25 years from the Arabidopsis genome: A Catalyst for Omics Breakthroughs in Plant Biology and Crop Research

About this Research Topic

Background

Twenty-five years ago, the release of the first complete Arabidopsis thaliana genome marked a pivotal turning point in plant science, providing the foundation to define and understand the function of coding genes, as well as the non-coding elements (epigenome, non-coding genes) unjustly labelled “junk” DNA for many years. Since then, sequencing in plant biology has expanded exponentially, thanks to the development of massive parallel sequencing. Second-generation sequencing, already allowed going from the genomic assembly of a single accession to pan-genomes spanning tenths of accessions, and to whole populations sequencing of rare genetic variants. Cost reduction also paved the way for more complex transcriptomic experiments, dissecting the dynamics of plants’ phenotypic plasticity under stress, from heterologous organisms and tissues to single cells resolution. More recently, the advent of long-read third generation sequencing led to refined telomere-to telomere genome assemblies for Arabidopsis and crop species and enabled direct detection of nucleic acid modifications (Nanopore technologies) providing unprecedented resolution in genome understanding.

Marking the 25th anniversary of the publication of the first complete Arabidopsis thaliana genome, this Research Topic aims to celebrate and reflect on the profound impact that this milestone has had on plant science. This collection seeks to highlight research made possible by having access to the first fully sequenced plant genome, showcasing recent breakthroughs in the field of plant sequencing. Particular emphasis will be placed on studies exploring the integration of novel sequencing techniques and their applications in understanding genome organization, transcriptional regulation, and epigenomics dynamics in Arabidopsis, at both fundamental level and/or in the context of stress responses or population genomics. As the future of plant sciences moves to functional translation into crop species from the model plant Arabidopsis, this Topic will also include translational research and novel sequencing studies on non-model organisms and crops that relied in previous knowledge generated in Arabidopsis, especially at the genomic level (i.e., genome annotations). By gathering the most recent advances and perspectives, this Research Topic will commemorate how 25 years of Arabidopsis genomics have revolutionized plant biology and continue to guide the next generation of research in plant systems and applied crop science

This Research Topic will welcome novel research in the fields below:

• Sequencing the non-coding genome — Exploring the epigenetic and epitranscriptomic landscapes through sequencing of DNA and RNA modifications, non-coding RNAs, and regulatory elements, particularly in the context of plant environmental responses and adaptation.
• Sequencing the dynamics of phenotypic plasticity under stress — Investigating stress-induced molecular dynamics using time-resolved transcriptomic and multi-omic sequencing approaches to capture the temporal and integrative responses underlying phenotypic plasticity.
• Novel sequencing technologies and large-scale applications — Employing advanced sequencing platforms such as long-read technologies (PacBio, Oxford Nanopore) for high-quality genome assembly, population-level structural variant detection, and direct detection of nucleic acid modification.
• Translational research on crops and non-model species enabled by previous knowledge from the Arabidopsis genome.

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Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Data Report
• Editorial
• FAIR² Data
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Arabidopsis Genome, 25 Years, Arabidopsis Sequencing

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