Whole genome Sequence of Atlantic Cod

Recently, scientists from Norway have investigated and present the genome sequence of Atlantic cod (Gadus morhua). The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. Genome sequence provided evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are conserved  feature of the adaptive immune system of jawed vertebrates and, are essential for the function of this pathway. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.

The study is published in the latest issue of Nature

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10342.html#/affil-auth

Medaka Hd-rR: Whole Genome Sequencing Project

Sequencing of the medaka genome was started at the Academia Sequencing Center of the National Institute of Genetics (NIG) in mid 2002. The project was supported by group grant Genome Science (Grant-in-Aid for Scientific Research on Priority Areas supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan).

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The sequencing was conducted by the whole-genome shotgun strategy using southern inbred strain, Hd-rR. The genome was assembled from 13.8 million reads, obtained from the whole genome shotgun plasmid, fosmid, and bacterial artificial chromosome (BAC) libraries. The total size of the assembled contigs was 700.4 megabases (Mb). 50% of nucleotides are covered in scaffolds (or contigs) of length 1.41Mb (9.8 kilobases) that are called N50 values. This contiguity is sufficient to characterize the genomic structures of genes.

Four versions of the medaka genome sequence data named 200406, 200506, version 0.9, and version 1.0  have been released to the public to provide users with timely information. The former two versions had shorter scaffolds that were not anchored on the medaka chromosomes because they were built in 2004 and 2005, before genetics markers were available. Versions 0.9 and 1.0 created in 2006, when comprehensive genetic markers were available, so that about 90% of their scaffolds and ultracontigs were located on the twenty-four medaka chromosomes. Versions 0.9 and 1.0 were built from the identical contigs and scaffolds, but the assembly of version 1.0 is longer than that of version 0.9 because more genetic markers could be used to generate version 1.0. Version 0.9 is left open to the public because most of the data analysis in the medaka genome paper published in Nature (2007) was based on version 0.9.

The University of Tokyo Medaka Genome Browser (UTGB Medaka) a web-based genome database browser, which provides various information related to medaka genomes, including assembly sequences, genes, clones, homologus genome sequences to other species, etc.

Takifugu rubripes: Whole Genome Sequence

Fifth Fugu Genome assembly v5 made available by the Institute of Molecular and Cell Biology (IMCB) in July 2010. The fugu (Takifugu rubripes or Fugu rubripes) genome project was initiated in 1989. In 1993, researchers showed that the fugu genome is only 390 Mb, yet it contains a similar repertoire of genes to humans, which is useful for discovering genes and gene regulatory elements in the human genome. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. A ‘draft’ sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the 'whole-genome shotgun' sequencing strategy. In the latest version, some gaps in the fugu assembly v4 have been filled and the scaffolds have been organized into chromosomes based on a genetic map of the fugu (a collaborative project between IMCB and University of Tokyo). The v5 assembly comprises 7,118 scaffolds covering 392 Mb. About 72% of the assembly (281,557,002 bp) is organized into 22 chromosomes. Another 14% of the assembly (55,560,038 bp) is assigned to chromosomes but the orientation and order of the scaffolds are not known (Chr_n_un). The remaining 14% of the assembly (54,753,918 bp) is concatenated into a single sequence (Chr_un).