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The cattle fever tick, Rhipicephalus (Boophilus) microplus is one of the most significant medical veterinary pests in the world, vectoring several serious livestock diseases negatively impacting agricultural economies of tropical and subtropical countries around the world. In our study, we assembled the complete R. microplus mitochondrial genome from Illumina and Pac Bio sequencing reads obtained from the ongoing R. microplus (Deutsch strain from Texas, USA) genome sequencing project. We compared the Deutsch strain mitogenome to the mitogenome from a Brazilian R. microplus and from an Australian cattle tick that has recently been taxonomically designated as Rhipicephalus australis after previously being considered R. microplus. The sequence divergence of the Texas and Australia ticks is much higher than the divergence between the Texas and Brazil ticks. This is consistent with the idea that the Australian ticks are distinct from the R. microplus of the Americas., (Published by Elsevier B.V.)

The chromosomal region 10q24 is involved in reciprocal translocations with one of the T-cell receptor loci in a significant proportion of human T-cell acute lymphoblastic leukemias. The breakpoints of these rearrangements cluster immediately upstream of the TLX1 homeobox gene and lead to its transcriptional activation. Genomic analysis using sequences located on the opposite side of the breakpoint cluster region identified a novel gene composed of three exons that is oriented in a head-to-head manner with TLX1. The novel gene, named TDI (TLX1 divergent) codes for a 1.9 kb transcript with an atypically long 5' leader sequence. Although predicted to be a transcriptional regulator of 13.4 kDa, the TDI protein has no significant sequence similarity to any known protein. The TLX1 and TDI genes are separated by a short spacer of only 161 bp that contains numerous GC boxes and a centrally located CCAAT box embedded within a CpG island. Using luciferase as the reporter in transient transfection assays, the intergenic region was found to be a functional promoter with robust bidirectional activity. TLX1 and TDI thus appear to represent another example of a divergently transcribed gene pair whose expression is regulated by a common promoter. Our finding that TDI is transcriptionally co-activated in leukemic cells that aberrantly express TLX1, additionally suggests that it may have the potential to act as a co-operating oncogene in leukemogenesis.

The relationship between the overall G+C content of the genome (GC) and the GC content at the third codon positions (GC3) of genes, which we refer to as a GC3-plot, was examined using 15 currently available complete genome sequences. A remarkably linear relationship was found between these two quantities, confirming previous observations of a strong positive correlation in the GC3-plot. In order to conduct a more detailed analysis of the GC3-plot, we examined the GC3 content by separating orthologous codons into three categories: synonymously different codons (namely identical amino acids, IA), different amino acids (DA), and identical codons (IC), for a pairwise comparison of two closely related species. When we took pairwise species comparisons between Mycoplasma genitalium (Mg) and Mycoplasma pneumoniae (Mp) and between Mycobacterium tuberculosis (Mt) and Mycobacterium leprae (Ml) as examples, we found that for Mp and Ml, the GC3 for IA deviated the most from the linear expectation in the GC3-plot, whereas for Mg and Mt the deviation was minimal. These findings suggest that the major changes of GC content took place in Mp and Ml, but not in Mg and Mt. This analysis also enables us to predict the future direction of the evolutionary changes of the genomic GC content.

Conventional matching is based on numbers of alleles shared between donor and recipient. This approach, however, ignores the degree of relationship between alleles and haplotypes, and therefore the actual degree of difference. To address this problem, we have compared family members using a block matching technique which reflects differences in genomic sequences. All parents and siblings had been genotyped using conventional MHC typing so that haplotypes could be assigned and relatives could be classified as sharing 0, 1 or 2 haplotypes. We trained an Artificial Neural Network (ANN) with subjects from 6 families (85 comparisons) to distinguish between relatives. Using the outputs of the ANN, we developed a score, the Histocompatibility Index (HI), as a measure of the degree of difference. Subjects from a further 3 families (106 profile comparisons) were tested. The HI score for each comparison was plotted. We show that the HI score is trimodal allowing the definition of three populations corresponding to approximately 0, 1 or 2 haplotype sharing. The means and standard deviations of the three populations were found. As expected, comparisons between family members sharing 2 haplotypes resulted in high HI scores with one exception. More interestingly, this approach distinguishes between the 1 and 0 haplotype groups, with some informative exceptions. This distinction was considered too difficult to attempt visually. The approach provides promise in the quantification of degrees of histocompatibility.