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Title: Identification of novel flowering genes using RNA-Seq pipeline employing combinatorial approach in Arabidopsis thaliana time-series apical shoot meristem data

Authors: Sumukh Deshpande; Anne James; Chris Franklin; Lindsey Leach; Jianhua Yang

Addresses: Faculty of Engineering, Environment and Computing, School of Computing, Electronics and Mathematics, Coventry University, Coventry CV1 2JH, UK ' Faculty of Engineering, Environment and Computing, School of Computing, Electronics and Mathematics, Coventry University, Coventry CV1 2JH, UK ' School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK ' School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK ' Faculty of Engineering, Environment and Computing, School of Computing, Electronics and Mathematics, Coventry University, Coventry CV1 2JH, UK

Abstract: Floral transition is a crucial event in the reproductive cycle of a flowering plant during which many genes are expressed that govern the transition phase. Identification of additional genes connected to flowering genes is vital since they may regulate flowering genes and vice versa. Through our study, expression values of additional genes have been found similar to flowering genes FLC and LFY in the transition phase. The presented approach plays a crucial role in this discovery. An RNA-Seq computational pipeline was developed for identification of novel genes involved in floral transition from A. thaliana apical shoot meristem time-series data. By intersecting differentially expressed genes (DEGs) from Cuffdiff, DEseq and edgeR, we identified 30 genes as principle regulators in the transition phase. Additionally, expression profiles of highly connected genes from network analysis revealed 76 genes with non-functional association and high correlation to FLC and LFY suggesting their potential role in floral regulation.

Keywords: apical shoot; flowering; pipeline; Cuffdiff; step analysis; differential expression; enrichment; Arabidopsis thaliana.

DOI: 10.1504/IJBRA.2020.104853

International Journal of Bioinformatics Research and Applications, 2020 Vol.16 No.1, pp.25 - 58

Received: 16 Mar 2017
Accepted: 27 Nov 2017

Published online: 02 Feb 2020 *

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