Genome assembled for tiny mouse

Weighing about as much as six paper clips, the endangered Pacific pocket mouse (PPM) aka Perognathus longimembris pacificus is the among the smallest rodents in the world. It historically occupied a stretch of sandy soil habitat along the coast of southern California, playing a vital role in ecosystem function by dispersing seeds of native plants and promoting nutrient cycling in the soil through the digging of its burrows. Thought to be extinct for several decades, PPM was rediscovered in 1993 in three small, isolated populations, and emergency listed under the U.S. Endangered Species Act.

Photos provided by Aryn Wilder, San Diego Zoo ( © San Diego Zoo)

In 2012, the San Diego Zoo Wildlife Alliance, in cooperation with the U.S. Fish and Wildlife Service and the California Department of Fish and Wildlife, established a conservation breeding program with the goal of reintroducing PPM into unoccupied regions in their historic range. In addition to facilitating the return of the species to their native habitat, the breeding program also serves as a useful model for studying the role of genetic load in inbreeding depression, and the patterns and impacts of karyotypic differences that have been observed in this species. In this way, exploring the genomics of PPM will help to better design management strategies to help preserve genetic diversity in this and other endangered species.

Today, we share the chromosome-length assembly for the Pacific pocket mouse. Scientists at the San Diego Zoo Wildlife Alliance generated an initial assembly of the Pacific pocket mouse genome in collaboration with Dovetail Genomics, and the Hi-C experiments and upgrade as been done by DNA Zoo. The genome annotation and a paper describing this research is in progress, so stay tuned!

About DNA Zoo

DNA Zoo is a multinational consortium whose goal is to accelerate conservation efforts by rapidly disseminating the DNA sequences of many life forms, and improving the methods for reconstructing such sequences. DNA Zoo is committed to open-source release of data and methods; genome assemblies produced by DNA Zoo are available without restriction at DNAzoo.org. To date, DNA Zoo has released chromosome-length genome assemblies for over 3% of mammalian species.

About San Diego Zoo Global

Bringing species back from the brink of extinction is the goal of San Diego Zoo Global. As a leader in conservation, the work of San Diego Zoo Global includes on-site wildlife conservation efforts (representing both plants and animals) at the San Diego Zoo, San Diego Zoo Safari Park, and San Diego Zoo Institute for Conservation Research, as well as international field programs on six continents. The work of these entities is made accessible to over 1 billion people annually, reaching 150 countries via social media, our websites and the San Diego Zoo Kids network, in children’s hospitals in 12 countries. The work of San Diego Zoo Global is made possible with support from our incredible donors committed to saving species from the brink of extinction.

About Dovetail Genomics LLC

Dovetail Genomics LLC is the world leader in proximity ligation technology for genome assembly and epigenetic chromatin conformation profiling. To date, Dovetail has delivered over 1500 high quality, chromosome-scale genome assemblies, across hundreds of taxa and to hundreds of researchers globally. Dovetail provides a complete sample-to-publishable assembly workflow for de novo assembly of virtually any organism and also provides proximity ligation kits for DIY assembly. Dovetail also provides a suite of epigenetics kits and services, including Micro-C, HiChIP and Omni-C for epigenetic chromatin profiling.

Fishing for catpliments

The fishing cat (Prionailurus viverrinus) gets their name from their love of water. Fishing cats have been observed “fishing” at the edge of water, scooping their prey seamlessly (1). They are one of the best swimmers around, equipped with webbing between their toes to help both with swimming and with walking in muddy wetlands without sinking (2). The fishing cat’s fur consists of two layers: a short and dense layer to conserve warmth and keep the skin dry when in the water, and a layer of longer hairs (referred to as guard hairs) which give the cat it’s colour pattern, used for camouflage (2). This pattern is a combination of spots and stripes, where the stripes run down from above the eyes between the ears onto the neck, breaking up on the shoulders. The short hair on the face is spotted, and its whiskers are short (1).

Fishing cat by kellinahandbasket, [CC BY 2.0], via flickr.com

Fishing cats are found in scattered areas of the Oriental Region. They inhabit the peninsular region of India, Sri Lanka, Malaysia, Thailand, Java, and Pakistan (1). Although fishing cats are attracted to all types of water and live in wetlands predominantly, they have been found in tropical dry forests and in the Indian Himalayas at elevations of 4,900 feet (1,500 meters) in dense vegetation near rivers or streams. Little is known about fishing cats in the wild, but it is thought that they have no natural predators other than humans (2).

Like many smaller felines, the fishing cat communicates with hisses, growls, and even meows. During a courtship, the male and female will make chittering sounds with the female signaling her willingness to breed and the male communicating submissiveness. The females give birth in the spring to an average of two kittens in a litter, raising their young without help from the male (how’s that for a catfish). The kittens will then learn to fish by watching their mother, and at 10 months will be ready to venture out on their own (2).

