This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.
Early studies have assumed that the basic structure of the sheep MHC was similar to that of other mammals, consisting of the telomeric class I, central class III and centromeric class II.
The anterior central class genes CapI-Scr and CapI-lox5 are expressed in segments T3 to T8 and T4 to T8, respectively.
After early surface ectodermal expression, the anterior and central class genes are expressed in small domains of putative neural precursor cells co-expressing ClSoxB1, suggesting an evolutionary early function of Hox genes in patterning parts of the nervous system.
Organized clusters of Hox genes, composed of anterior class (paralog groups Hox1, Hox2), Hox3, central class (Hox4 - 8) and posterior class (Hox9- 15) genes, are present in the annelid Capitella teleta [ 5], vertebrates and cephalochordates [ 15, 16], which suggests that Hox genes were indeed organized in a cluster in the last common ancestor of protostomes and deuterostomes.
The 21 functional genes have been divided into two sub-classes based on position and sequence similarity: 6 peripheral Class A Mups, and 15 central Class B Mups.
Capitella sp. I has a definitive Antp/PG7 gene, which clusters with other lophotrochozoan, ecdysozoan, and deuterostome central class genes, including the ecdysozoan Tribolium antp gene (Figure 1).
Our analysis suggests that a true anterior and posterior gene has been present in the bilaterian-cnidarian ancestor and that the central class genes are a novelty of the Bilateria.
As in previous phylogenetic analyses of acoel Hox genes [ 5, 45, 64], the anterior class Hox orthologs of acoels groups as the sister to all remaining Hox1/ labial genes, the central class Hox gene branches with Hox4/5 and the posterior Hox with the posterior class genes Hox9-14.
It is composed by three regions, the class I and class II regions flanking the central class III region.
