Design And Implementation Of An Algorithm To Determine Homologous Chromosome Segments In Genomes

Widespread occurrence of polyploidization is an important feature in plant genome evolution. Some researches found that all plant genomes which have been sequenced had been affected by polyploidy. To understand the function and associated biological processes of plant genomes, sorting of plant genome structure and evolution is very important for scientific significance and potential economic value.Accurately determining homologous chromosome segments in genomes is the basis for the genome researches and an extremely important step. However, because of the complexity in plants genomes, it needs more time and energy to determine homologous, especially the existing methods and software can not quickly and accurately determine them. So here the thesis aims at summarizing existing research theories and biological knowledge about grasses plants and cotton genome duplication events, transforming the specific biological practical problems into mathematical problems, modeling a mathematical model, improving Smith-Waterman dynamic programming algorithm, designing reasonable algorithm, developing a flexible and versatile software by C# to give homologous more efficiently and accurately, applying this software to test its correctness and validity in the genome sequence of grasses, finding 2092-14227 colinear genes and 60-468 homologous blocks, drawing the multiple alignment analysis figures, making three assumptions with the cotton and cacao homologous block results and verifying by computer simulation and drawing a conclusion that cotton had been a 5x polyploidization after the divergence from an ancestor shared with cacao.This work will lay a genomics foundation of further research, and provide useful approaches and tools to determine homologous chromosome segments in other complex genomes.