Welcome DNA Zoo Novosibirsk!

DNA Zoo Novosibirsk at the Institute of Molecular and Cellular Biology (Siberian Branch of Russian Academy of Sciences) joined the team of DNA-Zoo on August 25, 2020. The team is situated at the scientific hub - Academgorodok, Novosibirsk in the beautiful part of Russia - Southern Siberia.

Dr. Alexander Graphodatsky is a head of the team and the Department of Genomic Diversity at the Institute (https://www.mcb.nsc.ru/laboratory/lca; https://www.mcb.nsc.ru/laboratory/lcg). Dr. Graphodasky is a cytogeneticist who was at the forefront of comparative research of animal and human chromosomes by karyology, chromosome painting, and genomics in Russia. Dr. Graphodatsky’s leadership led to a gathering of our productive multidisciplinary team.

Chromosomal sets of animal species have a different number of chromosomes (2n or diploid number). Humans have 2n=46, the Indian muntjac has 2n=6, and the viscacha rat has 2n=102. Yet, we, mammals, all share almost the same genetic material. Why such a great difference in the number of chromosomes? We know from the research that changes in karyotypes during the evolution of mammals manifest in genome reshuffling events through fusions, fissions, inversions, and heterochromatin expansion of ancestral chromosomal elements leading to drastic changes in species diploid numbers. Still, underlying mechanisms and reasons for major genomic reshuffling are largely unknown.

DNA Zoo Novosibirsk will be using an extensive collection of fibroblast cell lines and frozen tissues of animals from across Europe and Asia as well as of World fauna assembled by the members of the team through the years. It is the largest collection of animal cell lines in Russia (https://www.mcb.nsc.ru/node/866)!

The diverse team of DNA-Zoo Novosibirsk includes cytogeneticists, molecular biologists, bioinformaticians, and ancient DNA geneticists. DNA-Zoo Novosibirsk collaborates with Zoos and reserves.

Our goal at DNA-Zoo is to assemble genomes of the fauna of Russia and neighboring countries to the chromosome level and to uncover underlying mechanisms of the genomic changes leading to the formation of our own human genome.

To mark the launch of DNA Zoo Novosibirsk, we have recently released the genome assemblies for the stone marten and the beech marten. Please check them out if you have not already! We follow up today with more genome assemblies based on the DNA Zoo Novosibirsk collection, the yellow-throated marten and the jaguarundi. Stay tuned for more!

Cytogenetics and Molecular Genetics

Alexander Graphodatsky

Vladimir Trifonov

Svetlana Romanenko

Polina Perelman

Violetta Beklemisheva

Natalya Serdyukova

Anastasiya Proskuryakova

Larisa Biltueva

Natalya Lemskaya

Guzel Davletshina

Maria Pobedintseva

Daria Andreyushkova

Ekaterina Tishakova

Zoology

Tatyana Bulionkova

Bioinformatics

Sergey Kliver

Dmitry Prokopov

Aleksey Makunin

Iliya Kichgin

Mikhail Fofanov

Ancient DNA

Nadejda Vorobieva

Anna Druzhkova

Maria Kusliy

Yulia Fedorova

Metagenomics

Anastasiya Kulemsina

The Soul of the Team

Yuliya Butakova

Current events

Stony coral are a major keystone species for coral reef ecosystems. Although coral reefs cover 1% of the ocean floor, they are home to more than 25% of the ocean’s known biodiversity and provide habitat for many marine organisms [1].

Unfortunately, coral reefs are in decline in the U.S. and around the world. Increased ocean temperatures and changing ocean chemistry are the greatest global threats to coral reef ecosystems. These threats are caused by warmer atmospheric temperatures and increasing levels of carbon dioxide in seawater. Ecological stress brought on by changes in temperature, salinity, or acidification levels can break down the symbiotic relationship between reef-building coral and their intracellular photosynthetic dinoflagellates in a phenomenon known as bleaching [2].

