The different genome sequencing projects aim for sequencing one individual of each species. This is to optimise the assembly of obtained sequences given that the genetic variation in many of these species are known or expected to be high. Several DNA extraction procedures have in most cases been tested to optimise yield and quality of the DNA. Even so, for some species we have obtained low levels of DNA and alternative methods for DNA library preparations have been utilised. All sequencing to this stage has been performed by the Illumina technology, generating paired-end reads of 100nt. The short fragment library to be sequenced has been of fragment sizes 150 or 300bp and for scaffolding, 3 or 5kbp fragments (mate-paired) have so far been used. The assembly is mainly by the CLC software, but also other platforms are being tested. Parallel PCR cloning and sequencing of specific genes in some of the species provides guiding to the optimisation of the assembly process. For all species RNA/cDNA sequencing is complementing the genome sequencing. Gene finding and gene structure is based on RNA and species-specific HMM gene descriptions.
During the fall 2012 we will initiate international collaborations for annotation of protein coding as well as ncRNA coding genes, and other chromosomal features. For further information on this or to indicate your interest in taking part in such activities, please contact Anders Blomberg (firstname.lastname@example.org), Kerstin Johanesson (email@example.com).
We plan to publish genomes during 2016-2017. Prior to the genome publication, the access to the current assembly data for a particular species can be arranged in terms of a collaborative project. If you are interested in such collaboration, please contact the project coordinators Kerstin Johannesson and Anders Blomberg.
In 2011 CeMEB launched IMAGO – Infrastructure for MArine Genetic model Organisms. Under IMAGO we will develop 8 marine species into new experimentally amenable genetic models. The chosen species represent key-species in NE Atlantic coastal ecosystems.
The IMAGO initiative is funded by VR, Formas, University of Gothenburg (through the CeMEB grant)