以fosmid末端序列研究分析草蝦基因體

本研究針對草蝦(Penaeus monodon)fosmid末端序列進行分析研究，以探討草蝦基因體中諸如重複序列、轉置子、轉錄序列及草蝦特有之重複序列等基因體特徵之比例、組成與分佈。本研究共分析11,850個clone所定序之20,926條末端序列，總長度為草蝦基因體的0.5%，其平均長度為531bp，平均GC組成為45.6%。GC組成分佈呈常態分佈，並經由同一個clone兩端之末端序列之GC組成比較分析得知在小範圍內GC組成也會有大幅度之變化。重複序列分析結果顯示約49.7%的末端序列皆含有重複序列，其中以simple sequence repeat，low complexity repeat，rRNA及LTR/gypsy為最主要之重複序列種類。重複序列佔草蝦基因體所有核苷酸約15.2％，代表重複序列分佈雖廣，但長度多為短小之序列。以末端序列分別對C.elegans、D.melanogaster以及H.sapiens蛋白質資料庫進行BLASTX分析，共發現294個末端序列含有長度大於300bp的轉錄序列，並表示草蝦基因體共含有約58,000個基因。密碼子使用偏差(codon usage bias)分析顯示全部64個密碼子之中共有44密碼子有顯著的使用偏差情形。草蝦轉錄序列中88％可依基因功能(Gene Ontology)分類，而其中約一半為binding或cellular process相關。以self-BLAST分析發現16條草蝦特有之重複序列片段，與NCBI之NR資料庫比對結果顯示其中10條草蝦特有之重複序列為首度發現之重複序列，並以GENSCAN預測其內含基因或是轉錄序列之可能性。本研究藉由草蝦末端序列之研究瞭解其基因體內各項特徵的比例、組成與分佈，並提供未來草蝦基因體計畫重要的資訊。

關鍵字

草蝦；基因體；末端序列；重複序列；轉錄序列

並列摘要

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.

並列關鍵字

Penaeus monodon ； tiger shrimp ； genome analysis ； fosmid end sequence ； repetitive sequence ； protein coding region

參考文獻

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國際替代計量

以fosmid末端序列研究分析草蝦基因體

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