Identifying transgene insertions in <i>Caenorhabditis elegans</i> genomes with Oxford Nanopore sequencing.

ABSTRACT: Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of Caenorhabditis elegans commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human α-synuclein), a model for Parkinson's research. After scaffolding to the reference, the final assembled sequences were ∼102 Mb with N50s of 17.9 Mb and 18.0 Mb, respectively, and L90s of six contiguous sequences, r

SUBMITTER: Adams PE 

PROVIDER: S-EPMC11404476 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature