Escalating concern regarding the impacts of reduced genetic diversity on the conservation of endangered species has spurred efforts to obtain chromosome-level genomes through consortia such as the Vertebrate Genomes Project. However, assembling reference genomes for many threatened species remains challenging due to difficulties obtaining optimal input samples (e.g., fresh tissue, cell lines) that can characterize long-term conservation collections. Here, we present a pipeline that leverages genome synteny to construct high-quality genomes for species of conservation concern despite less-than-optimal samples and/or sequencing data, demonstrating its use on Hector’s and Māui dolphins. These endemic New Zealand dolphins are threatened by human activities due to their coastal habitat and small population sizes. Hector’s dolphins are classified as endangered by the IUCN, while the Māui dolphin is among the most critically endangered marine mammals. To assemble reference genomes for these dolphins, we created a pipeline combining de novo assembly tools with reference-guided techniques, utilizing chromosome-level genomes of closely related species. The pipeline assembled highly contiguous chromosome-level genomes (scaffold N50: 110 MB, scaffold L50: 9, miniBUSCO completeness scores >96.35%), despite non-optimal input tissue samples. We demonstrate that these genomes can provide insights relevant for conservation, including historical demography revealing long-term small population sizes, with subspecies divergence occurring ~20 kya, potentially linked to the Last Glacial Maximum. Māui dolphin heterozygosity was 40% lower than Hector’s and comparable to other cetacean species noted for reduced genetic diversity. Through these exemplar genomes, we demonstrate that our pipeline can provide high-quality genomic resources to facilitate ongoing conservation genomics research.

Foot-and-mouth disease virus (FMDV) is widespread throughout much of the world, including parts of South East Asia. As part of the World Organisation for Animal Health (OIE)’s South East Asia and China Foot‐and‐Mouth Disease Project (SEACFMD), field sampling was performed to help understand evidence of widespread virus exposure observed previously. Serum and dry mucosal swabs were collected to evaluate the presence of FMDV RNA on the nasal, oral, and dorsal nasopharyngeal mucosal surfaces of 262 healthy cattle (n=38 in Laos; n=47 in Myanmar) and buffalo (n=12 in Laos; n=2 in Myanmar) immediately following slaughter in three slaughterhouses. Swabs and serum were tested by the OIE FMD world reference laboratory using pan‐serotypic real‐time reverse transcription‐PCR (RT‐PCR) and serum was evaluated using the FMD PrioCHECK non-structural protein (NSP) ELISA. In total, 7.3% of animals had detectable FMDV RNA in one or more of the three sites including 5.3% of nasopharyngeal swabs, 2.3% of oral swabs, and 1.5% of nasal swabs. In all animals, serum was found not to contain detectable FMDV RNA, and 37.8% of animals were positive for NSP antibodies, indicating likely past exposure to FMDV. Results were comparable for Laos and Myanmar, and were similar for both cattle and buffalo. The current study demonstrates the utility of detection by swabbing the nasopharynx in the post-mortem context, in situations such as post-mortem where probang samples are not feasible. Additionally, FMDV present on the oral and nasal mucosa of clinically-healthy large ruminants in Laos and Myanmar, if viable, may potentially play a role in the epidemiology of FMD in these countries, and perhaps more widely within Southeast Asia.