Evolutionary-flexibility-in-flooding-response-2019

Code and supplementary files used in analysis for "Evolutionary flexibility in flooding response circuitry in angiosperms" (2019)

Title: Evolutionary flexibility in flooding response circuitry in angiosperms

Authors: Mauricio A. Reynoso, Kaisa Kajala, Marko Bajic, Donnelly A. West, Germain Pauluzzi, Andrew Yao, Katie Hatch, Kristina Zumstein, Margaret Woodhouse, Joel Rodriguez-Medina, Neelima Sinha, Siobhan M. Brady, Roger B. Deal, Julia Bailey-Serres

Journal: Science

Abstract:

Flooding due to extreme weather threatens crops and ecosystems. To understand variation in gene regulatory networks activated by submergence,we conducted a high-resolution analysis of chromatin accessibility and gene expression at three scales of transcript control in four angiosperms, ranging from a dryland-adapted wild species to a wetland crop. The data define a cohort of conserved submergence-activated genes with signatures of overlapping cis-regulation by four transcription factor families. Syntenic genes are more highly expressed than nonsyntenic genes, yet both can have the cismotifs and chromatin accessibility associated with submergence up-regulation. Whereas the flexible circuitry spans the eudicot-monocot divide, the frequency of specific cis-motifs, extent of chromatin accessibility, and the degree of submergence activation is more prevalent in thewetland crop andmay have adaptive importance.

Code used by topic

• ATAC-seq
• RNA mapping for rice
• Differential Gene Expression by limma-voom
• Ribotaper for periodicity
• Clustering
• Cross-species comparisons using Phytozome gene families

Other resources by topic

• Genome browser - CoGe viewer of ATAC-seq, nuclear RNA, total RNA, TRAP RNA and Ribo-seq
• Syntenic relationships for cross-species comparisons
• Cytoscape files for Figure 4