Leveraging a de-novo long read assembly for comparative and functional genomics of the Octopus bimaculoides
Authors: Gabrielle Coffing 1; Jeremea Songco 2; Judit Pungor 2; Denise Piscopo 2; Adam Miller 2; Cris Niell 2; Andrew Kern 1
Affiliations: 1) Institute of Ecology and Evolution, University of Oregon; 2) Institute of Neuroscience, University of Oregon
Keywords: Comparative genomics & genome evolution
The California two-spot octopus (Octopus bimaculoides) was the first cephalopod genome to be sequenced (Albertin et al., 2015). While this was a landmark accomplishment, the genome assembly is highly fragmented, and thus problematic for in-depth transcriptional and single-cell analysis. As the genomes of more cephalopod species are being sequenced, comparative genomics studies will have improved power, thus it is essential to have high-quality genome assemblies and annotations (i.e., Li et al., 2019, Zhang et al., 2021). Here, we describe a de-novo assembly of a high-quality, near chromosome-level O. bimaculoides genome. The genome was sequenced to 28x coverage using Pacific Bioscience’s (PacBio) HiFi long read technology and subsequently scaffolded with Hi-C sequencing. The re-assembled O. bimaculoides genome is 2.56 Gb with a scaffold N50 of 2,761,593 bp from a total of 386.65 Gb unique PacBio HiFi data. To generate gene annotations, we mapped existing bulk RNA-sequencing data and new PacBio Iso-Seq reads onto this genome assembly. Using our novel genome, we conducted a comparative phylogenomics study to understand lineage specific evolution of octopuses and more generally, cephalopods. We examined the repeat landscape, identified novel O. bimaculoides genes, and have begun to infer whether any specific gene families played a role in developing the octopus’s unique phenotypes.