17 beeutiful genome assemblies

Sweat bees (Hymenoptera: Halictidae) encompass a wide range of social behaviors, from solitary individuals that live and reproduce independently to eusocial colonies with overlapping generations and a non-reproductive worker caste. Some species are capable of producing both social and solitary nests, often depending on environmental context.

Within the sweat bees, there have been two independent gains and a dozen losses of eusociality. These replicated gains and losses of social behavior enable a comparative approach to identify the core factors that shape the emergence and breakdown of eusociality and provide insights into the most costly aspects of social life. We performed this exact comparative analysis in our latest preprint "Convergent selection on juvenile hormone signaling is associated with the evolution of eusociality in bees".

For these genomic comparisons we needed, you guessed it, genome assemblies. Today, together with the Kocher Lab at Princeton University we share 17 chromosome-length sweat bee genome assemblies that span solitary, eusocial and polymorphic species to accompany the preprint.

17 sweat bees with shiny new chromosome-length genome assemblies. Photo attributions can be found on individual assembly pages.

The assembled species include:

1. Bicolored striped sweat bee (Agapostemon virescens): www.dnazoo.org/assemblies/Agapostemon_virescens

2. Pure green sweat bee (Augochlora pura): www.dnazoo.org/assemblies/Augochlora_pura

3. Golden green sweat bee (Augochlorella aurata): www.dnazoo.org/assemblies/Augochlorella_aurata

4. Ligated furrow bee (Halictus ligatus): www.dnazoo.org/assemblies/Halictus_ligatus

5. Giant furrow bee (Halictus quadricinctus): www.dnazoo.org/assemblies/Halictus_quadricinctus

6. Orange-legged furrow bee (Halictus rubicundus): www.dnazoo.org/assemblies/Halictus_rubicundus

7. White-legged sweat bee (Lasioglossum albipes): www.dnazoo.org/assemblies/Lasioglossum_albipes

8. Common furrow bee (Lasioglossum calceatum): www.dnazoo.org/assemblies/Lasioglossum_calceatum

9. Figueres' sweat bee (Lasioglossum figueresi): www.dnazoo.org/assemblies/Lasioglossum_figueresi

10. White-banded sweat bee (Lasioglossum leucozonium): www.dnazoo.org/assemblies/Lasioglossum_leucozonium

11. Sharp-collared sweat bee (Lasioglossum malachurum): www.dnazoo.org/assemblies/Lasioglossum_malachurum

12. Margined sweat bee (Lasioglossum marginatum): www.dnazoo.org/assemblies/Lasioglossum_marginatum

13. Evening primrose sweat bee (Lasioglossum oenotherae): www.dnazoo.org/assemblies/Lasioglossum_oenotherae

14. Lobe-spurred sweat bee (Lasioglossum pauxillum): www.dnazoo.org/assemblies/Lasioglossum_pauxillum

15. Viereck's sweat bee (Lasioglossum vierecki): www.dnazoo.org/assemblies/Lasioglossum_vierecki

16. Zephyr sweat bee (Lasioglossum zephyrum): www.dnazoo.org/assemblies/Lasioglossum_zephyrum

17. Alkali bee (Nomia melanderi): www.dnazoo.org/assemblies/Nomia_melanderi

The same genome assemblies and gene annotations are also available through the Princeton Halictid Genome Browser.

We searched the chromosome-length genome assemblies for genes that both experienced positive selection when eusociality arose and relaxed selection when eusociality was secondarily lost in the sweat bees. Strikingly, the analysis highlighted proteins that bind and transport juvenile hormone – a key regulator of insect development and reproduction. Read more about this in the preprint, and see also the Kocher lab twittorial!

To give you some taste of the data, see a collage of chromosome-length contact maps below, and visit the individual assembly pages for more information!

A collage of chromosome-length contact maps for the 17 sweat bee species. For individual contact maps visit https://tinyurl.com/yfy6agsx or follow the species-specific links above.

Fun fact: these genome assemblies constitute our 200-216th assembled species. Can you beelieve it?!

Genome assembled for an oceanic dolphin species

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).

Flipping over genomes

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.