Biomphalaria and beyond, gastropod immunogenomics
Professor Coen Adema, University of New Mexico, USA
The Biomphalaria glabrata (Hygrophila, Panpulmonata) genome characterisation was initiated in the mid-2000s as a traditional, multi-institute project, and generated an amalgam of several types of short read sequence data (<800 bases): BES, Sanger, 454 and PE (short,3k,8k) Illumina. The resulting genome assembly (Newbler-SOAP) was fragmented, also due to genome complexity (~1Gbp, 63% AT content, ~50% repetitive content). While effective for annotation of genes functioning in immunity and other aspects of snail biology, the assembly includes gaps and inversions within scaffolds, split-, incomplete- and missing genes. Long reads (Nanopore MinION, ≤79kb) from select BAC clones (~136kb average, restriction digested) help greatly to resolve such problems. For comparative immunogenomics, genomes of additional panpulmonata were captured (Illumina Nextseq, 150b PE reads, modest coverage), including several Stylommatophora and hygrophilids from the families Planorbidae, Lymnaeidae and Physidae. With public NGS data this enables the tracking of phylogenetic distribution of snail immune genes. Examplified by revealing intraspecifically diverse mitogenomes in Physella acuta; identifying phylogenetic branch points for evolution of gastropod immunity (eg the Laevapex fuscus (Ancylidae) genome for tracking FREP gene expansion in Planorbidae); and connecting molecular immunology to field study by ecogenomics, “omics” data inspire and compel broad and in-depth, collaborative consideration of molluscan biology.
Natural selection on immune function
Otto Seppälä, University of Innsbruck, Austria
Parasites threaten all free-living species. The immune system is the most important barrier against infections and understanding the form and strength of natural selection on immune activity is crucial for predicting the evolution of parasite resistance. Ecoimmunological studies that examine selection on immune defence typically measure the end products of one or maximum few immunological cascades in invertebrates. This approach was initially motivated by the assumed simplicity of invertebrate immune systems. Over recent decades, however, comparative immunology with aid from genomics has shown that invertebrate immune systems are highly complex and diverse. This provides new challenges for evolutionary ecological research on immune function. Here, Otto Seppälä presents ongoing work on natural selection on immune activity in Lymnaea stagnalis snails. First, Professor Seppälä shows how natural selection operates on two phenotypic immune traits. Then, Professor Seppälä will show how this work is expanded to cover a broader range of immunological mechanisms at the gene expression level. To identify relevant components of snail immune system their transcriptome responses to bacterial and trematode pathogens were characterised by applying Illumina based RNAseq. In current experiments, the expression levels of selected target genes that cover different branches of snail immune system are used to estimate selection on immune activity.
The genome of the invasive zebra mussel, Dreissena polymorpha
Dr Michael McCartney, University of Minnesota, USA
The Eurasian zebra mussel (Dreissena polymorpha) continues to spread across Europe and North America, causing billions of dollars in damage and dramatically altering aquatic ecosystems. Yet its genome has not been sequenced, and zebra mussels diverged from their closest sequenced relative more than 450 million years ago. Here we use long-read sequencing and Hi-C scaffolding, and generate the most contiguous chromosome-level mollusk assembly to date. Using comparative analysis and transcriptomics, we shed light on processes that influence invasive spread, including shell formation, byssal thread synthesis, and high temperature tolerance. The McCartney group identify several Steamer-Like Elements, retrotransposons linked to transmissible cancer in marine clams. Finally, the talk describes the unique D. polymorpha mitochondrial genome— the longest ever reported in Eumetazoa, with its abundant tandem repeats. Together these findings create a rich resource for research and control of this destructive invasive, and for genomic studies of several underexplored branches of the bivalve tree of life.