Lamprey genome guide

[Updated on October 20, 2018]

In this page, I summarize some of the details of publicly available resources of the lamprey genome sequences for the users convenience.

Petromyzon marinus

Version 3
Sanger read production was started by The Genome Institute at Wash. U. (WUTGI) as early as in 2005 or so (if I remember correctly) [see the original project page]. The Sanger reads lead to the first publicly available genome assembly (version 3) now still accessible at UCSC Genome Browser (note that this version is called 'petMar1.0' at UCSC). The genome assembly is available at the WUTGI FTP site .

Version 7
The assembly version 'version 7' became available primarily at NCBI Genome. This assembly was later adopted by Ensembl at EBI to provide their own 'genebuild' [see this file for the detail]. Researchers using this resource at Ensembl should be warned with the fact that only about 10,000 protein-coding genes are annotated on this genome assembly. It is likely that many loci not included in this count are found in the genome assembly but not annotated by a possibly too conservative genebuild pipeline. The USCS browser has also adopted this version 7 [browse!]. At this site, this version is again named in their own naming 'petMar2.0'.

In February 2013, a paper compiling various analyses based on this version of the assembly was published online in Nature Genetics.

Germline (Pmar_germline 1.0)
In early 2018, the genome assembly based on the DNA extracted from sperm was released (Smith et al., 2018).

Lethenteron camtschaticum (or japonicum) 

LetJap1.0 (testes)
A bit later than the release of the Petromyzon genome assembly v7 above, the first L. camtschaticum genome assembly was published as part of an original study reporting its reduced Hox gene clusters (Mehta et al., 2013).