The Full Genome Sequence of an Antarctic Microbe Constructed Using a Rapid, Portable Sequencer and a Hybrid Assembly

• Main Author: Boles, Bruce Wyatt
• Format: Text
• Language: unknown
• Published: TRACE: Tennessee Research and Creative Exchange 2019
• Subjects: Bioinformatics; Biology; Environmental Microbiology and Microbial Ecology; Genomics; Antarctic; Antarc*
• Online Access: https://trace.tennessee.edu/utk_eureca/2019/artsscience/22; https://trace.tennessee.edu/cgi/viewcontent.cgi?article=1261&context=utk_eureca

Microbial genomes contain combinations of nucleotides that code for genes which subsequently determines the function of the cell. This information provides significant insight into the unique niche of microbes from extreme environments. Here we use two sequencing technologies, the Oxford Nanopore MinION with accompanying software and Illumina HiSeq, to generate a hybrid genome for a Shewanella strain isolated from an Antarctic glacier. Bioinformatic programs, Albacore and SPAdes, allowed us to decrease the time of genome assembly while also obtaining a large quantity of information related to the Shewanella sp. Our combined approach yielded a high quality genome assembly 5.3 Mb in length, consisting of 24 scaffolded contigs with an N50 value of 2.8 Mb. The hybrid assembly method allowed for use of higher quality data than older methods to generate the genome sequence. After gene annotation, using prokka, we found several genes that inform us on the lifestyle of this isolate including a potentially horizontally transferred fabf gene, polar flagellar synthesis pathway, and the QseC-QseB (quorum sensing) two-component regulatory system. Ultimately, we aim to modify our pipeline for remote genome sequencing to extract information from microbial field samples in remote locations allowing us to understand microbial life in environmental conditions.