The Atlantic white-sided dolphin (Lagenorhynchus acutus) is just as curious and playful as the famous bottlenose dolphin and yet it is widely unknown to the public due to its preference for deep oceanic waters. When encountered, Atlantic white-sided dolphins regularly perform spectacular aerial behaviour and enjoy riding the bow-wave created by boats, giving passengers the perfect opportunity to spot their name-giving white patch that lies below their dorsal fin on both sides of their body.

Atlantic white-sided dolphin by Anna, [CC BY-SA 4.0], via Wikimedia Commons

Atlantic white-sided dolphins are social animals, usually existing in pods of up to 50 individuals, but sometimes they come together in their hundreds to form “super pods” where they work together to herd large shoals of fish or travel long distances. They will also not hesitate to join other cetacean species for social or feeding interactions, such as other oceanic delphinids or even large baleen whales like the fin or humpback whale [1].


Generally, these dolphins are thought to be quite abundant and are not listed as endangered by the IUCN, but there is no overall abundance estimate available for the whole species and it is virtually unknown what impact the changing environment, entanglement in fishing gear or pollution has on their populations.


Whole‑genome assemblies are an important tool for conservation scientists to help shine a light on the population structure of these charismatic but elusive dolphins. They can also enable detection of potential threats, like the ones mentioned above, by combining genetic data with metadata, eventually facilitating a more precise assessment of their overall conservation status.


Today, we release the chromosome-length genome assembly for the Atlantic white-sided dolphin. This is a $1K genome, with a scaffold n50 = 103 Mb and a contig n50 = 87 Kb. For assembly procedure details, see our Methods page.


This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The specimen used for this genome assembly was provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program.


Check out how the chromosomes in the new assembly relate to those of the Pacific white-sided dolphin Lagenorphynchus obliquidens previously upgraded by DNA Zoo from data shared by Canada's Genomic Enterprise, and don't forget to explore the chromosome-length contact map on the assembly page!

Whole-genome alignment plot between the Pacific (ASM367639v1_HiC) and the Atlantic (Lagenorhynchus_acutus_HiC) white-sided dolphin genome assemblies.

Citations:

1. Weinrich, M. T., Belt, C. R. & Morin, D. Behavior and Ecology of the Atlantic White-Sided Dolphin (Lagenorhynchus Acutus) in Coastal New England Waters. Mar. Mammal Sci. 17, 231–248 (2001).

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  • Ben Neely

Today we release the genomes of three dolphins of the genus Stenella: Pantropical spotted dolphin (Stenella attenuata), Atlantic spotted dolphin (Stenella frontalis), and Eastern spinner dolphin (Stenella longirostris orientalis).


All three are relatively small dolphins ranging from approximately 5 to 7 feet long (1.5 to 2 meters) and weighing 200 to 300 pounds (90 to 140 kg). As their names imply, the two spotted dolphin species develop spots with age, though they are born without spots. Spinner dolphins get their name from being one of the most aerial dolphins, often leaping from the water and spinning up to seven times.


Spinner dolphins and pantropical dolphins can be found across tropical and subtropical oceans (sometimes schooling together!), whereas the Atlantic spotted dolphin can be found in temperate, subtropical and subtropical waters throughout the Atlantic. There are four subspecies of spinner dolphins, and this genome is of the Eastern spinner dolphin (S. l. orientalis) specifically. Like all marine mammals, these dolphins are protected under the Marine Mammal Protection Act.

Pantropical Spotted Dolphin (Stenella attenuata) by NOAA Photo Library, [CC-BY-2.0], via flickr.com
Atlantic spotted dolphin (Stenella frontalis) by NOAA Southeast Fisheries Science Center, Public domain, via Wikimedia Commons
Spinner dolphin (Stenella longirostris) by Alexander Vasenin, [CC BY-SA 3.0], via Wikimedia.org

All genomes were generated following the $1K strategy described in (Dudchenko et al., 2018). See our Methods page for more details.


