Lamprey genome guide

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

At the moment, publicly available genome-wide sequence resources are limited to the sea lamprey (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 latest public version 'version 7' became available primarily at NCBI Genome. This assembly has been adopted by Ensembl at EBI to provide their own 'genebuild' [see this file for the detail]. Researchers using this resource at Ensembl should be fully 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 way 'petMar2.0'. I heard that more information, such as more thorough gene annotation, will be added to this UCSC browser in the near future.

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