Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea

Ya Min,Elena M Kramer

doi:10.1038/s41598-020-76750-7

Ya Min, Elena M Kramer

Open Access

https://doi.org/10.1038/s41598-020-76750-7

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Journal: Scientific Reports	Publication Date: Nov 12, 2020
Citations: 12	License type: open-access

Affiliation: Harvard University

Abstract

The earliest phases of floral development include a number of crucial processes that lay the foundation for the subsequent morphogenesis of floral organs and success in reproduction. Currently, key transcriptional changes during this developmental window have been characterized in the model species Arabidopsis thaliana, but little is known about how transcriptional dynamics change over the course of these developmental processes in other plant systems. Here, we have conducted the first in-depth transcriptome profiling of early floral development in Aquilegia at four finely dissected developmental stages, with eight biological replicates per stage. Using differential gene expression analysis and weighted gene co-expression network analysis, we identified both crucial genes whose expression changes mark the transitions between developmental stages and hub genes in co-expression modules. Our results support the potential functional conservation of key genes in early floral development that have been identified in other systems, but also reveal a number of previously unknown or overlooked loci that are worthy of further investigation. In addition, our results highlight not only the dynamics of transcriptional regulation during early floral development, but also the potential involvement of the complex, essential networks of small RNA and post-translational regulation to these developmental stages.

Highlights

The earliest phases of floral development include a number of crucial processes that lay the foundation for the subsequent morphogenesis of floral organs and success in reproduction
Using a candidate gene approach, previous studies have revealed the sub-functionalization of the B-class organ identity g enes[10,11,12] and that the JAGGED homolog is crucial for initiation of the floral organ primordia[13], but genome scale studies to date have focused on late stage floral organ d evelopment[14,15,16]
Similar studies at finely dissected stages of early floral development have only been done in the model species A. thaliana[79,80,81], analyses have been performed in tomato shoot apical meristems (SAMs), and early inflorescences of model monocot species[82,83]

Summary

Introduction

The earliest phases of floral development include a number of crucial processes that lay the foundation for the subsequent morphogenesis of floral organs and success in reproduction. The earliest phase of floral meristem (FM) development requires exquisite coordination among many different developmental processes These include the proper initiation and patterning of the floral organs, maintenance of the size of the FM during organ initiation, the eventual termination of the FM activity to ensure the correct number of whorls, and the overlay of the floral organ identity programs onto the primordia so that the boundaries of gene expression domains synchronize precisely with the physical boundaries between the primordia. Coordination of these processes is achieved through crosstalk between numerous regulatory frameworks at multiple levels, ranging from transcriptional regulation, to RNA stability, to epigenetic modification, and protein stability. Using a candidate gene approach, previous studies have revealed the sub-functionalization of the B-class organ identity g enes[10,11,12] and that the JAGGED homolog is crucial for initiation of the floral organ primordia[13], but genome scale studies to date have focused on late stage floral organ d evelopment[14,15,16]

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Results

Conclusion