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Genome Sequencing Study Reveals Apparent Adaptations in Whale Lineage

NEW YORK (GenomeWeb News) – By sequencing the minke whale and several related species, an international team led by investigators in Korea and China has gained a genetic look at the marine mammals' adaptations to ocean life.

As they reported online yesterday in Nature Genetics, the researchers began by sequencing and assembling the genome of the common minke whale, Balaenoptera acutorostrata. Along with analyzing sequencing in that reference, they also did re-sequencing and comparative genomic analyses involving three more minke whales, one fin whale, a bottlenose dolphin, and a finless porpoise.

With this sequence data, the team tracked down mutations, gene set expansions, and other genomic patterns suspected of contributing to several characteristic whale features, including the animals' ability to withstand low oxygen levels, elevated salt, and other conditions that cause stress in related land mammals.

"The genome data not only can help us know much more about the mechanisms underlying minke whale [adaptations], but also provides invaluable resource for marine mammal's future studies such as diseases control and prevention, species conservation, and protection," co-first author Xuanmin Guang, with BGI-Shenzhen, said in a statement.

The cetacean order that houses whales, dolphins and porpoises falls into the same clade as the order containing cows, hippopotami, and pigs, Guang and company noted. That has prompted interest in the genetic and physiological features that have helped cetaceans adapt to life in water — particularly adaptations for surviving in the low oxygen conditions that the animals experience during deep very deep underwater dives.

For the current study, the researchers began by generating a reference sequence for one of the most widespread baleen whales, the common minke whale.

Using Illumina's HiSeq 2000, they sequenced genomic DNA from a male minke whale's muscle tissue, generating enough sequence to put together a de novo assembly with an estimated 128-fold coverage, on average, of the almost 2.5 billion base genome.

To that, the team added lower-coverage genome sequence data for three more minke whales, a bottlenose dolphin, a finless porpoise, and a fin whale, as well as transcript sequence data representing several minke whale tissue types.

An analysis of the minke whale reference sequence unearthed nearly 2,600 non-coding RNAs and 20,0605 predicted protein-coding genes, including members of 12,675 orthologous gene families shared with the bottlenose dolphin, cow, and/or pig.

But the team saw several differences detected within the clade, too. For instance, the minke whale genome contained fewer representatives from gene families involved in smell, taste perception, and some forms of cellular signaling.

The researchers also saw lower-than-usual representation of genes from keratin and other hair growth-related families, along with pseudogenized versions of genes suspected of coding for tooth components in other animals.

On the other hand, the minke whale and other members of the whale lineage appeared to carry a relatively large repertoire of genes and gene mutations expected to help in maintaining appropriate blood pressure and salt levels, in performing anaerobic respiration, and in dealing with reactive oxygen species and other potential stressors in low oxygen conditions.

"Overall, the whale genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment," Guang and co-authors noted, "marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species, and high salt levels."

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