GeneTargeter: Automated In Silico Design for Genome Editing in the Malaria Parasite, Plasmodium falciparum

AutoESDCas: A Web-Based Tool for the Whole-Workflow Editing Sequence Design for Microbial Genome Editing Based on the CRISPR/Cas System

Genome editing is the basis for the modification of engineered microbes. In the process of genome editing, the design of editing sequences, such as primers and sgRNA, is very important for the accurate positioning of editing sites and efficient sequence editing. The whole process of genome editing involves multiple rounds and types of editing sequence design, while the development of related whole-workflow design tools for high-throughput experimental requirements lags. Here, we propose AutoESDCas, an online tool for the end-to-end editing sequence design for microbial genome editing based on the CRISPR/Cas system. This tool facilitates all types of genetic manipulation covering diverse experimental requirements and design scenarios, enables biologists to quickly and efficiently obtain all editing sequences needed for the entire genome editing process, and empowers high-throughput strain modification. Notably, with its off-target risk assessment function for editing sequences, the usability of the design results is significantly improved. AutoESDCas is freely available at https://autoesdcas.biodesign.ac.cn/with the source code at https://github.com/tibbdc/AutoESDCas/.

CRISPR-Cas13 in malaria parasite: Diagnosis and prospective gene function identification

Malaria caused by Plasmodium is still a serious public health problem. Genomic editing is essential to understand parasite biology, elucidate mechanical pathways, uncover gene functions, identify novel therapeutic targets, and develop clinical diagnostic tools. Recent advances have seen the development of genomic diagnostic technologies and the emergence of genetic manipulation toolbox comprising a host of several systems for editing the genome of Plasmodium at the DNA, RNA, and protein level. Genomic manipulation at the RNA level is critical as it allows for the functional characterization of several transcripts. Of notice, some developed artificial RNA genome editing tools hinge on the endogenous RNA interference system of Plasmodium. However, Plasmodium lacks a robust RNAi machinery, hampering the progress of these editing tools. CRISPR-Cas13, which belongs to the VI type of the CRISPR system, can specifically bind and cut RNA under the guidance of crRNA, with no or minimal permanent genetic scar on genes. This review summarizes CRISPR-Cas13 system from its discovery, classification, principle of action, and diagnostic platforms. Further, it discusses the application prospects of Cas13-based systems in Plasmodium and highlights its advantages and drawbacks.

AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms

Advances in genetic manipulation and genome engineering techniques have enabled on-demand targeted deletion, insertion, and substitution of DNA sequences. One important step in these techniques is the design of editing sequences (e.g. primers, homologous arms) to precisely target and manipulate DNA sequences of interest. Experimental biologists can employ multiple tools in a stepwise manner to assist editing sequence design (ESD), but this requires various software involving non-standardized data exchange and input/output formats. Moreover, necessary quality control steps might be overlooked by non-expert users. This approach is low-throughput and can be error-prone, which illustrates the need for an automated ESD system. In this paper, we introduce AutoESD (https://autoesd.biodesign.ac.cn/), which designs editing sequences for all steps of genetic manipulation of many common homologous-recombination techniques based on screening-markers. Notably, multiple types of manipulations for different targets (CDS or intergenic region) can be processed in one submission. Moreover, AutoESD has an entirely cloud-based serverless architecture, offering high reliability, robustness and scalability which is capable of parallelly processing hundreds of design tasks each having thousands of targets in minutes. To our knowledge, AutoESD is the first cloud platform enabling precise, automated, and high-throughput ESD across species, at any genomic locus for all manipulation types.