Van Houtan, K. | bioRxiv Science

bioRxiv2023

Transcriptomics Reveals Tumorigenesis and Pathogen Response in Scombrid Puffy Snout Syndrome

Scombrids represent some of the most economically important fisheries globally. However, increased interest in creating aquaculture systems for these fish has also increased the risk for disease emergence. One such disease, Puffy Snout Syndrome (PSS), causes collagenous tissue growths on the face in numerous scombrid taxa. PSS has mainly been documented in captive-held fish populations and can lead to high mortality rates. Despite this, little is known about the causative agent(s) of PSS and the immune response they elicit. Therefore, we leveraged transcriptomic data of PSS symptomatic-captive, asymptomatic-captive, and healthy-wild Pacific Mackerel (Scomber japonicus) to evaluate the physiological characteristics of PSS infections and identify a potential mechanism of disease. Captive symptomatic and asymptomatic mackerel showed distinct gene expression patterns from their wild counterparts. Genes involved in tumorigenesis, immune response, and tissue remodeling were overexpressed in captive-held fish. WNT9 was the most overexpressed gene in captive groups, and the WNT signaling pathway itself showed a [~]3 fold increase in KEGG pathway enrichment analysis in captive animals. When captive fish were compared, asymptomatic fish showed lower expression of inflammation genes, but high expression of tumor suppressor genes compared to symptomatic-captive fish. Together, these host pathophysiological data and our past visual identification of RNA virus-like particles in afflicted tissues suggest that viral-mediated oncogenesis may be driving PSS in captive mackerel.

genomics↗

bioRxiv2018

DNA analysis of a large collection of shark fins from a US retail shop: species composition, global extent of trade and conservation - a Technical Report from the Monterey Bay Aquarium

We identified shark fins sampled across the entirety of a shark fin shop that had operated on the west coast of the United States until 2014. From these specimens we obtained 963 species identifications with Cytochrome oxidase (COI) sequencing and 1,720 identifications with control region (CR) sequences. We found 36-39 distinct species with COI and 38-41 with CR. Of the species identified, 16-23 are currently listed as Endangered or Vulnerable on the IUCN Red List, an additional 2 are considered data deficient, and 7 currently listed under CITES Appendix II. Of the 2.5 tonnes of fins from this collection, we estimated 56-66% (CR or COI, respectively) come from CITES-listed species or those the IUCN considers threatened or data deficient. Most of these species occur outside of the United States EEZ, comprising a global set of species that is common in most fin surveys. The principal target shark fishery in the United States (spiny dogfish; Squalus acanthias) has no fins in our collection. Fins seen abundantly in our collection include pelagic species such as thresher, mako, oceanic whitetip, silky, blue and hammerhead sharks, as in previous samples of the shark fin supply chain. However, in addition, we see a large flood of blacktip, dusky, sandbar, and smalltail sharks that are common in shallow coastal waters. This may indicate that the global market for shark fins takes sharks from nearshore coastal zones, all over the world. Abundant species in the fin shop included globally-distributed species such as scalloped hammerheads and shortfin mako sharks, but also regionally-restricted species such as finetooth, blacknose, and Caribbean Reef sharks found only in the western Atlantic or Caribbean. Specimens identified from rare species of particular conservation concern included the wedgefish genus Rhyncobatus and the white shark. Both molecular markers performed well in identifying most fins, achieving a similar degree of taxonomic certainty. The universal primers for COI regularly amplified bacteria in wet fin samples, but the CR primers were able to return shark sequences even from these degraded samples. However, the CR primers amplified a second gene, likely a pseudogene, in some important and abundant species, and seriously underestimated some species of high conversation concern such as the thresher sharks.

genetics↗