Fintastic beasts and where to find them

We celebrate the World Marine Mammal Conference held in Barcelona this week by releasing three new chromosome-length marine mammal genome assemblies: for the harbor porpoise (Phocoena phocoena), here; the long-finned pilot whale (Globicephala melas), here; and the melon-headed whale (Peponocephala electra), here.

The long-finned pilot whale assembly is an upgrade based on the draft generated by the Canada’s Genomic Enterprise. The harbor porpoise and the melon-headed whale are the $1K-model DNA Zoo genomes, see (Dudchenko et al., 2018) for details. The samples used for this work were received from the National Marine Mammal Tissue Bank maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository.

The harbor porpoise (Phocoena phocoena) is one of six species of porpoise, commonly observed inhabiting coastal areas of Asia, North America, Europe and Africa (the individual assembled by the DNA Zoo came from Homer, Alaska). The name ‘porpoise’ derives from the Latin word ‘porcus’, which means hog and ‘piscis’ meaning fish, literally meaning sea pig. (Interesting since pigs and cetaceans are both even-toed ungulates. The latin name, Phocoena phocoena, on the other hand, means ‘big seal’, which is a pinniped in the distantly related carnivora order...) The harbor porpoise is roughly the size of a human, with a dark gray back, intermediate shades of gray along their sides, white belly and a white throat with a gray chin patch. The most apparent difference between a harbor porpoise and dolphin is that the harbor porpoise has no beak, a smaller, less curved dorsal fin, and small pointed flippers.

Image by skeeze from Pixabay [Pixabay License], via pixabay.com

The long-finned pilot whale (Globicephala melas), named for its unusually long pectoral fins, is a toothed whale approximately 20 feet long that mainly eats soft squid. They are social creatures that have at times formed groups of up to a thousand animals. They prefer the deep temperate to subpolar oceanic waters of the North Atlantic and southern Pacific (the individual assembled by the DNA Zoo came from the North Atlantic).

Pilot whale spyhop, photo by Barney Moss [CC BY 2.0 (https://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons

The melon-headed whale (Peponocephala electra) is also a toothed whale, but is small to medium sized at about 10 feet long. These whales prefer deep tropical/subtropical waters across the globe (the individual assembled by the DNA Zoo came from Hawaii). Similar to pilot whales, these whales can form groups of up to 1000 individuals. Studies have shown that they maintain a matrilineal structure such that females remain in groups with their mothers, whereas males move between groups (similar to some killer, sperm and pilot whales).

NOAA/Andrea Bendlin MMPA#15240

Like all marine mammals, the melon-headed whale, the long-finned pilot whale and the harbor porpoise are protected under the Marine Mammal Protection Act.

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 specimens used in this study was collected by: Carol A. Stephens (harbor porpoise; Homer, Alaska), the New England Aquarium (Belinda Rubenstein; long-finned pilot whale; Brewster, Breakwater Beach, Massachusetts) and the Hawaii Pacific University (Kristi West; long-finned pilot whale; Kahului, Hawaii). 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 and the Alaska Marine Mammal Tissue Archival Project.

Along with the research highlighted this week at the World Marine Mammal Conference, we hope that the continued generation of high-quality genome assemblies will help advance the marine mammal science and conservation efforts. If you have specimens that you can share make sure to reach out, and stay tuned for more marine mammal genome assemblies coming out in the next few weeks on the DNA Zoo website!

Top bat

The Little Brown Bat (Myotis lucifugus) is one of the most widely distributed and recognizable species of bats in North America. As their name suggests, they are a small (5-14g), brown-colored bat. They are frequently found roosting in old buildings, taking breaks in trees, and hibernating in caves and mines [1-2].

There are two main reasons why researchers are interested in having good genomic resources for the Little Brown Bat. First, accounting for body size, the Little Brown Bat lives longest of any mammal. Second, a fungus-caused disease known as the White Nose Syndrome is killing off the little brown bat by the millions. We hope that upgrading the current draft genome assembly, created in 2010 by the Broad Institute, to chromosome-length will help address these questions. The upgraded genome assembly is available here. The upgrade is done in collaboration with Vincent J Lynch (University of Buffalo), Juan Manuel Vazquez (University of Chicago) as well as Richard Miller, Bill Kohler and Melissa Han (University of Michigan).

White Nose Susceptibility and Viral Resistance

A major issue affecting bats today is the emergence and rampage of White Nose Syndrome (WNS), caused by the fungus Pseudogymnoascus destructans. Originating from Europe, P. destructans has decimated Eastern and Midwestern bat populations as it has moved westward throughout North America [5]. Little Brown Bat has been severely affected. Interestingly, it appears that some populations of M. lucifugus have shown signs of resistance to WNS relative to other populations [6]. Access to better genomics resources for M. lucifugus can help determine how differences between populations contribute to their resistance or susceptibility to the WNS.

Peto’s Paradox and Longevity in the Little Brown Bat

Generally speaking, life span in mammals is linked with size: bigger animals live longer. According to this general rule, the little brown bat life expectancy is up to 19 years. Yet, the oldest little brown bat on record was 34 years old, almost twice the prediction! Hopefully, understanding how the Little Brown Bat manages to beat the curve will have benefits for human health.

