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

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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.

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Most cited references 31

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Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known. Comparison with established databases showed that 25% of our domain set could not be deduced from SwissProt and 41% could not be annotated by Pfam. SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homologous domains in focal adhesion kinases; (ii) previously unknown domain families, including a citron-homology domain; (iii) putative functions of domain families after identification of additional family members, for example, a ubiquitin-binding role for ubiquitin-associated domains (UBA); (iv) cellular roles for proteins, such predicted DEATH domains in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY domains in both marenostrin/pyrin and Midline 1; (vi) domains in unexpected phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exemplified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.

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The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling.

Y Helariutta, H Fukaki, J Wysocka-Diller … (2000)

Asymmetric cell divisions play an important role in the establishment and propagation of the cellular pattern of plant tissues. The SHORT-ROOT (SHR) gene is required for the asymmetric cell division responsible for formation of ground tissue (endodermis and cortex) as well as specification of endodermis in the Arabidopsis root. We show that SHR encodes a putative transcription factor with homology to SCARECROW (SCR). From analyses of gene expression and cell identity in genetically stable and unstable alleles of shr, we conclude that SHR functions upstream of SCR and participates in a radial signaling pathway. Consistent with a regulatory role in radial patterning, ectopic expression of SHR results in supernumerary cell divisions and abnormal cell specification in the root meristem.

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The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root.

Laura Di Laurenzio, Joanna W. Wysocka-Diller, Jocelyn Malamy … (1996)

In the Arabidopsis root meristem, initial cells undergo asymmetric divisions to generate the cell lineages of the root. The scarecrow mutation results in roots that are missing one cell layer owing to the disruption of an asymmetric division that normally generates cortex and endodermis. Tissue-specific markers indicate that a heterogeneous cell type is formed in the mutant. The deduced amino acid sequence of SCARECROW (SCR) suggests that it is a member of a novel family of putative transcription factors. SCR is expressed in the cortex/endodermal initial cells and in the endodermal cell lineage. Tissue-specific expression is regulated at the transcriptional level. These results indicate a key role for SCR in regulating the radial organization of the root.

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Author and article information

Contributors

Deepak Singla: deepak@pau.edu

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 31 August 2020

Publication date PMC-release: 31 August 2020

Publication date Collection: 2020

Volume: 10

Electronic Location Identifier: 14338

Affiliations

GRID grid.412577.2, ISNI 0000 0001 2176 2352, School of Agricultural Biotechnology, , Punjab Agricultural University, ; Ludhiana, 141004 India

Article

Publisher ID: 71240

DOI: 10.1038/s41598-020-71240-2

PMC ID: 7459283

PubMed ID: 32868844

SO-VID: 3587c4f1-7577-476a-af21-34acc1f34970

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 20 April 2020

Date accepted : 6 August 2020

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ScienceOpen disciplines: Uncategorized

Keywords: data mining,computational biology and bioinformatics,plant sciences,phylogenetics

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ScienceOpen disciplines: Uncategorized

Keywords: data mining, computational biology and bioinformatics, plant sciences, phylogenetics

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

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Abstract

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Irish Journal of Agricultural and Food Research

Most cited references 31

SMART, a simple modular architecture research tool: identification of signaling domains.

The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling.

The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root.

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