We tested SoDA against a set of 120 artificial immunoglobulin sequences generated by simulation of recombination and compared the results with two other widely used programs. SoDA inferred the correct gene segments more frequently than the other two programs. We further tested these programs using 30 human immunoglobulin genes from Genbank and here highlight instances where the recombinations inferred by the three programs differ. SoDA appears generally to find more likely recombinations.

Background: The processes involved in the somatic assembly of antigen receptor genes are unique to the immune system and are driven largely by random events. Subtle biases, however, may exist and provide clues to the molecular mechanisms involved in their assembly and selection. Large-scale efforts to provide baseline data about the genetic characteristics of immunoglobulin (Ig) genes and the mechanisms involved in their assembly have recently become possible due to the rapid growth of genetic databases.

Marsupials are a distinct lineage of mammals notable for giving birth to highly altricial (relatively less developed) young. The recent discovery of a unique TCR chain in marsupials, TCRμ, raises questions about its possible role in early development. Here we compare the timing of V(D)J recombination and appearance of TCRμ transcripts relative to the conventional TCRα, β, γ, and δ mRNA during postnatal development in the opossum. There are two TCRμ transcript isoforms, TCRμ1.0 and TCRμ2.0. TCRμ1.0, which uses prejoined V(D)J segments, is detectable as early as day 1, when the thymus is primarily undifferentiated epithelium. The other isoform, TCRμ2.0, which requires V(D)J recombination and contains an unusual double V configuration, is not detectable until day 13 when the thymus is histologically mature. Surprisingly, we were able to detect TCRα, β, and δ mRNA transcribed from loci that had completed V(D)J recombination as early as day 1 as well. At this early age there is apparent evidence for preference in the V segments used in the TCRα and β genes. In the case of Vα this preference appears to be associated with position in the TCRα/δ locus. In Vβ, however, preference may be due to the use of microhomology in the V, D, and J segments. Mature TCRγ transcripts were not detected until day 8, suggesting that, in contrast to eutherian mammals, in the opossum αβ T cell development precedes γδ T cell development. The results support that there may be differences in T cell subset development between marsupials and placental mammals.