Genome Spotlight: Christmas Island Rat (Rattus macleari)

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Rats once ruled Christmas Island, a 135-square-kilometer isle about 350 kilometers south of Indonesia’s Java. While chubby bulldog rats (Rattus nativitatis) roamed the island’s forest floors, it was Christmas Island rats (Rattus macleari), with their long, thick fur and rounded ears, that truly had the run of the place. According to British paleontologist Charles William Andrews, who wrote a monograph about his 1897 observations of the island, “swarms” of them appeared everywhere as soon as the sun set. Yet the last documented sighting of the species would occur a mere 18 years later. By 1908, the rats were extinct, likely the victims of a disease brought to their shores by stowaway brown rats (Rattus rattus).

Such losses were once considered irreversible. But now, with ever-improving genetic technologies, researchers are exploring the possibility of de-extinction, which can involve resurrecting a species by engineering the genome of a living species to match its long-lost kin. The recency of the Christmas Island rat’s demise, as well as its somewhat close genetic relation to extant species, make it an excellent case study for the feasibility of such projects, researchers write in a March 9 Current Biology paper.  

See “CRISPR May Prove Useful in De-Extinction Efforts”

The first step toward editing the animal back to life is assembling a high-quality genome sequence. So the team obtained skin samples from Christmas Island rat pelts, originally collected between 1900 and 1902, from the Oxford University Museum of Natural History. Given the age of the samples, the team employed short-read Illumina and BGISeq sequencing, which are ideal for degraded DNA, and rather than assembling the genome de novo, the researchers mapped the short reads they obtained to the Norway rat (Rattus norvegicus) genome. The paper’s authors deemed Norway rats an ideal candidate for editing to resurrect the Christmas Island rat because they’re close kin of the extinct species, with an estimated divergence time of 2.6 million years, plus there is an “excellent quality” reference genome for the species.

The constructed genome was missing sizable chunks. It had an average of 60.81x coverage, but only mapped to 95.15 percent of the Norway rat sequence. The researchers estimate that 2,500 of the Christmas Island rat’s roughly 34,000 genes are missing from the assembly. Poor DNA quality—which resulted in nearly 1 percent of the bases being ambiguous, as well as very short average read lengths (nearly half were 50 base pairs or less)—likely contributed to the sequences’ unmappability, the authors note, but further comparisons among living rat species suggested that divergence between the two genomes was a major factor in the apparent gaps. Roughly one-quarter of the missing genome sequence likely consisted of genes, and coverage analyses revealed that immune and olfactory genes had particularly low coverage. The authors write that “it is clear that the non-random distribution of these genes would have consequences for the resulting biology of the reconstructed animals, potentially precluding reintroduction of the species to its original environment.”

The extent of missing DNA surprised experts in the field, Science reports. Douglas McCauley, an ecologist at the University of California, Santa Barbara, who was not involved with the study, tells the outlet that it “shows both how wonderfully close—and yet—how devastatingly far” researchers are from actually reviving extinct species. “We could make something, but it seems clear it will never be a Christmas Island rat,” he notes. “In which case, what is the point?”

See “The Booming Call of De-extinction”

It’s possible improving technologies could lead to more-complete ancient genomes, and thus greater success in recreating extinct species—but even still, some experts question whether de-extinction is a worthy endeavor. “As a science, it’s awesome,” coauthor Tom Gilbert, an evolutionary biologist at the University of Copenhagen, tells Science News. However, he wonders “is this the best use of the money in a world where we can’t keep our rhinos alive?”

Runners Up:

Neosho madtom (Noturus placidus)

In the waters of the Arkansas River Basin lives a unique little catfish known as the Neosho madtom. About the size of a person’s thumb, these tiny fish were listed as threatened in 1990 after human activities destroyed much of their ancestral habitat. But conservation efforts have been hampered by a lack of knowledge about the species’ genetics. Ten whole genomes published February 21 in G3 Genes|Genomes|Genetics stand to change that. The study authors were able to locate single nucleotide polymorphisms among the genomes, which revealed little population differentiation despite geographic separation, and provided the first estimates of genetic diversity for the species. The work will aid current and future conservation efforts, the authors write, “and demonstrates that using whole-genome sequencing provides detailed information of population structure and demography using only a limited number of rare and valuable samples.”

South African bread wheat (Triticum aestivum) cultivar Kariega

Genetic engineering has the potential to improve agriculture by increasing yields, steeling crops against pathogens, and broadening tolerable growing conditions. But identifying and cloning key genes for such gains remains fraught, as the often large and repeat-rich genomes of crop species are difficult to sequence. The genomes of wheats used for flour have proven especially tricky to master but, in a March 14 paper in Nature Genetics, researchers report an assembly of a South African cultivar known for its resistance to fungal stripe rust disease that is an order of magnitude more contiguous than previous sequences. The breakthrough was enabled by long-read sequencing and other cutting-edge genetic technologies, the authors write, and the high-quality genome allowed them to identify an allele that could possibly be used to confer resistance on other varieties of wheat. The findings demonstrate “the feasibility of generating chromosome-scale wheat assemblies from any wheat line to guide gene cloning projects,” the authors conclude.

Genome Spotlight is a monthly column for The Scientist’s Genetics & Genomics newsletter that highlights recently published genome sequences and the mysteries of life they may reveal.

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