singla Deepak D

Scientific reports 20200831 1

GRAS genes belong to the plant-specific transcription factors (TF's) family that are known to be involved in plant growth and development. In this study, we have identified 37 genes from the bottle gourd genome that encodes for GRAS TF's. Except for the SCLA, we were able to identify at least one gene from each of the 17 subfamilies. Gene structure and chromosomal analysis showed that maximum seven genes are present on Chr7 followed by six genes on Chr1. The subcellular location analysis reveale ...[more]

PMID: 32868844

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Project description:The GRAS [GRI (Gibberellic Acid Insensitive), RGA (Repressor of GAI-3 mutant), and SCR (Scarecrow)] transcription factors play a pivotal role in the development and stress responses of plants. Eucalyptus is an important fast-growing tree species worldwide, yet its poor cold tolerance limits its cultivation range. This study conducted a bioinformatics analysis of Eucalyptus grandis GRAS family and investigated the expression patterns of GRAS genes in different ploidy Eucalyptus under cold treatment. This study identified 92 EgrGRAS genes, which were divided into eight subfamilies. Interspecies synteny analysis found that E. grandis and Populus trichocarpa have more syntenic GRAS gene pairs. Chromosome localization analysis revealed that 90 EgrGRAS genes were found to be unevenly distributed across 11 chromosomes. Gene structure analysis found similar intron-exon structures in EgrGRAS genes. Protein motif analysis revealed that proteins within the same subfamily have certain structural similarities. The physical and chemical properties of the proteins encoded by EgrGRAS genes vary, but the ranges of amino acid numbers, molecular weights, and isoelectric points (pI) are similar to those of GRAS proteins from other species. Subcellular localization prediction using software found that 56 members of EgrGRAS family are localized in the nucleus, with a few members localized in the cytoplasm, chloroplasts, and mitochondria. Tobacco subcellular localization experiments verified a nuclear-localized GRAS transcription factor. Cis-acting element analysis predicted that EgrGRAS genes are involved in the growth as well as the response to hormones, light induction, and low-temperature stress. Transcriptome data analysis and quantitative real-time PCR (qRT-PCR) experiments in diploid and triploid Eucalyptus urophylla found that some EgrGRAS genes exhibited upregulated expression under different cold treatment durations, with certain genes from the LISCL, PAT1, and DELLA subfamilies significantly upregulated in triploid Eucalyptus. These EgrGRAS transcription factors may play an important role in Eucalyptus response to cold stress. The study lays a molecular foundation for the breeding of cold-resistant Eucalyptus varieties.

Project description:BackgroundThe cysteine-rich receptor-like kinases (CRKs) family in plants have been reported to perform multiple functions against various stresses. However, the CRK family in bottle gourd (Lagenaria siceraria) has not been well-explored. Herein, a comprehensive genome-wide identification and characterization of the CRK gene family has been carried out in bottle gourd under Genome-wide characterization of CRK genes in bottle gourds under Fusarium oxysporum f. sp. lagenariae infection.ResultsA stringent set of bioinformatic analyses identified 18 LsCRKs in the bottle gourd genome. Chromosomal mapping of the identified LsCRKs revealed that the LsCRKs were distributed in 4 chromosomes in the bottle gourd genome. The phylogenetic analysis of LsCRKs divided them into two subgroups on the tree. The synteny and collinearity analysis of the LsCRKs among themselves and other plant CRKs provided insights into their conservancy and expansion. Gene ontology analysis of the identified LsCRKs suggested their possible roles in regulating different physiological processes and stress responses in bottle gourd. To assess the involvement of the LsCRKs under F. oxysporum f. sp. lagenariae infection, bottle gourd seedlings were transplanted into the pots with F. oxysporum-infected soil. The expression analysis revealed that multiple LsCRKs exhibited induced expression, suggesting their involvement in bottle gourd-F. oxysporum interactions. Additionally, the protein-protein interaction analysis suggested some important interacting partners of LsCRKs crucial to different physiological processes in bottle gourd.ConclusionsThe present work explored and analyzed the LsCRKs in bottle gourd. Functional predictions and interaction network analysis suggested the roles of LsCRKs in modulating multiple physiological processes in bottle gourd. The expression dynamics of LsCKRs under fungal pathogen infection suggest their involvement in stress response in bottle gourds. Overall, the results of the study provide basic information about the CRK family in bottle gourds and their involvement in fungal pathogen response.

Dataset Information

Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome.

Publications

Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome.

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