Entosphenus tridentatus

Overview
Full NameEntosphenus tridentatus
GenusEntosphenus
Speciestridentatus
Common NamePacific Lamprey
AbbreviationEtri
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.
Feature Summary
The following features are currently present for this organism
Feature TypeCount
supercontig376,756
exon312,118
polypeptide84,272
CDS50,716
gene33,556
mRNA33,556
three_prime_UTR12,854
five_prime_UTR10,972
Downloads
Entosphenus tridentatus male Genome Assembly (ETRm) ETRm_v1.fasta
Entosphenus tridentatus female Genome Assembly (ETRf) ETRf_v1.fasta
ETRm Transcripts etrm.transcripts.renamed.fasta
ETRf Transcripts etrf.transcripts.renamed.fasta
ETRm Proteins etrm.proteins.renamed.fasta
ETRf Proteins etrf.proteins.renamed.fasta
ETRm GFF3 etrm.genes.renamed.gff
ETRf GFF3 etrf.genes.renamed.gff



See Data Analysis page for a listing of the Analyses performed on ETRm and ETRf genome assemblies and gene models. The FASTAs and GFF are also there for download as well as other analysis.

Data Analyses

All data loaded into SIMRbase has an "Analysis Page". These pages provide information about the methods and provide a link to download the files.

Name Program Sourcesort descending
Entosphenus tridentatus female ETRf Mapped GFF MAKER etrf.genes.renamed.gff
Entosphenus tridentatus female ETRf IPRSCAN IPRSCAN etrf_iprscan.gz
Entosphenus tridentatus female ETRf Protein FASTA MAKER etrf.proteins.renamed.fasta
Entosphenus tridentatus female ETRf Transcript FASTA MAKER etrf.transcripts.renamed.fasta
Entosphenus tridentatus female Genome Assembly (ETRf) ETRf ETRf_v1.fasta
Entosphenus tridentatus female ETRf BLASTX Cavefish e!100 BLASTX ETRf_vs_cavefish
Entosphenus tridentatus female ETRf BLASTX Celegans e!100 BLASTX ETRf_vs_celegan
Entosphenus tridentatus female ETRf BLASTX Fly e!100 BLASTX ETRf_vs_fly
Entosphenus tridentatus female ETRf BLASTX Human e!100 BLASTX ETRf_vs_human
Entosphenus tridentatus female ETRf BLASTX Lamprey e!100 BLASTX ETRf_vs_lamprey
Entosphenus tridentatus female ETRf BLASTX Medaka e!100 BLASTX ETRf_vs_medaka
Entosphenus tridentatus female ETRf BLASTX Mouse e!100 BLASTX ETRf_vs_mouse
Entosphenus tridentatus female ETRf BLASTX Nematostella e!Metazoa46 BLASTX ETRf_vs_nematostella
Entosphenus tridentatus female ETRf BLASTX Smed smesg BLASTX ETRf_vs_smed
Entosphenus tridentatus female ETRf BLASTX Uniprot BLASTX ETRf_vs_uniprot
Entosphenus tridentatus female ETRf BLASTX Xenopus e!100 BLASTX ETRf_vs_xenopus
Entosphenus tridentatus female ETRf BLASTX Yeast e!100 BLASTX ETRf_vs_yeast
Entosphenus tridentatus female ETRf BLASTX Zebrafish e!100 BLASTX ETRf_vs_zebrafish
Entosphenus tridentatus male ETRm Mapped GFF MAKER etrm.genes.renamed.gff
Entosphenus tridentatus male ETRm IPRSCAN IPRSCAN etrm_iprscan.gz
Entosphenus tridentatus male ETRm Protein FASTA MAKER etrm.proteins.renamed.fasta
Entosphenus tridentatus male ETRm Transcript FASTA MAKER etrm.transcripts.renamed.fasta
Entosphenus tridentatus male Genome Assembly (ETRm) ETRm ETRm_v1.fasta
Entosphenus tridentatus male ETRm BLASTX Cavefish e!100 BLASTX ETRm_vs_cavefish
Entosphenus tridentatus male ETRm BLASTX Celegan e!100 BLASTX ETRm_vs_celegans
Entosphenus tridentatus male ETRm BLASTX Fly e!100 BLASTX ETRm_vs_fly
Entosphenus tridentatus male ETRm BLASTX Human e!100 BLASTX ETRm_vs_human
Entosphenus tridentatus male ETRm BLASTX Lamprey e!100 BLASTX ETRm_vs_lamprey
Entosphenus tridentatus male ETRm BLASTX Medaka e!100 BLASTX ETRm_vs_medaka
Entosphenus tridentatus male ETRm BLASTX Mouse e!100 BLASTX ETRm_vs_mouse
Entosphenus tridentatus male ETRm BLASTX Nematostella e!Metazoa46 BLASTX ETRm_vs_nematostella
Entosphenus tridentatus male ETRm BLASTX Smed smesg BLASTX ETRm_vs_smed
Entosphenus tridentatus male ETRm BLASTX Uniprot BLASTX ETRm_vs_uniprot
Entosphenus tridentatus male ETRm BLASTX Xenopus e!100 BLASTX ETRm_vs_xenopus
Entosphenus tridentatus male ETRm BLASTX Yeast e!100 BLASTX ETRm_vs_yeast
Entosphenus tridentatus male ETRm BLASTX Zebrafish e!100 BLASTX ETRm_vs_zebrafish