Publication Roundup: CLC Genomics Workbench in the Literature
We frequently hear that scientists run into frustrating bottlenecks when analyzing data. Our CLC Genomics Workbench offers researchers a platform for easy analysis and visualization of NGS data. We’ve rounded up a few recent examples from the literature to show how this analysis tool contributes to the advancement of scientific knowledge.
Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment
First author: Tengguo Li
The Journal of Clinical Microbiology published a study about a universal human papillomavirus (HPV) typing assay. The work was completed by a team from the CDC, which used target enrichment and whole-genome sequencing for universal HPV typing. They used CLC Genomics Workbench for sequence analysis and mapping to reference sequences. Results of the study could lead to a better understanding of HPV epidemiology.
Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes
First author: Leonie Jahn
Frontiers in Microbiology ran a study by Danish scientists who analyzed the evolution of antibiotic resistance, which is a global threat to human health. The team compared different approaches to investigate how the selection regime influences the resulting genotypes and phenotypes. Their work included the use of CLC Genomics Workbench to align reads of the E. coli k12u00096 reference genome and to determine SNP and indel sites. The results contribute to increased clarity around the adaptation potential specific to genetic and phenotypic flexibility in environmental conditions.
Biosynthesis of Volatile Terpenes that Accumulate in the Secretory Cavities of Young Leaves of Japanese Pepper (Zanthoxylum Piperitum): Isolation and Functional Characterization of Monoterpene and Sesquiterpene Synthase Genes
First author: Yoshiyuki Fujita
The leaves of Japanese pepper (Zanthoxylum piperitum) contain volatile terpenes, which have antimicrobial properties and a pleasant aroma and are commonly used in the flavor, aromatherapy, cleaning product, and agrochemical industries. A team from Japan looked at the secretory cavities on the leaves of young Japanese peppers to study terpene formation. They used CLC Genomics Workbench to run total reads of RNA sequencing, and submitted their findings to Plant Biotechnology. The report provides the first characterization of three terpene synthases, clarifying our understanding of how terpenes are created.
Insights into Reston Virus Spillovers and Adaption from Virus Whole Genome Sequences
First author: César Albariño
A team at the CDC used CLC Genomics Workbench for sequence and phylogenetic analysis of Reston virus (RESTV) — one of the Ebolavirus genus, in a report from PLOS One. Though Reston virus is non-pathogenic for humans, it is associated with highly lethal hemorrhagic fever in non-human primates and pigs in the Philippines. Through this study, the team gained insight into RESTV diversity and ascertained its multiple, independent introductions into breeding facilities of non-human primates and swine farming operations in the Philippines.
Genomic and Transcriptomic Resources for Marker Development in Synchytrium endobioticum, an Elusive but Severe Potato Pathogen
First author: Friederike Busse
A team of German scientists delved into the genomic causes of Synchytrium endobioticum — a robust, tenacious pathogen that causes wart disease in potato crops. They shared their findings in a report in Phytopathology. CLC Genomics Workbench was used throughout the process to trim raw reads, assemble reads, and conduct comparative sequence analyses. The research yielded high-quality genomic and transcriptome sequencing data, including molecular markers for diagnosis and the identification of polymorphisms and differentiated pathotype groups, all of which could inform future molecular studies.