In addition to the β-globin and α-globin clusters, we obtained sequences for three more gene clusters: CCL, IFN, and CYP2abf.
As might be expected, genome size and number of secondary metabolite biosynthetic gene clusters are positively correlated, as larger genomes can accommodate more gene clusters devoted to secondary metabolism.
In addition to the two globin clusters and the KIR cluster, we used CHAP 2 to obtain X- and N-orthologous alignments for three more gene clusters: CCL, CYP2abf, and IFN (fig. 7 C H ).
Production, health and reproduction traits involved more gene clusters of tightly linked genes than body conformation traits, indicating that genetic mechanisms of production, health and reproduction were more complex than those of body conformation traits.
Two more gene clusters, 93 (3-β-hydroxy-D 5-C27-steroid oxidoreductase-like protein) and 95 (no confident annotation, but shows homology to collagen-like protein 1), showed strong evidence of positive selection in PAML site tests (P ≤ 0.0001).
The results clearly indicated that the group comprising LS, QY, SQ, and WC had four more gene clusters than the group containing the other Chinese locally raised breeds, which means LS, QY, SQ, and WC were more closely related and uniform.
Note that this region also includes a few genes with quite low log2 [gDNA Sliv /gDNA Scoe ] value but were not designated as absent/divergent in S. lividans simply because they did not co-localize as three- or more-gene clusters and hence did not satisfy out absence criteria (see Methods section).
This striking observation is exemplified by the sp9 and otp genes and more complex gene clusters including the hox loci.
However, CN produces fewer and more distinct gene clusters with enhanced difference between lung AC and normal samples.
We also observed that there are more significant gene clusters on chromosomes 5, 7, 12 X than any other chromosomes.
Another interesting finding is that, compared with the Chrysopicola clade, lineages within the Citri clade have more unique gene clusters.
