The use of long-read sequencing technologies for characterization of molluscan pathogens
Higher resolution and more accurate nucleic-acids based diagnostic methods are required to account for the high genetic diversity of pathogens affecting molluscs. Long-read, single-molecule high throughput sequencing (HTS) technologies, also known as third-generation sequencing, offers several advantages for the characterization of molluscan pathogens. These technologies allow the sequencing of fragments with tens to thousands of kilobases in length and its accuracy has improved considerably in the last years. The availability of low-cost, small and portable long-read sequencing equipment is also noteworthy. Cefas has been using these technologies for the sequencing of the genome of bacteria and viruses that infected molluscs using metagenomics or PCR tilling approaches. In contrast with short-reads HTS, long-read sequencing can resolve the assembly of challenging genomics sequences containing structural variants and repeats. Cefas has also been using these technologies in metabarcoding studies for the characterization of microbiota and specific taxa targeting reads with more than 1.4 kbp and hence increasing taxonomic resolution. Additionally, Cefas has been using long-read sequencing for the discovery of new pathogens affecting molluscs.
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