The world is changing. Fast. High quality reference genomes have become essential tools in understanding the processes that shape patterns of diversity. They offer new ways to study longstanding taxing problems including interactions among drift, migration, and selection and the prevalence of adaptation versus gene flow in marine metapopulations. They provide, with various other kinds of genomic data, windows onto the past and into the future of populations, species, and communities.
This site aims to briefly introduce a variety of collaborative comparative projects seeking to use genomics to better understand the interactions of marine organisms with their environments and with each other.
Why comparative analyses? Very simply, it is one of the oldest and most powerful approaches in biology. It offers the ability to understand the diversity of life in the seas by associating the differences/similarities in genomic data with differences/similarities in phylogeny and function. Through these associations, we start on the path toward understanding causes and consequences.
Why marine genomes? Marine systems are in many ways alien to humans, so they are easy to misunderstand; the massive abundance of many of the organisms featured here, as well as the tremendous evolutionary distance from the majority of well characterized genomes, which are predominantly of terrestrial organisms, means that we may expect novel findings in marine species.
Schiebelhut, L.M., M.B. DeBiasse, L. Gabriel, K.J. Hoff, M.N. Dawson (2023) A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides, Journal of Heredity, https://doi.org/10.1093/jhered/esad054
Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts.
Paggeot, L.X., M.B. DeBiasse, M. Escalona, C. Fairbairn, M.P.A. Marimuthu,O. Nguyen, R. Sahasrabudhe, M.N Dawson. Reference genome for the California ribbed mussel, Mytilus californianus, an ecosystem engineer. Journal of Heredity 113:681–688. https://doi.org/10.1093/jhered/esac041
The California ribbed mussel, Mytilus californianus, is an ecosystem engineer crucial for the survival of many marine species inhabiting the intertidal zone of California. Here, we describe the first reference genome for M. californianus and compare it to previously published genomes from three other species: M. edulis, M. coruscus, and M. galloprovincialis. This high-quality genome assembly provides a foundation for population genetic analyses that will give insight into future conservation work along the coast of California.
DeBiasse, M.B., L.M. Schiebelhut, M. Escalona, E. Beraut, C. Fairbairn, M.P.A. Marimuthu,O. Nguyen, R. Sahasrabudhe, M.N Dawson. 2022. A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting. Journal of Heredity 113:689–698. https://doi.org/10.1093/jhered/esac044
Efforts to protect the ecologically and economically significant California Current Ecosystem from global change will greatly benefit from data about patterns of local adaptation and population connectivity. To facilitate that work, we present a reference-quality genome for the giant pink sea star, Pisaster brevispinus, a species of ecological importance along the Pacific west coast of North America that has been heavily impacted by environmental change and disease. The reference genome for P. brevispinus is an important first step toward the goal of producing a comprehensive, population genomics view of ecological and evolutionary processes along the California coast. This resource will help scientists, managers, and policy makers in their task of understanding and protecting critical coastal regions from the impacts of global change.
Last week, the California Conservation Genomics Project launched a new tracking system to keep up with the progress of their reference genomes assemblies (https://www.ccgproject.org/reference-genomes-tracking). With over 100 new species being sequenced, this website tracker will show you the progress of each of the key steps.
The first HiFi reads for a MariNet genome reference genome were finalized over a week ago, we are well on our way to having a chromosome-level genome of Mytilus californianus. Thread your byssals around that news!