12 Dicembre, 2016 14:30 in punto

Sezione di Geometria, Algebra e loro applicazioni

Using spacial graphs to study reoccurring patterns of scrambled genes

Natasha Jonoska, University of South Florida

Aula seminari III piano

Nucleotide rearrangements occur at both evolutionary and developmental levels, and are often studied through model organisms such as ciliate species Oxytricha and Stylonychia. These processes can be modeled by 4-regular rigid vertex graphs, called assembly graphs. They are closely related to double occurrence words, chord diagrams, and circle graphs. Edges of these graphs represent double-stranded DNA molecules, while vertices correspond to DNA recombination sites. We present graph invariants of these assembly graphs and investigate genome-wide the range of scrambled gene architectures that describe the precursor-product relationships. We find that there are two general patterns, reoccurring genome wide, that describe over 90% of the Oxytricha’s scrambled genes. We further investigate the patterns of interleaving genes and find that there are specific star-like graph structures that describe most complex interleaving patterns.