Rute da Fonseca
Marine Genomics
We produced the genome of a giant squid (Architeuthis dux; Steenstrup, 1857) is giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked.
Drawing by Alex Hayward
With Angela Ribeiro and other collaborators, I wrote this review presenting an overview of the applications of genomics to the study of marine life, from evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine.
In this collaboration with Filipe Castro from CIIMAR and others, we sequenced and annotated the genome of European sardine (Sardina pilchardus, Walbaum 1792). This species exhibits significant commercial relevance, but has showed a steady and sharp decline in capture levels. We have an ongoing project exploring the genetic diversity of sardine populations to advance current practices in culture husbandry.
This paper published in MBE was the result of a collaboration with researchers from CIIMAR. We showed that key molecular components responsible for skin sebum production have been rendered nonfunctional in Cetacea species (toothed and baleen whales). Pseudogenization events took place prior to the diversification of modern Cetacea lineages.Partial loss profiles were also detected in non-Cetacea aquatic mammals, such as the Florida manatee, and in terrestrial mammals displaying specialized skin phenotypes such as the African elephant, white rhinoceros and pig. Our findings reveal a unique landscape of “gene vestiges” in the Cetacea sebum-producing compartment, with limited gene loss observed in other mammalian lineages: suggestive of specific adaptations or specializations of skin lipids.
With Angela Ribeiro, I explored the diversity in blue mussel population in polluted and non-polluted areas in the Northwest of the Iberian Peninsula. In the paper published in Marine Genomics we describe how the transcriptomes of 72 individuals from 9 populations of Mytilus galloprovincialis collected along a ca. 130-km north-south transect on the Western coast of the Iberian Peninsula show that polluted areas are acting as a barrier to gene flow, potentially because of the detrimental effect of anthropogenic chemicals on larvae carried from more pristine environments. Furthermore, we observed an increase in genetic diversity in populations from polluted site, which could be indicative of higher mutagenicity driven by the environment.