Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture1,2. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates3,4, but we show that Atlantic cod has lost the genes for MHCII, CD4 and Ii that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions5. We find a highly expanded number of MHCI genes and a unique composition of its Toll-like receptor (TLR) families. This suggests how the Atlantic cod immune system has evolved compensatory mechanisms within both adaptive and innate immunity in the absence of MHCII. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.

No abstract

DiSSU1, a mobile intron in the nuclear rRNA gene of Didymium iridis, was previously reported to contain two independent catalytic RNA elements. We have found that both catalytic elements, renamed GIR1 and GIR2, are group I ribozymes, but with differing functionality. GIR2 carries out the several reactions associated with self‐splicing. GIR1 carries out a hydrolysis reaction at an internal processing site (IPS‐1). These conclusions are based on the catalytic properties of RNAs transcribed in vitro. Mutation of the P7 pairing segment of GIR2 abrogated self‐splicing, while mutation of P7 in GIR1 abrogated hydrolysis at the IPS‐1. Much of the P2 stem and all of the associated loop could be deleted without effect on self‐splicing. These results are accounted for by a secondary structure model, in which a long P2 pairing segment brings the 5′ splice site to the GIR2 catalytic core. GIR1 is the smallest natural group I ribozyme yet reported and is the first example of a group I ribozyme whose presumptive biological function is hydrolysis. We hypothesize that GIR1‐mediated cleavage of the excised intron RNA functions in the generation and expression of the mRNA for the intron‐encoded endonuclease I‐DirI.

Group I introns are genetic elements interrupting functional genes. They are removed from precursors at the RNA level and most catalyze their own splicing. The catalytic part of these constitutes one of the major classes of catalytic RNAs, the group I ribozymes. However, group I introns have a lot more to offer than their own elimination by splicing. Intron RNA can circularize in at least three different ways and introns are mobile both at the DNA and RNA level. Some group I introns have a very complex organization incorporating functional genes and other sequence elements and have established deep relationships with their host genomes. Finally, group I introns can develop into new ribozymes with new biological functions.