Editorial: CRISPR-Cas in Agriculture: Opportunities and Challenges

CRISPR-Cas genome editing technology is developing at a rapid pace and new molecular tools, such as CRISPR nucleases, are becoming regularly available. As part of this Research Topic, Bandyopadhyay et al. provide a comprehensive overview of Cas12a, a CRISPR nuclease formerly known as Cpf1. In their review article, the authors cover structural and mechanistic aspects of Cas12a in comparison with Cas9, the most commonly used CRISPR nuclease. They also highlight uses of Cas12a for the purpose of improving agriculturally important traits in various crops. An overview of Cas9 genome editing applications in plants is provided by El-Mounadi et al. who introduce the reader to the mechanism of Cas9 activity, methods of its delivery to plant cells (i.e., transformation techniques), give examples of improving crop traits using CRISPR-Cas9, and touch on biosafety and regulatory aspects associated with genome editing. A number of countries (e.g., the USA, Brazil, Argentina, and Japan) have already exempted genome edited crops, which do not carry transgenic DNA or novel combination of genetic material (i.e., not similarly achievable through conventional breeding), from being regulated similarly to Genetically Modified Organisms (GMOs) as genetically engineered (GE) organisms (Schmidt et al., 2020). Although the above-mentioned countries have passed legislation allowing cultivation of genome edited crops without GE regulation, the public dialogue and policy developments on the issue are evolving. In the case of Japan, Tabei et al. analyse Twitter conversation on genome-edited foods and their labelling over the period from May to October 2019. The analysis reveals that 54.5% of relevant tweets were statements opposed to food produced using genome edited crops, while only 7% were statements in favour of it. The remaining 38.5% of tweets were statements deemed neutral. Although the analysis was not necessarily representative of the wider Japanese society due to bias among Twitter users, the study underlines the importance of a continuous public dialogue on the issue of genome edited crops in Japan and the rest of the world

The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation

Chlamydomonas reinhardtii, a unicellular green alga, has been exploited as a reference organism for identifying proteins and activities associated with the photosynthetic apparatus and the functioning of chloroplasts. Recently, the full genome sequence of Chlamydomonas was generated and a set of gene models, representing all genes on the genome, was developed. Using these gene models, and gene models developed for the genomes of other organisms, a phylogenomic, comparative analysis was performed to identify proteins encoded on the Chlamydomonas genome which were likely involved in chloroplast functions (or specifically associated with the green algal lineage); this set of proteins has been designated the GreenCut. Further analyses of those GreenCut proteins with uncharacterized functions and the generation of mutant strains aberrant for these proteins are beginning to unmask new layers of functionality/regulation that are integrated into the workings of the photosynthetic apparatus

A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA metabolism and silencing.

Post-transcriptional gene silencing (PTGS) is a major mechanism regulating gene expression in higher eukaryotes. To identify novel players in PTGS, a forward genetics screen was performed on an Arabidopsis thaliana line overexpressing a strong growth-repressive gene, ETHYLENE RESPONSE FACTOR6 (ERF6). We identified six independent ethyl-methanesulfonate mutants rescuing the dwarfism of ERF6-overexpressing plants as a result of transgene silencing. Among the causative genes, ETHYLENE-INSENSITIVE5, SUPERKILLER2 and HASTY1 have previously been reported to inhibit PTGS. Notably, the three other causative genes have not, to date, been related to PTGS: UTP:RNA-URIDYLYLTRANSFERASE1 (URT1), C-TERMINAL DOMAIN PHOSPHATASE-LIKE3 (CPL3) and RESURRECTION1 (RST1). We show that these genes may participate in protecting the 3' end of transgene transcripts. We present a model in which URT1, CPL3 and RST1 are classified as PTGS suppressors, as compromisation of these genes provokes the accumulation of aberrant transcripts which, in turn, trigger the production of small interfering RNAs, initiating RNA silencing