Japanese Lamprey Genome

Lampreys and hagfishes (cyclostomes) are the only living group of jawless vertebrates and therefore are an important group for the study of vertebrate evolution. Cyclostomes differ from their sister group, the jawed vertebrates (gnathostomes), by possessing a single medially-located nostril and a notochord that persists in adults. In addition, cyclostomes lack hinged jaws, mineralized skeleton, paired appendages, pancreas and spleen that are characteristic of gnathostomes. Although cyclostomes possess an adaptive immune system, it differs from that of gnathostomes. Cyclostomes use variable lymphocyte receptors assembled from leucine-rich repeat proteins, whereas gnathostomes use T-cell and B-cell antigen receptors generated from the immunoglobulin superfamily. These contrasting features of cyclostomes and gnathostomes combined with their sister group relationship makes cyclostomes a crucial group for understanding the evolution of vertebrates and their morphological and physiological diversity.

We are using the Japanese lamprey (Lethenteron japonicum, Family Petromyzontidae) as a model lamprey genome because of its relatively small genome (~1.6 Gb). Our preliminary studies indicated that the Japanese lamprey contains approximately 20% repetitive sequences compared to ~35% repetitive sequences in the 2.3 Gb genome of the sea lamprey (Petromyzon marinus). The Japanese lamprey is a parasitic, anadromous species that inhabits the Sea of Japan and migrates into Japanese rivers such as the Miomote River in Niigata and the Ishikari River in Hokkaido for breeding.

Assembly statistics

A draft assembly of the Japanese lamprey genome (LetJap1.0) was generated by sequencing DNA from the testis of a single individual using the Roche 454 platform (Mehta et al., 2013). The assembly has been deposited at DDBJ/EMBL/GenBank under the accession APJL00000000. The assembly consists of 86,125 scaffolds spanning 1,030,662,718 bp with N50 scaffold size of 924 kb (N50 scaffold number 187); and 179,499 contigs with N50 contig size of 9.2 kb (N50 contig number 23,681). The estimated genome size is ~1.6 Gb.

Protein-coding genes:17,829
Protein-coding transcripts:17,829
Repetitive sequences:21%
Average GC content:48%


Mehta, T.K., Ravi, V., Yamasaki, S., Lee, A.P., Lian, M.M., Tay, B., Tohari, S., Yanai, S., Tay, A., Brenner, S. and Venkatesh, B. (2013) Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). Proc. Natl. Acad. Sci. USA. 110: 16044-16049. [Open Access]

Queries to jlamp at imcb.a-star.edu.sg

LAST UPDATED: 2-Oct-2013

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