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Figure 1 B-cell clonotypes proliferate within MMΦCs while acquiring mutations in the variable region of Ig genes. (A) Translated sequences of the CDR3 of the dominant clones within a single MMΦC (F4UKCa) and the number of putative daughter cells. Lineage tree using BRILIA shows only the different CDR3 sequences (there are 183 unique sequences in this clone but only 24 unique CDR3 sequences). Each dot of the left hand tree represents a unique sequence, and each dot color corresponds to a unique CDR3 sequence. The dot size reflects the total copy number of each sequence. The x-axis shows the percent of Hamming distance calculated based on the number of nucleotides at which two sequences of the same length differ. (B) An example of part of a smaller lineage tree using BuildTrees, IgPhyML (HLP19 model) and Alakazam (igraph), CDR3 nucleotide sequences of all the unique sequences (the size of this sub-clone is 35 sequences). A few of the CDR3 sequences are unique to specifc sequences with mutated nucleotides (underlined nucleotides). Some branches have their defining mutation outside of the CDR. The scale bar represents the branch length (expected number of substitutions per codon site). The analysis was done using IgPhyML and BRILIA. HAM %, is the percent of Hamming distance which is calculated based on the number of nucleotides at which two sequences of the same length differ.