This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The Pantropical spotted dolphin (Stenella attenuata) specimen used for this study was collected by Kristi West (Hawaii Pacific University) and Greg Levine from Oahu, HI. The Atlantic spotted dolphin (Stenella frontalis) specimen used for this study was collected by Wayne McFee (NOAA) and Jessica Conway from Hunting Island, SC. The Eastern spinner dolphin (Stenella longirostris orientalis) specimen used for this study was collected by Erin Meagher (University of North Carolina, Wilmington) from the Eastern Tropical Pacific. The specimens were provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program.


See the alignment plots below for information on how the assembled chromosomes across these three species relate to each other and to those of the Pacific white-sided dolphin previously assembled to chromosome-length by the DNA Zoo and used here as an outgroup.

Coarse whole-genome alignments of the three new assemblies to the ASM367639v1_HiC genome assembly, i.e. the chromosome-length upgrade for the Pacific white-sided dolphin. Keep in mind that some some differences may be a result of a misassembly rather than an evolutionary rearrangement (e.g. this may be the case behind the differences in the equivalent of chr12 in the Pacific white-sided dolphin).

There are more Stenella dolphins in the queue, so be sure to keep an eye out for new data. If you want to be notified about the new genome assemblies subscribe to the email-list at the bottom of the page or follow us on twitter @thednazoo.

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The Eastern Water Dragon (Intellagama lesueurii) is one of Australia's largest dragon lizards and can be found living in both natural waterways and within highly developed city centres. Previously Physignathus, Intellagama has only recently been considered its own distinct genus translating to "smart dragon". The specific name lesueurii honours the French naturalist Charles-Alexandre Lesueur (1778-1846) who collected this species on the Baudin expedition of 1800.

Photo Description – The Eastern Water Dragon (Intellagama lesueurii). Photo credits: Celine Frere, University of the Sunshine Coast [CC].

Water Dragons are found in eastern Australia, where there are two subspecies. The Eastern subspecies (Intellagama lesueurii lesueurii), occurs along the east coast of Australia from Cooktown in the north down to the New South Wales south coast (approximately at Kangaroo Valley) where it is replaced with the Gippsland subspecies (Intellagama lesueurii howittii), which is distributed as far south and into the Gippsland region of eastern Victoria.


Water Dragons are a charismatic species that can live in large social groups often communicating through a variety of dominant and submissive signals including head-bobbing, arm waving and push-ups. The Water Dragon is a familiar sight in Australian cities and urban areas, where they have become habituated in parks and botanical gardens. Several inner-city populations narrowly separated by urban landscape have begun to diverge from one another, becoming genetically and morphologically distinct. These city slicker dragons have demonstrated that under some circumstance’s evolution can proceed at a significantly faster pace that initially thought.


Although not listed as threatened, Water Dragons are protected in all states and territories where they occur naturally: Queensland, New South Wales, Australian Capital Territory and Victoria.


Today, we share the chromosome-length assembly for the Eastern Water Dragon. DNA Zoo has been working with Associate Prof Celine Frere, Dr Dan Powell and Nicola Kent at The University of Sunshine Coast, Australia to deliver this much required key fundamental genomic resource.


The assembly is based on a draft hybrid assembly effort supported by The Australian Amphibian and Reptile Genomics Initiative (AusARG), a collaborative at Bioplatforms Australia framework initiative building genomic resources for thorough understanding of evolution and conservation of Australia’s unique native Amphibians and Reptiles that are now under threat, through climate, disease or habitat modification. The draft genome assembly was created using high-fidelity long reads from Pacific Biosciences technology (circular consensus sequencing). The reads were assembled using the long-read assembler Hifiasm (Cheng et al., 2021).


The above draft was scaffolded with 118,960,506 PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!


The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.


The new genomic tools and resources for the Eastern Water Dragon (Intellagama lesueurii) will enable detailed investigations into their unique ability to adapt to life in our highly urbanised cities and facilitate a better understanding of how reptiles can respond to rapid environmental change.


The following people contributed to the Hi-C chromosome-length upgrade of the draft assembly: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.


Blog by: Parwinder Kaur, Nicola Kent, Dan Powell and Celine Frere.


Citations:

Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). https://doi.org/10.1038/s41592-020-01056-5

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