Genome visualization of the southern Luzon slender-tailed cloud rat (Phloeomys cumingi, waterhouse 1839) based on standard karyotyping and whole chromosome analysis
Date
2010
Degree
Bachelor of Science in Biology
Major Course
Major in Zoology
College
College of Arts and Sciences (CAS)
Adviser/Committee Chair
Leticia E. Afuang
Request Access
To request access of this material, please email the administrator at uscs-mainlib.uplb@up.edu.ph
Abstract
For genome visualization, standard karyotype was used to regionally map GC rich bands of Phloeomys cumingi (2n=44) metaphase chromosomes.
The standard karyotypes across three studies (Heaney-Rickart, Bellomo- Schaunberg, and this study) were collated for comparative analysis using
histogram plots obtained from 3D-surface plots of vectorized images of each chromosome and matched the image plots using pattern recognition software (Image Comparer‟s pattern recognition algorithm). The g-bands were annotated at the 400-bands resolution. Google Layout 2.0, Image J and Circos 0.52, a PERL program, were used to handle karyotypes, the ideogram constructs and circular genomic data layout. Each karyotype differs in banding resolution depending on the chromosome preparation and source of metaphase cells, thus making it more difficult to assess band formation. Virtually, with enough standard karyotype from previous studies, band formation is reproducible in spite these differences. Synteny-like plots were prepared using a circular genome layout to visualize cytogenetic band data. Analysis of the X chromosome shows banding pattern highly conserved with syntenic map shown by circos 2D link data visualization. Circos genome visualization program proves to be efficient in presenting data across the ideograms of the karyotypes by exploiting g-band data, pixel histogram, and image properties via content-based color-texture analysis.
Language
English
Recommended Citation
Fajardo, Leemuel DG., "Genome visualization of the southern Luzon slender-tailed cloud rat (Phloeomys cumingi, waterhouse 1839) based on standard karyotyping and whole chromosome analysis" (2010). Undergraduate Theses. 2088.
https://www.ukdr.uplb.edu.ph/etd-undergrad/2088
Document Type
Thesis