Antarctic Flies and Mangrove Killifish: A Tale Of Two Assemblies

Emerging sequencing technologies and assembly algorithms make possible the de novo assembly of genomes of interesting and unique organisms. However, these technologies also come with challenges and limitations, including short read length, error rates and error types, such as mismatches and insertions and deletions. Additionally, existing biological variation such as heterozygosity, large-scale rearrangements, and repetitive elements, complicate the de novo assembly process. I present advances in two contrasting assembly projects with unique challenges. The first is the genome assembly and annotation of the only fly endemic to Antarctica, Belgica antarctica. The first look at the genome reveals an unusually small genome with a low repeat content, including a lack of transposable elements, which are mainly limited to retro-elements. Comparison to other dipteran genomes reveals that genes associated with cell membrane and nucleotide metabolism are positively enriched in the B. antarctica genome, whereas genes implicated in dehydration survival in other midge species are notably absent. I will also describe the assembly successes and challenges of the approximately one gigabase genome of the mangrove rivulus, Kryptolebias marmoratus, an internally self-fertilizing hermaphroditic vertebrate. A draft assembly is generated through a combination of long- and short-insert libraries sequenced on multiple platforms: SOLiD sequencing of long mate pair libraries, Illumina HiSeq 2000 sequencing of short-insert libraries and Ion Torrent PGM long reads and mate pair sequencing. The two assemblies highlight the exciting possibilities for biological interpretation from new genome projects.