Yesprit and Yeaseq: Applications for designing primers and browsing sequences for research using the fourSchizosaccharomycesspecies

Abstract

The polymerase chain reaction (PCR)-based gene targeting method, which can delete a specific gene or introduce tags, has been widely utilized to study gene function in fission yeast. One of the critical steps in this method is to design primers for amplifying DNA fragments of deletion or tagging modules and for checking the integration of those DNA fragments at designated loci. Although the primer design tool Pombe PCR Primer Program (PPPP) is available for Schizosaccharomyces pombe, there is no such publicly available application for the other three fission yeast species, S. cryophilus, S. japonicus, and S. octosporus. Likewise, no application enabling DNA/protein sequence retrieval for these three fission yeast species is available either. Therefore, access to such functionality would substantially assist in retrieval of gene sequences of interest and primer design in these fission yeast species. In this report, we describe two applications for fission yeast study: Yesprit and Yeaseq.Yesprit is a primer design tool for strain construction using the PCR-based method, and Yeaseq is a sequence viewer that can acquire the DNA/protein sequences of specific genes. Both tools can be run on the Windows, macOS, and Linux platforms.We believe that the Yesprit and Yeaseq will facilitate research using the four fission yeast species. Take Aways• Yesprit designs primers for gene deletion/tagging in the four fission yeasts.• Gene deletion and tagging using Yesprit-designed primers verified its utility.• Yeaseq can retrieve DNA/protein sequences of the four fission yeast species.• Yeaseq helps construct temperature-sensitive mutants of S. japonicus. K E Y W O R D S fission yeast, PCR-based gene targeting, primer design tool, sequence viewer 1 | INTRODUCTION Fission yeasts are model organisms that have been extensively used in biological research because, although unicellular, they share many biological processes with metazoans, such as the eukaryotic cell cycle,

GetPrimers: A generalized PCR‐based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems

“…• GetPrimers was validated across multiple organisms and experimental setups. genome of S. cerevisiae and S. pombe (Cummings et al, 2015;Penkett et al, 2006;Wang et al, 2021;Yofe & Schuldiner, 2014).…”

“…Moreover, to verify whether the cassette integration is correct and precise, researchers still must manually design verification primers for each targeted gene locus. Therefore, a couple of bioinformatic tools have been developed to perform automatic primer designing based on the reference genome of S. cerevisiae and S. pombe (Cummings et al, 2015; Penkett et al, 2006; Wang et al, 2021; Yofe & Schuldiner, 2014). Unfortunately, for fusion PCR‐based gene targeting method, no automatic primer design tool is available so far.…”

GetPrimers: a generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems

“…Moreover, to verify whether the cassette integration is correct and precise, researchers still must manually design verification primers for each targeted gene locus. Therefore, a couple of bioinformatic tools have been developed to perform automatic primer designing based on the reference genome of Saccharomyces cerevisiae and Schizosaccharomyces pombe [Penkett, Birtle, and Bähler 2006; Yofe and Schuldiner 2014; Cummings, Joh, and Motamedi 2015; Wang, Xu, Wang, Liu, Lou, and Sugiyama 2021]. Unfortunately, for fusion-PCR-based gene targeting method, no automatic primer design tool is available so far.…”