Cancer resistance is of particular importance for longevity research. While nearly all multicellular species are susceptible to cancer, some species should be more susceptible than others. Within a species, for example, cancer risk is positively correlated with increases in body size and lifespan. Between different species, however, there are no correlations between a species’s body size or lifespan, and cancer risk. This observation, known as Peto’s Paradox, can only be explained if species evolve enhanced tumor suppression mechanisms alongside increases in size and lifespan. Many open questions remain in this puzzle, including whether the evolution of enhanced tumor suppression precedes, follows, or evolves in tandem with these two factors; and which molecular and genetic mechanisms do bats and other long-lived species use to suppress their overall cancer risk.

Myotis Lucifugus and Bat Genomics

This is the fourth bat genome assembly at the DNA Zoo, and the first chromosome-length assembly in the microbat suborder (Microchiroptera). Below, we include a few whole-genome alignment plots to help elucidate how the little brown bat genome relates to those previously shared. It is worth noting that even with the recent push in bat genomics over 99% of all bat species remain unsequenced, and there are likely many more unknown bat species which are yet to be discovered [3-4]. We would like to thank Richard Miller, Bill Kohler and Melissa Han, who provided these cell lines to us for sequencing and molecular studies. Working with the DNA Zoo and other collaborators we hope to break the status quo, so stay tuned!

Whole-genome alignment of the chromosome-length genome assembly upgrade for the little brown bat (Myoluc2.0_HiC) and other bats shared by the DNA Zoo: the Madagascan flying fox (Pteropus_rufus_HiC), the large flying fox (Pvam_2.0_HiC, upgrade from Lindblad-Toh et al., 2011) and the straw-colored fruit bat (ASM46528v1_HiC, upgrade from Parker et al., 2013).

References:

1- Fenton, M., R. Barclay. 1980. Myotis lucifugus. Mammalian Species, 142: 1-8.

2- Barbour, R., W. Davis. 1969. Bats of America. Lexington, Kentucky: The University Press of Kentucky.

3- Simmons, N.B. and A.L. Cirranello. 2019. Bat Species of the World: A taxonomic and geographic database. Accessed on 12/02/2019

4- Agnarsson, Ingi, Carlos M Zambrana-Torrelio, Nadia Paola Flores-Saldana, and Laura J May-Collado. n.d. “A time-calibrated species-level phylogeny of bats (Chiroptera, Mammalia).” PLoS Currents 3: RRN1212. https://doi.org/10.1371/currents.rrn1212.

5- Zukal J, Bandouchova H, Bartonicka T, et al. White-nose syndrome fungus: a generalist pathogen of hibernating bats. PLoS One. 2014;9(5):e97224. Published 2014 May 12. doi:10.1371/journal.pone.0097224

6- Langwig Kate E., Hoyt Joseph R., Parise Katy L., Frick Winifred F., Foster Jeffrey T. and Kilpatrick A. Marm. “Resistance in persisting bat populations after white-nose syndrome invasion.” 372. Phil. Trans. R. Soc. B. http://doi.org/10.1098/rstb.2016.0044

When life gives you lemurs…

The mongoose lemur (Eulemur mongoz) is a small primate in the family Lemuridae (lemurs), native to dry deciduous forests in northwestern Madagascar. Clearing of these forests for pastureland and charcoal production is a big threat to the survival of mongoose lemurs [1]. Their numbers have dwindled by about 80% over a period of the last 25 years, and the International Union for Conservation of Nature (IUCN) has rated their conservation status as "critically endangered" [2]. If you want to help, consider donating to facilities that house captive mongoose lemurs, e.g. the Duke Lemur Center!

Today we release the chromosome-length genome assembly for the mongoose lemur, here. The assembly was done following the $1K-model, see (Dudchenko et al., 2018) for details. The blood sample for library prep was donated by a male individual and provided to us by SeaWorld.

Together with the upgrade to the blue-eyed black lemur genome assembly, here, (based on the draft from Meyer et al., 2015), this is our second chromosome-length genome in the Lemuridae family, so that we can start, for the first time, comparing lemur genomes and exploring how they might have evolved. See below how the assemblies of the mongoose lemur and the blue-eyed black lemur compare to each other, and to the assemblies of their cousins in the DNA Zoo collection: the gray mouse lemur (Microcebus murinus, shared here) and the Coquerel’s sifaka (Propithecus coquereli, shared here).

Whole-genome alignments between the new genome assembly for the mongoose lemur (2n=60, Eulemur_mongoze_HiC) and those of the blue-eyed black lemur (2n=46, Eflavifronsk33QCA_HiC), gray mouse lemur (2n=66, Mmur_3.0_HiC) and Coquerel’s sifaka (2n=48, Pcoq_1.0_HiC).

Notice a big inversion on chrX (#40 in the Eulemur_mongoz_HiC genome assembly) in Eulemurs as compared to their primate relatives (circled in the plots above). This is a fairly unique: the metacentric X chromosome comprising approximately 5% of the genome is a relatively constant feature of all mammalian karyotypes.