Samples sharing the same HVS-I and HVS-II D-loop sequence as noted above were assigned to the same mtDNA X-haplogroup lineage.
We did, however, observe a higher recombination rate in the Gifu × L. burttii population than in the Gifu × MG20 population (Fig. 1C) in the genomic interval located at the top of chromosome 1 in the MG-20 reference sequence, as noted previously.
Because of the high-copy number of mitochondrial sequences in the Balamuthia sequencing run, as noted previously for Naegleria fowleri [ 33], we performed an additional NGS run of 14.1 million 250 bp single-end reads, and computationally subtracted reads aligning to the mitochondrial genome.
The technology can achieve this using fragmentation, peptide sequencing and, as noted above, comparison with proteins that have been predicted from genome and transcriptome sequences [ 57- 59].
The estimated proportion of nonsyntenic genes in this region was very high (87 %; 449 in 517 sequences) compared with the proportion (57 %) in the entire chromosome 6B based on our survey sequence data, as noted previously [ 24].
We observed that the PGMs from these Clostridial, δ-protoebacterial and Methanosarcinale organisms, many of which are thermophilic, frequently grouped together in our TBLASTN outputs indicating their sequence similarity, as noted previously [15], [35].
While a tetramer-based PWC analysis clearly shows the positioning dependency of various sequence words, as noted above, it does not unambiguously describe the functional elements that produce the observed word distributions.
V. fischeri strain ES114 (isolate MJM1100) was used for all of the sequence analysis except as noted.
As one might expect, the species with the most third FN type III domains, the mouse, has some repeats that are very similar to each other: domains 3D and 3F have identical amino acid sequences, as previously noted by Neidhardt et al. [ 19].
