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

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

<p>Abstract</p> <p>Background</p> <p>Transcriptome sequences provide a complement to structural genomic information and provide snapshots of an organism's transcriptional profile. Such sequences also represent an alternative method for characterizing neglected species that are not expected to undergo whole-genome sequencing. One difficulty for transcriptome sequencing of these organisms is the low quality of reads and incomplete coverage of transcripts, both of which compromise further bioinformatics analyses. Another complicating factor is the lack of known protein homologs, which frustrates searches against established protein databases. This lack of homologs may be caused by divergence from well-characterized and over-represented model organisms. Another explanation is that non-coding RNAs (ncRNAs) may be caught during sequencing. NcRNAs are RNA sequences that, unlike messenger RNAs, do not code for protein products and instead perform unique functions by folding into higher order structural conformations. There is ncRNA screening software available that is specific for transcriptome sequences, but their analyses are optimized for those transcriptomes that are well represented in protein databases, and also assume that input ESTs are full-length and high quality.</p> <p>Results</p> <p>We propose an algorithm called PORTRAIT, which is suitable for ncRNA analysis of transcriptomes from poorly characterized species. Sequences are translated by software that is resistant to sequencing errors, and the predicted putative proteins, along with their source transcripts, are evaluated for coding potential by a support vector machine (SVM). Either of two SVM models may be employed: if a putative protein is found, a protein-dependent SVM model is used; if it is not found, a protein-independent SVM model is used instead. Only <it>ab initio </it>features are extracted, so that no homology information is needed. We illustrate the use of PORTRAIT by predicting ncRNAs from the transcriptome of the pathogenic fungus <it>Paracoccidoides brasiliensis </it>and five other related fungi.</p> <p>Conclusion</p> <p>PORTRAIT can be integrated into pipelines, and provides a low computational cost solution for ncRNA detection in transcriptome sequencing projects.</p

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

High-Throughput Sequencing, Characterization and Detection of New and Conserved Cucumber miRNAs

Micro RNAS (miRNAs) are a class of endogenous small non coding RNAs involved in the post-transcriptional regulation of gene expression. In plants, a great number of conserved and specific miRNAs, mainly arising from model species, have been identified to date. However less is known about the diversity of these regulatory RNAs in vegetal species with agricultural and/or horticultural importance

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

PLncDB: Plant long non-coding RNA database

10.1093/bioinformatics/btt107Bioinformatics2981068-1071BOIN