Its dependence on water is likely to cause trouble for the species, as it is estimated around 50 percent of Southeast Asia wetlands are disappearing as the human population grows (2). Of the remaining wetlands, they are affected by pollution, over-farming and chemical fertilizer runoff, overfishing by humans, and drainage issues (2). In addition to this, the fishing cat is also a victim of poaching. They are often hunted for food, medicine, or various body parts (1). Accordingly, the fishing cat is listed as vulnerable on the International Union for Conservation of Nature and Natural Resources (IUCN) Red List (IUCN 2003) and is included on Appendix II of the Convention on International Trade in Endangered Species (3).

Today, we share a 1K de novo assembly for the species (see Dudchenko et al., 2018). See our Methods page for more detail! We thank San Antonio Zoo for the sample that was used for this assembly!

This work was in part supported by DNA Zoo Australia, The University of Western Australia (UWA), with compute at the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

Blog by: Ashling Charles and Parwinder Kaur

Stone on the beech

The stone marten, or beech marten (Martes foina), is a medium-sized animal from the weasel family (Mustelidae). Its range covers most of Europe and extends towards the Far East, with two major zones (IUCN 2020) separated by Central Asia. In Europe, the stone marten inhabits a variety of habitats – forests, open areas and mountain ranges, but often lives close to human dwelling, including big cities. Its range partially overlaps the range of the more arboreal pine marten (Martes martes), and hybrids are not uncommon in regions where the two species are sympatric. Stone martens are agile predators, but their diet also includes a variety of fruit and insects; they are mostly nocturnal. In 2016, a stone marten caused a shutdown of the Large Hadron Collider in Switzerland.

Martes foina by Bohuš Číčel, [CC BY-SA 3.0], via wikimedia.org

In a way, the stone marten is a cornerstone of carnivore genetics. Sorting chromosomes of this species were used as probes in Zoo-FISH experiments on dozens of species and will be used in many more. The stone marten itself is well-studied from the cytogenetic point of view. Zoo-FISHs with dog, cat and human probes (Figure 1) were done for this species (Graphodatsky, Perelman, and O’Brien 2020; Nie et al. 2012). This data was used to study genome architecture and rearrangements in carnivores (Nie et al. 2012) and can be used to connect assembly and karyotype, building one more bridge between genomics and cytogenetics.

Figure 1. Martes foina karyotype and Zoo-FISH with dog (CFA), cat (FCA) and human (HSA) (Graphodatsky, Perelman, and O’Brien 2020; Nie et al. 2012).

We present the chromosome-length assembly for the stone marten with all C-scaffolds (Lewin et al. 2019) assigned to the corresponding chromosomes. This genome is a first in many ways: it is the first genome assembly of such integrity within the genus Martes; the first genome generated by the Marten Genome Team; and last but not least, it is the first genome for the DNA Zoo Novosibirsk! The initial analysis of whole-genome alignment between this assembly and the domestic cat genome demonstrated strict agreement with ZooFISH in three Robertson translocations and revealed many inversions (Figure 2).

Figure 2. Dotplot for whole genome alignment of stone marten genome to domestic cat assembly (Felis_catus_9.0).

We thank Dr. Rogell Powell (North Carolina State University) for funding 10x Genomics linked-read sequencing for the draft assembly and Dr. Klaus Koepfli for organizing this sequencing and bringing all of the collaborators together. The cell culture of an individual used both for the linked read and HiC sequencing was provided by Kunming Cell Bank of the Chinese Academy of Sciences, Kunming, Yunnan, China through Drs. Malcolm Ferguson-Smith and Fengtang Yang at Department of Veterinary Medicine, University of Cambridge, UK to Animal Cytogenetics Laboratory at the Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Dr. Alexander Graphodatsky).

The initial assembly was performed by Sergei Kliver (DNA Zoo Novosibirsk, Institute of Molecular and Cellular Biology). Hi-C experiments and scaffolding to chromosomes was done by Polina Perelman, Ruqayya Khan and Olga Dudchenko. The genome annotation and a paper describing this research is in progress.

New marten genomes coming soon!

Blog post by Sergei Kliver, Tatiana Bulyonkova, Aleksandra Mironova

References:

Graphodatsky, Alexander, Polina Perelman, and Stephen J. O’Brien. 2020. Atlas of Mammalian Chromosomes. John Wiley & Sons, Incorporated.

IUCN. 2020. “IUCN 2020. The IUCN Red List of Threatened Species. Version 2020-2.”

Lewin, Harris A et al. 2019. “Precision Nomenclature for the New Genomics.” GigaScience 8(8): giz086.

Nie, W et al. 2012. “Chromosomal Rearrangements and Karyotype Evolution in Carnivores Revealed by Chromosome Painting.” Heredity 108(1): 17–27.