Acropora millepora in the Great Barrier Reef by Petra Lundgren, Juan C Vera, Lesa Peplow, Stephanie Manel and Madeleine JH van Oppen, [CC BY 4.0], via wikimedia.org

Today, we highlight a chromosome-length genome assembly from our recent manuscript, for the species Acropora millepora, a scleractinian coral that inhabits coral reefs across the planet’s shallow ocean water. This chromosome-length assembly was generated via a Hi-C upgrade (using 3D-DNA and Juicer, see our Methods page for more details) of a draft genome assembly from (Ying et al., 2019). The A. millepora tissue used to generate the Hi-C data for the upgrade was obtained from a healthy coral identified by its skeletal morphology, particularly the arrangement of peripheral and axial coralites[DC1] . The sample was taken from a mature adult A. millepora that has established itself as a colony with a calcium carbonate skeleton.

To our knowledge, this is the first three-dimensional 3D-genome assembly of the A. millepora genome, and the first stony coral to have its genome three dimensionally mapped. A recently published excellent independent effort focusing on Genome Wide Association Studies (GWAS) of bleaching across 253 different coral larvae relied on a linkage map-based chromosome-level genome assembly [2]. We hope that Hi-C data will not only help with improving the chromosome-length assembly for A. millepora and the associated downstream analyses, but also contribute to our understanding of the complex regulatory landscape associated with the complex phenomenon of bleaching, e.g., shed some light on the 3D arrangement of the locus encoding transcription of the heat-shock co-chaperone sacsin.

Mala (rufous hare-wallaby)

An important ancestral figure in the mythology of the Warlpiri people, the last wild mala (rufous hare-wallaby, Lagorchestes hirsutus) population in central Australia went extinct in the early 1990s, succumbing to the impacts of destructive wildfires and feral predators like foxes and cats. These small macropods are now making a comeback behind the conservation fences, thanks to captive breeding programs.

Photo 60046491, (c) Michael Hains, some rights reserved [CC BY-NC], via iNaturalist.org

The mala is a small marsupial covered in a greyish-orange fur. It grows to about 30cm tall. If you spot a smaller one it is likely to be male. On average they weigh only 1-2kg! The animals resemble hares in looks (hence the hare-wallaby), but with larger hind legs and a long thin tail, used for balance. Their scientific name ‘Lagorchestes hirsutus’ means ‘shaggy dancing hare’. This refers both to the shaggy fur on their lower back and the similarities the wallaby has to hares.

Mala prefers to go out at night and will hide underground during the day throughout most of summer. Their diet consists of seeds, fruits and leaves, with no water required. This is because they are typically found in semi-arid climates an obtain the moisture they need from their food. Females breed throughout the year (no set breeding season) and may have up to three young, which the mother carries around in her pouch. Joeys will be kept in their mother’s pouch for around 125 days.

They primarily use body language to communicate with each other. However, when frightened they may scream. Or rather, they produce a high-pitched squeak. In sanctuaries, the wallabies tend to have a lifespan of up to 13 years, which is longer than in the wild.

The rufous hare-wallaby is an important animal to Aboriginal culture. For the Anangu, or Aboriginal people, the Mala or "hare wallaby people" are important ancestral beings. Mala Tjukurpa, the Mala Law, is essential to culture and celebrated in dance and stories.

Rufous hare-wallaby listed as an endangered in WA, extinct in NT, endangered in SA and endangered species status nationally in Australia.

Today, we share the chromosome-length genome assembly for rufous hare-wallaby. The sample for the genome assembly was provided by Natasha Tay, Harry Butler Institute, Murdoch University. This is a $1K genome assembly, with contig N50=57kb, and scaffold N50=401Mb. See our Methods page for more detail on the assembly procedure. Check out the interactive Hi-C contact map for 10 chromosomes of the rufous hare-wallaby below and on the relevant assembly page.

The work was enabled 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.

A high-quality genome sequence is an essential resource required to implement genomics data into conservation management initiatives. More than 80% of the current 200 Australian national vertebrate recovery plans have genetic action listed in the species recovery plan with less than 15% of them having any genomic data available. Reach out if you have access to sample to help us address the gap!