碩士 / 國立臺灣大學 / 動物學研究研究所 / 95 / In this study, we report the analysis of 20,926 fosmid end sequences (FESs), providing an initial view of the genomic composition of the tiger shrimp. We analyzed the composition of repeat elements, protein-coding regions, microsatellite contents and tiger shrimp specific repeat elements.
The total length of the FESs is 0.5% of the shrimp genome, with an average length of 531 bp and average GC content of 45.6%. The GC content is normally distributed, and analyses of pair FESs indicate GC contents withing local regions can be heterogenous.
An average of 49.7% of the FESs contained repetitive sequences, covering an average of 15.2% of the total sequences. Simple sequence repeats, low complexity repeats, rRNA, and LTR/gypsy are the four most abundant repetitive sequences found in the shrimp genome.
BLAST analyses identified 294 FESs that contain protein coding regions with lengths greater than 300 bp and with annotation in any two of the three BLAST analyses, which leads to an estimated gene count of 58,000 genes for the tiger shrimp. Codon usage bias was observed in 44 of the possible 64 codons.
Sixteen P.monodon specific repetitive sequences (PMSRs) were identified by self-BLAST analyses. In search against the NCBI NR database, ten PMSRs are novel repetitive sequences.
The fosmid end sequences, along with the fosmid clone library, provides an overview of the genomic landscape as well as a valuable resource for future physical mapping, whole genome sequencing and other genomic related studies.
| Identifer | oai:union.ndltd.org:TW/095NTU05312015 |
| Date | January 2007 |
| Creators | You-Yu Lin, 林友瑜 |
| Contributors | Hon-Tsen Yu, 于宏燦 |
| Source Sets | National Digital Library of Theses and Dissertations in Taiwan |
| Language | zh-TW |
| Detected Language | English |
| Type | 學位論文 ; thesis |
| Format | 45 |
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