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International Team Sequences Tammar Wallaby Genome

NEW YORK (GenomeWeb News) – An international team reported in Genome Biology online last night that it has sequenced the first genome of a kangaroo species, the tammar wallaby Macropus eugenii.

The researchers used Sanger sequencing, combined with sequence data from a variety of high-throughput platforms, to sequence the 2.9 billion base genome of a female tammar wallaby kangaroo from South Australia's Kangaroo Island. With the genome sequence in hand, the researchers were able to begin finding genes involved in everything from reproduction and development to immune function and scent perception in the animal. The study is expected to offer genetic clues about other marsupials as well.

"The tammar wallaby sequencing project has provided us with many possibilities for understanding how marsupials are so different to us," co-corresponding author Marilyn Renfree, a zoology researcher at the University of Melbourne, who is also affiliated with the Australian Research Council Centre of Excellence in Kangaroo Genomics, said in a statement.

As a group, marsupials are thought to share a common ancestor with eutherian mammals going back some 130 to 148 million years. Two other marsupials — the Brazilian grey short-tailed opossum and the Tasmanian devil — have also had their genomes sequenced.

Like other marsupials, tammar wallaby young are not completely developed when they're born and need to spend several months in their mother's pouch. Even before the animals are born, tammar wallabies spend a full year gestating, including a whopping 11 months in a form of suspended development known as embryonic diapause.

That trait, and other tammar features — including its diminutive size and a genome that's organized into relatively few large chromosomes — made the animal a compelling candidate for whole-genome sequencing, researchers explained.

"The tammar has many unusual biological characteristics," they wrote, "including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding, and prolonged and sophisticated lactation within a well-defined pouch."

Collaborators from the Baylor College of Medicine Human Genome Sequencing Center and the Australian Genome Research Facility got around two times coverage of the genome by whole-genome shotgun Sanger sequencing.

The researchers also generated nearly six-fold additional genome sequence data through paired-end sequencing with the ABI SOLiD platform. Roche 454 GS-FLX Titanium and Illumina GAIIx reads were also used to help anchor and assemble the genome.

Sanger and Roche 454 approaches were also used to do transcriptome sequencing in samples from tammar testis, ovary, mammary gland, and other tissues and from various developmental stages.

The team's analyses of the genome turned up 18,258 predicted genes, including nearly 15,300 protein-coding genes, some 1,500 apparent pseudogenes, hundreds of microRNA genes, and a few dozen genes for long, non-coding RNAs. That is likely an under-estimate, the study authors noted, owing to the relatively low coverage of the genome.

Compared with human and opossum genomes, the team found that the tammar genome contains several rearrangements, along with some retrotransposon, microRNA, and regulatory elements that haven't been detected in the past

Like the opossum genome, the new genome contained expansions to regions involved in major histocompatibility class II function, apoptosis, and sensory perception. The tammar's MHC region also contained distinct rearrangements compared to other animals.

Among the other genetic patterns identified, researchers found genes coinciding with some known features of tammar biology such as reproduction and lactation genes. They also identified genes in the cathelicidin family that appear to contribute to the antibiotic properties of a mother kangaroo's milk, which help ward of bacterial and other infections in newborns.

Overall, researchers said, "Analyses of these resources enhance our understanding of marsupial evolution, identify marsupial-specific conserved non-coding elements, and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution."

"These initial tammar genome analyses have already provided many unique insights into the evolution of the mammalian genome and highlight the importance of this emerging model system for understanding mammalian biology," the study authors concluded.

Several related studies are set to appear in the journals BMC Genomics, EvoDevo, BMC Immunology, BMC Molecular Biology, BMC Genetics, BMC Developmental Biology, and BMC Evolutionary Biology.