Unraveling shark secrets: sequencing genomes and microbiomes for research and conservation
About Shaili Johri
Shaili Johri is a geneticist with a research focus in conservation genomics of wildlife populations. She completed her BSc. and M.S. in India and moved to the United States for her PhD in Genetics. She did her post-doctorate at the Center for Conservation Biology at the University of Washington in Seattle and is currently a research professor at San Diego State University in association with Dr. Elizabeth Dinsdale’s laboratory. Shaili works at the intersection of marine conservation policy and interdisciplinary research and her research career spans projects relating to conservation of tigers in western India, wolves in northwest USA, killer whales in the Pacific Northwest and now sharks and rays in the southwest US and India. Shaili’s role as a project lead involves developing genomic and metagenomic tools to assist with biodiversity assessments and population health monitoring of marine megafauna such as sharks and killer whales. In parallel to her research, Shaili works in close collaboration with fishing communities to develop science-based conservation policies through cross-sector collaborations, outreach and education. In addition to her research, Shaili engages in capacity building for genomic methods among wildlife research communities in the US and abroad and this is where the Oxford Nanopore MinION device has been a game changer.
Chondrichthyes - sharks, rays and chimaeras (‘sharks’) evolved 500 million years ago and are one of the oldest extant vertebrates today. Sharks have extraordinarily long-life spans, exceptional wound healing capabilities and large genomes – qualities which make them ideal candidates for understanding mechanisms contributing to genome stability and immunological resilience. As apex predators, sharks are also vital to top-down regulation of oceanic ecosystems and are therefore crucial to maintaining commercial fish stocks and human food security. However, sharks are disproportionately targeted to meet the international demand for shark fins and as a result an estimated 25-50% of species are threatened by extinction. 50% of shark species are also data deficient, making it difficult to conserve remaining populations and to study their evolutionary adaptations. Our goal is to reduce data deficiency of shark populations through on-site genomic and metagenomic studies in shark biodiversity hot-spots, including the USA, India, Tanzania, Mexico, Australia, and Philippines. Shark samples are collected from free swimming sharks or from specimens found in fish markets. Genomic DNA is sequenced on-site by trained undergraduate and graduate students on the MinION. We sequenced four new chondrichthyan genomes including the Silky shark (Carcharhinus falciformis), Sharpnose guitarfish (Glaucostegus granulatus), and two manta rays (Mobula japonica and Mobula tarapacana). Long-read sequencing on the MinION allowed high depth of sequencing coverage of shark genomes, which are typically 1-6 gigabases in size. Our studies increased the number of sequenced chondrichthyan genomes by 40%. Ongoing genome assessments for population size and structure will allow determination of conservation status for these shark species. Genome comparisons across taxa will increase understanding of mechanisms which impart evolutionary resilience to this species group. Further, our microbiome analyses of free-swimming whale sharks (Rhincodon typus) in locations across the globe revealed that microbiomes are similar with respect to taxonomic composition and functional profiles in genetically diverse and geographically separated whale shark populations, providing key insights about the biogeography of whale sharks. Analyses of functional profiles of the microbiome in wild thresher sharks (Alopias vulpinus) revealed a10-fold higher proportion of heavy metal-metabolizing genes in sharks as compared to the water column in coastal San Diego, suggesting either bioaccumulation of heavy metals or a novel baseline microbiome specific to thresher sharks. In summary, use of portable sequencing technology from Oxford Nanopore has improved the data deficiency of shark populations through local capacity building and will facilitate greater protection of endangered species in the future.