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Bioinformatics studies on structures, functions and diversifications of rolling leaf related genes in rice (Oryza sativa L.)

Published online by Cambridge University Press:  11 November 2020

Md. Jahangir Alam Open the ORCID record for Md. Jahangir Alam [Opens in a new window] ,
Md. Alamin ,
Most. Humaira Sultana ,
Md. Asif Ahsan ,
Md. Ripter Hossain ,
S.M. Shahinul Islam  and
Md. Nurul Haque Mollah Open the ORCID record for Md. Nurul Haque Mollah [Opens in a new window]
Md. Jahangir Alam
Affiliation:
Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi6205, Bangladesh
Md. Alamin
Affiliation:
Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi6205, Bangladesh
Most. Humaira Sultana
Affiliation:
Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi6205, Bangladesh
Md. Asif Ahsan
Affiliation:
Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi6205, Bangladesh
Md. Ripter Hossain
Affiliation:
Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi6205, Bangladesh
S.M. Shahinul Islam
Affiliation:
Plant Biotechnology and Genetic Engineering Laboratory, Institute of Biological Sciences, University of Rajshahi, Rajshahi6205, Bangladesh
Md. Nurul Haque Mollah*
Affiliation:
Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi6205, Bangladesh
*
*Corresponding author. E-mail: mollah.stat.bio@ru.ac.bd
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Abstract

Leaf morphology of crop plants has significant value in agronomy. Leaf rolling in rice plays a vital role to increase grain yield. However, collective information on the rolling leaf (RL) genes reported to date and different comparative bioinformatics studies of their sequences are still incomplete. This bioinformatics study was designed to investigate structures, functions and diversifications of the RL related genes reported till now through several studies. We performed different comparative and functional analyses of the selected 42 RL genes among 103 RL genes using different bioinformatics techniques including gene structure, conserved domain, phylogenetic, gene ontology (GO), transcription factor (TF), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein–protein network. Exon-intron organization and conserved domain analysis showed diversity in structures and conserved domains of RL genes. Phylogenetic analysis classified the proteins into five major groups. GO and TF analyses revealed that regulation-related genes were remarkably enriched in biological process and 10 different TF families were involved in rice leaf rolling. KEGG analysis demonstrated that 14 RL genes were involved in the KEGG pathways, among which 50% were involved in the metabolism pathways. Of the selected RL proteins, 55% proteins were non-interacting with other RL proteins and OsRL9 was the most interacting RL protein. These results provide important information regarding structures, conserved domains, phylogenetic revolution, protein–protein interactions and other genetic bases of RL genes which might be helpful to the researchers for functional analysis of new candidate RL genes to explore their characteristics and molecular mechanisms for high yield rice breeding.

Keywords

diversificationgene ontology and transcription factor analysisgene structure and functionKEGG pathway analysisphylogenetic analysisprotein–protein interaction networkricerolling leaf related genes
Type
Research Article
Information
Plant Genetic Resources , Volume 18 , Issue 5 , October 2020 , pp. 382 - 395
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press on behalf of NIAB

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