Genome: Petromyzon marinus

Credit: Jeramiah Smith

Category
Other Vertebrates
Taxonomy
Non-Mammalian Vertebrate
Scientific Name
Petromyzon marinus
Common Name
Sea Lamprey

Biology

Lampreys are eel-like in appearance, but have a soft skeleton composed of cartilage. They lack paired fins but have well developed fins on their back. In the adult, the mouth is a longitudinal slit when closed, but forms a curved disk at the tip of the snout when open, and is armed with many horny, hooked teeth arranged in numerous (11 to 12) rows, the innermost the largest. The sea lamprey can hardly be mistaken for any other fish, its eel-like appearance coupled with two dorsal fins and the jawless mouth identifying it at a glance.

Smaller specimens are white below and uniformly colored above, usually described as blackish blue, or as lead colored, and more or less silvery. Large specimens usually are olive brown above, or of varying shades of yellow-brown, green, red, or blue, mottled with a darker shade of the same color, or sometimes nearly black if the dark patches are confluent. The lower surface is whitish, gray, or of a pale shade of the same hue as the ground color of the back. During breeding season, the landlocked form takes on more brilliant hues, with the ground tint turning bright yellow. The length at the time of transformation from the larval stage is about 4 to 8 inches (100-200 mm.). Sexually mature individuals, taken in American tributaries to the Atlantic Ocean, average 2 to 2 1/2 feet long, up to a maximum of about 3 feet. One of 33 inches weighed 2 1/4 pounds.Sexually mature sea lampreys collected from tributaries to the Great Lakes are often much smaller.

The sea lamprey breeds in freshwater, but it is selective of its breeding habitat. Ideal habitats are a gravelly bottom in rapid water for their spawning beds, with muddy or sandy bottom in quiet water nearby, for the larvae. As the two sexes mature, the males develop a strong ridge along the back, the females a crest-like fin between the anus and the caudal fin. Spawning, commencing when the temperature of the water is about 50 F. (10 C.), is completed by the time it has warmed to about 68-70 F (20-21 C.). A sea lamprey has been found to contain 236,000 ova. The eggs are laid in depressions about 3-6 inches deep, dug by both males and females. Adults all die after spawning.

The larvae are different in appearance from the adults: blind, toothless, with mouths and fins of different shape. They continue in this state for a period estimated as 3 to 4 years, during most of which time they live in burrows in the mud or sand, or hide under stones. At the end of this larval period, when they have grown to a length of 4 to 6 inches, they undergo metamorphosis to the parasitic form and structure, an event that is often highly synchronized. The metamorphosis typically starts in early July and may last up to ten months. After this radical metamorphosis, they run down to the ocean or lakes to live and grow there for one or two years, so that large ones, not yet mature, are to be found in salt water all the year round.

While at sea, the lampreys prey on fish by attaching to the body by 'sucking on' with the strong mouth. As soon as the victim is bled dry, the lamprey moves on to another fish. Occasionally they are found fast to driftwood, even to boats. When not clinging to anything they are strong, vigorous swimmers, progressing by an undulating motion.

-- Adapted from The Gulf of Maine Research Institute

Habitat

Sea lampreys (Petromyzon marinus) are found in Atlantic Ocean; from the west coast of Greenland to Florida in the western side of the Atlantic; from northern Norway to the Mediterranean in the eastern; running up fresh rivers to breed, and landlocked in certain American lakes, as the Laurential Great Lakes.

Sequencing Plan

The 2.1-2.4 Gb genome of Petromyzon marinus has been targeted by the NHGRI for a high quality draft and assembly. Preliminary studies indicate that the genome is A/T rich and repetitive. The repetitive genome confounds the assembly process, causing stacking of repetitive elements into a few blocks of contigs with very deep coverage per contig. In addition, the heterozygosity rate for a single animal is very high, again impeding an effective assembly.

Following extensive discussion among TGI scientific staff and representatives of the Petromyzon community, including Drs. Marianne Bronner-Fraser, Tatjana Sauka- Spengler, Zeev Pancer, and Weiming Li, regarding all the difficulties anticipated, the following sequencing plan was formulated. The DNA has been prepared in Dr. Bronner-Fraser's laboratory from an animal designated animal 11, and is in house.

  • 6X WGS (5.7X WGS in plasmids and 0.3X in fosmids)
  • 0.1X BAC end sequencing
  • Generate Cot curve data
  • Sequence sampling of the highly repetitive Cot fractions for repeat-masking purposes
  • cDNA sequencing on 454 (6 libraries)--aiming for full length products as much as possible
  • Conventional cDNA sequencing libraries already in existence and provided by the community. This will assist gene annotation and provide clones for interested investigators.
  • Finishing of regions identified through BAC filter probing that contain much of the immunoglobulin precursor regions of the genome (estimate 12 BACs)

Genome survey sequencing has been completed to determine the genomic landscape for Petomyzon. Discussions regarding the best approach for this A/T rich and highly repetitive genome have been completed and sequencing is ongoing. The National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) is providing funding for the sequence characterization of the Petromyzon marinus genome.

Data Links

Species Name Data Type
Petromyzon marinus FTP Link
Petromyzon marinus NCBI Genome Page Link
Petromyzon marinus NCBI Trace Archive Link
Petromyzon marinus NCBI BioProject ID Link