J is for jaguarundi

According to the Cat Classification Task Force of the IUCN Cat Specialist Group jaguarundi (Puma yagouaroundi) is a monotypic species (Kitchener et al., 2017) and one of the three living representatives of Puma lineage diverged from the last common ancestor around 5 million years ago. Historically, jaguarundi was included in the genus Herpailurus, but recently, phylogenetic and phylogenomic studies have positioned it among the Puma lineage together with the African cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor) (Johnson, et al., 2006; Li, et al., 2016; O'Brien, et al., 2008; O'Brien and Johnson, 2007).

Jaguarundi by Cloudtail the Snow Leopard, [CC BY-NC-ND 2.0], via flickr.com

Jaguarundi displays a very unique appearance among other cats - slender, elongated body, short legs, a small flattened head, long “otter-like” tail, and a sleek, unmarked coat. Coats occur in two main color variations: gray/dark or reddish. Color variants showed significant association with specific habitats, where gray/dark variants are common within moist and dense forests while reddish variants are more prevalent for open and arid areas (da Silva, et al., 2016).

Although jaguarundi is listed as Least Concern on the IUCN Red List they still suffer from population decline due to habitat fragmentation and habitat loss. They are also affected by persecution for killing poultry in local areas. Puma yagouaroundi species is protected over much of its range and hunting is prohibited in Argentina, Belize, Bolivia, Colombia, Costa Rica, French Guiana, Guatemala, Honduras, Mexico, Panama, Paraguay, Suriname, Uruguay, U.S. and Venezuela. In Peru hunting is regulated. They are not legally protected in Brazil, Ecuador, El Salvador, Guyana or Nicaragua.

The first jaguarundi whole genome assembly became publicly available in 2021 (Tamazian et al, 2021). A genome of a male jaguarundi specimen was sequenced with 10X Genomics linked reads and assembled with supernova2. The assembled genome contains series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of African cheetah and mountain lion, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. This assembly was used as a draft for HiC-scaffolding, shared today on www.dnazoo.org.

The primary fibroblast cell line (HYA-1) at passage 10 was used to make the Hi-C library. The skin biopsy was collected by Dr. Mitchell Bush (Smithsonian National Zoological Park, Washington DC) in 1981 in Blijdorp Zoo (Rotterdam, Netherlands) from a 9-year old captive breeding male jaguarundi originally from Mexico. The cell line was established by Mary Thompson in December 1981 and stored at the Laboratory of Genomic Diversity headed by Dr. Stephen O’Brien (LGD, Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD) and later the LGD cryo collection was preserved by Drs. Melody Roelke, Carlos Driscoll, Christina Barr and David Goldman. The cells of the primary fibroblast cell line at passage 10 were used for high-molecular weight DNA extraction for 10X Genomics by Nataliya Serdyukova at the (Dr. Grafodatsky’s Laboratory of Animal Cytogenetics at the Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia). This four decades old jaguarundi sample story shows the worthiness of wildlife samples cryopreservation.

Browse the interactive Hi-C contact map showing how the 19 chromosomes of the jaguarundi fold in 3D below and on the corresponding assembly page!

Blog post by Pasha Dobrynin, Polina Perelman, and Sergei Kliver

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.