Unravelling the supergene for colour polymorphism in the grove snail Cepaea nemoralis
Dr Suzanne Saenko, Naturalis Biodiversity Centre, The Netherlands
Professor Menno Schilthuizen, Naturalis Biodiversity Centre, the Netherlands
The land snail Cepaea nemoralis has been one of the most important models in studying colour polymorphism in an ecological and evolutionary context. The shell colour is partially controlled by a supergene, ie a cluster of genes inherited as a single locus due to tight physical linkage. Functional dissection of this locus can provide important insights into supergene evolution and the role of genome structure in adaptation, but has so far been prevented by lack of genomic resources. Obtaining high-quality genome assembly, however, is challenging because of the size and repetitive nature of snail genomes. Here, the results of C. nemoralis whole genome sequencing using PacBio long-read technology and the (dis)advantages of several genome assemblers will be discussed. Furthermore, the preliminary data on the identification of the shell colour supergene will be presented as well.
Evolution of light-sensing proteins informs the multiple origins of eyes in bivalves
Dr Jeanne Serb, Iowa State University, USA
Understanding the evolutionary origin of eyes is of great interest to biologists because eyes provide insight into how complex phenotypes can arise through redeployment and elaboration of genetic pathways. Yet, this goal cannot be realised without studying closely related lineages that include eyeless and eyed taxa with independently-derived eye types. To understand how spatiotemporal changes to gene expression have played a role in the evolution of eyes, a combination of tissue-specific transcriptomes and genome assembly will be used to identify genes involved in phototransduction from species spanning the taxonomic and ocular diversity of pteriomorphian bivalves. Data will be analysed in a phylogenetic framework to address the following questions: 1) Do lineages with eyes also have expansions of phototransduction gene families? 2) How similar are the phototransduction pathways between the different photoreceptive structures within and among species? and 3) Do eyes acquire phototransduction pathways using the same evolutionary process or does each eye type have a unique evolutionary trajectory to photoreception? The project will identify molecular mechanisms underlying mantle, eyespot, and ocular photoreception across morphologically diverse structures while determining the roles of adaptation and exaptation in eye evolution.
MolluscDB: open access to genomes and transcriptomes of many species
Professor Mark Blaxter, Wellcome Sanger Institute, UK
The mollusc research community has generated large scale genomic and transcriptomic datasets for many species. These data, generated for diverse purposes, from deep phylogeny to supporting shellfish farming, are largely dispersed and inaccessible in an integrated way. We have developed GenomeHubs, a system for the display, sharing and interrogation of genomic data based on the stable Ensembl database model, GenomeHubs make the integration of data from diverse sources possible through public application programming interfaces. We have built MolluscDB, a GenomeHubs database for Mollusca. Importantly, for MolluscDB, we have adapted the underlying database to be able to include species that only have transcriptome data. Currently, MolluscDB presents genomes and reassembled transcriptomes for 23 species, including 15 for which only transcriptome data are available. I will illustrate the exploitation of these data in phylogenetics and in identifying clade-specific gene family expansions. As the Earth BioGenome Project and the UK Darwin Tree of Life projects get underway, with the prospect of many hundreds of new mollusc genomes, resources such as MolluscDB will become invaluable for the wider community. MolluscDB v1 was built by Carlos Caurcel and Richard Challis with assistance from Dominik Laetsch and Kevin Cocot. Development was funded by an EU ITN award.
Cephalopod genomics and the evolution of novelty
Dr Carrie Albertin, Marine Biological Laboratory, Woods Hole, USA
Coleoid cephalopods (octopuses, squid, and cuttlefish) have a suite of evolutionary innovations, including complex centralised nervous systems and camera-like eyes, which are classic examples of convergent evolution with vertebrates. Coleoids also present a number of true novelties that have no obvious correlations in other animals, such as their adaptive coloration system and sucker-lined arm crown. To study the genetic bases underlying these morphological innovations, the Albertin group sequenced the genome of the longfin inshore squid Doryteuthis pealeii. The group found that the D. pealeii genome is substantially larger than that of Octopus bimaculoides. The expansions of protocadherins, a family of cell adhesion molecules important for wiring vertebrate brains, and of C2H2 zinc-finger transcription factors described in octopus appears to be even larger in squid. Most importantly, our chromosome-scale assembly also identifies many local expansions of genes expressed in novel cephalopod structures. Some of these gene clusters are cephalopod-, or even squid-specific, while others appear to be local expansions of genes found in distantly related animals. This data highlights a major role for the acquisition of novel genes and the selective expansion of known gene families in the evolution of cephalopod morphological innovations.