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Pairwise comparison of the genome sequences revealed that the majority of SNPs were found in two major clusters, including (i) the plasticity zone (PZ); and (ii) the major polymorphic membrane (pmp) gene cluster (Fig. 1).
In rats and humans, POAGAL neurons are predominantly found in three major clusters, including the VLPO and extended VLPO; the medial preoptic nucleus; and the supraoptic nucleus11.
We were able to identify at least seven main MUs for M. boninensis, which were OTJ, natural trees in CCJ, natural trees in KWK, SKM, man-made trees in CCJ and KWK and two major clusters including individuals in IGM and LPS (Green and Pink).
Using the protein alignment which included 122 sequences, we constructed the neighbour-joining tree which showed four major clusters, including shadoos, shadoo2s and prion protein-likes (cluster 1), fish prion proteins (cluster 2), tetrapode prion proteins (cluster 3) and doppels (cluster 4).
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The first of the major clusters included metabolic maps related to the degradation of aromatic compounds, such as amino benzoate, bisphenol, toluene, and naphthalene, among others.
Cluster 6 was a major cluster, including four genes in the C1 class, seven in the S14 (Clp) class, two in the M1 class, and four other classes.
An intriguing observation was that, using a 70% similarity cut-off value for cluster analysis (approximately equivalent to less than or equal to eight PFGE fragment differences) resulted in most infection isolates being grouped into one major cluster (including PFGE clusters B, C, D and E), with 68% of infection isolates and 17% of carriage isolates (P < 0.01).
The first major cluster included Z. diploperennis (Tz09), Z. perennis (Tz01 and Tz02), Z. luxurians (Tz05 and Tz06) and Z. nicaraguensis (Tz10).
The fourth major cluster includes Dpls.
The third major cluster includes the tetrapode PrPs.
The first major cluster includes Shos, Sho2s and PrP-likes.
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