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DNA recombination occurs at both evolutionary and developmental scales, and is often studied through model organisms such as ciliate species Oxytricha and Stylonychia. These species undergo massive genome rearrangements during their development of a somatic macronucleus from a zygotic micronucleus. Gene segments that recombine during such rearrangement processes may be organized on the chromosome in a variety of ways. They can overlap, interleave or one may be a subsegment of another. We use colored directed graphs to represent contigs containing rearranged segments where edges represent recombined segment organization. Using graph properties, to each graph we associate a point in a Euclidean space such that cluster formations and analysis can be performed with methods from topological data analysis. We find that there are specific star-like graph structures that describe most complex interleaving gene patterns. We also use word patterns to investigate genome-wide scrambled gene architectures that describe the precursor-product relationships. Our studies show that there are two general patterns, reoccurring genome wide, whose iterative appearance describe over 90\% of the Oxytricha's scrambled genes.

Please contact Mariel (mrlvazquez@ucdavis.edu) if you want to meet with the speaker.