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Identification and Bioinformatics of Pseudogenes from Whole Genome Sequences of Phaeodactylum Tricornutum

Author: JiChangMian
Tutor: LiuWenLing
School: Tianjin University of Science and Technology
Course: Marine biology
Keywords: Phaeodactylum tricornutum pseudogenes pseudogene fragment bioinformatic analysis
CLC: Q943
Type: Master's thesis
Year: 2012
Downloads: 5
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Abstract


Pseudogenes are sequences that share sequence similarities to functional genes, but in general are unable to be transcribed in to proteins.Pseudogene was used to be considered as a typical kind of non-coding "junk DNA". Along with increasing study, however,more and more evidences have shown that pseudogenes play important roles in gene regulation and genome evolution. Identification of pseudogenes is very important for genome annotation. Phaeodactylum tricornutum is a marine diatom that is rich in polyunsaturated fatty acid (PUFA). The genome sequences of P. tricornutum have been complete sequenced. T(identify pseudogenes from P. tricornutum, we developed a pipeline that enabled us to discover and characterize pseudogenes. In total, we identified1654’true’processed pseudogenes,714duplicated pseudogenes and4729pseudogenes fragments. The distribution of processed psuedogene, molecular evolution, GC content favoritism,the correlation between chromosome length and number of pseudogene were identified as well as interrelation of identity and completeness. Overall, processed pseudogenes are very similar to their closest corresponding human gene, being95%and92%complete for’True’ processed pseudogene and ’Putative’ processed pseudogene.Their chromosomal distribution appears random and dispersed, with the numbers on chromosomes proportional to length, suggesting sustained "bombardment" over evolution. However, it does vary with GC-content:Processed pseudogenes occur mostly in intermediate GC-content regions.The results indicated that the genome sequences of P. tricornutum contained many pseudogenes and pseudogenes fragments.

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