sMartening up

The yellow-throated marten (Martes flavigula) is a flamboyant oddball in the genus Martes, which also includes the sable, pine marten, stone marten, Japanese marten, and American martens. Unlike any other marten species, yellow-throated martens hunt in packs, usually made up of siblings, and are frighteningly good at that: they successfully take down much bigger animals, such as water deer and macaques. In fact, they appear to be much more advanced socially than their loner relatives – while the overall color of their coat is an olive-tinged agouti-to-black gradient, providing good camouflage in lush foliage, some markings almost definitely serve the purpose of biocommunication: the contrasting black head and white chin, bright yellow chest, and long, black tail are amazingly similar to patterns seen in highly social simians, such as squirrel monkeys.

Martes flavigula, yellow-throated marten by Rushen, [CC BY-SA 2.0], via flickr.com

As of now, the yellow-throated marten is listed as LC (Least Concern) by the IUCN due to wide distribution and considerable numbers, as well as its presence in a number of protected territories. However, like most other martens, it prefers large continuous stretches of old-growth primeval forests, and uncontrolled logging and consequent habitat fragmentation and loss are causing an ongoing decline of its numbers in some parts of its range, which stretches from Pakistan in the west to the Russian Far East in the east and the island of Borneo in the south. In the Russian Far East, the yellow throated-marten, locally known as kharza, coexists with another member of the genus - the sable (Martes zibellina), albeit not always peacefully.

The unusual for martens combination of morphological, genetic and behavioral differences has led some researchers to believe that Martes flavigula, together with its sister species, the Nilgiri marten (Martes gwatkinsii) should be assigned a genus of their own. Further genomic research will help to assess whether this suggestion is founded. Moreover, the species as a whole is poorly studied, and there are reasons to believe that some of the isolated patches that make up its range may in fact host distinct subspecies or even separated species.

Today, we present the chromosome-length assembly for the third marten species of this year. All C-scaffolds of the yellow-throated marten were assigned to the corresponding chromosomes via a Zoo-FISH experiment with the stone marten chromosomes used as probes. In contrast to other marten species, Martes flavigula have more chromosomes: 2n=40 instead of 2n=38. (Fig. 1): you can see the chromosome corresponding to chr8 in the stone marten into two chromosomes (chr9 and 19) in the yellow-throated marten in the whole-genome alignment plot below!

Figure 1. Dotplot for whole genome alignment of yellow-throated marten genome to stone marten assembly

We thank Dr. Rogell Powell (North Carolina State University) for funding 10x Genomics linked-read sequencing for the draft assembly and Dr. Klaus Koepfli and Dr. Alexander Graphodatsky for organizing this sequencing and bringing all of the collaborators together. Also we thank Olga Shilo (deputee director), Rosa Solovyova (head of carnivore department) and Svetlana Verkholantseva (veterinarian) from Rostislav Shilo Novosibirsk Zoo (Russia, Novosibirsk) who provided samples for a cell line. Samples were collected postmortem from a 15-year old male individual called Dixi. These cells were used for both DNA extraction for linked read sequencing and for the Hi-C experiment. DNA extraction and Zoo-FISH experiments were performed by Natalia Serdyukova and Dr Violetta Beklemisheva. The initial assembly was performed by Sergei Kliver. Hi-C experiments and scaffolding to chromosomes were done by Dr. Polina Perelman, Ruqayya Khan and Dr. Olga Dudchenko. The genome annotation and a paper describing this research is in progress.

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!