Entosphenus tridentatus

Pacific lamprey (Entosphenus tridentatus): The Pacific lamprey is an anadromous parasitic lamprey species native to the West Coast of North America. The species is an important cultural food resource to the Columbia River Treaty Tribes of the U.S. Pacific Northwest and has been since time immemorial. The Columbia River discharges to the Pacific Ocean, is the largest river of the Pacific Northwest region of North America occupying a basin size of 258,000 square miles, and is the center of abundance of Pacific lamprey. The genome was sequenced in part to support ongoing conservation efforts of the species which has been heavily impacted by dams and other forms of anthropogenic habitat loss. The Pacific lamprey is one of few lamprey species that can actively climb vertical rock surfaces and historically large numbers of animals traversed a 40 foot waterfall at Willamette falls (127 miles upstream of the mouth of the Columbia River) to reach upstream spawning habitat. Notably, many of the animals that traverse the falls will fast for nearly a year or more before spawning in a subsequent spring/summer. Further upstream in the Columbia River basin, Pacific lamprey traversed the historic site of Celilo Falls (200 miles upstream of the mouth of the Columbia River, now submerged by the Dalles Dam since 1957) and migrated several hundreds more miles into the upper reaches of the Columbia and Snake rivers. Their numbers in the interior Columbia River have fallen significantly in recent years although adults continue to make the arduous migration. Two adults captured in the Yakima River (378 miles upstream of the mouth of the Columbia River) were spawned at a nearby hatchery to be used for supplementation of the population before they were used for genome sequencing.

The Pacific lamprey was also sequenced because it is highly informative with respect to understanding the evolution of genes and gene regulatory functions in the lamprey genome, and vertebrate genomes in general. The Pacific lamprey is a representative of a clade of lampreys (genera Entosphenus, Lethenteron and Lampetra) that diverged from the lineage represented by the sea lamprey (Petromyzon marinus) ~40 MYA. This evolutionary distance provides a basis for understanding which parts of the genome encode specific functions tied directly to their sequence, such as genes regulatory sequences because these are expected to change more slowly over time than other parts of the genome. The Krumlauf lab is particularly interested in using this species to understand the evolution of Hox regulatory pathways and other pathways that are required for proper patterning of vertebrate brains and the vertebrate body plan in general.

Like other lamprey species, the Pacific lamprey also undergoes programmed genome rearrangements that result in the precise physical removal of a portion of the genome from most cells during early embryonic development. The entire genome is only retained by a small number of cells that give rise to the germline (reproductive tissues). Similar processes are only known to occur in a few vertebrate species and lampreys therefore provide a unique perspective on genome stability, gene regulation and genetic functions within the germline.

Two versions of the Pacific lamprey genome are available: one from a female that represents the somatically retained portions of the genome and another from a male that represents the entire genome (germline-specific and somatically retained). The male was targeted for assembly of germline-specific regions because extraction of highly pure germline DNA can be readily achieved using small samples of sperm from reproductively mature males.