BAC end sequencing of Pacific white shrimp <Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>: a glimpse into the genome of Penaeid shrimp |
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Authors: | Cui?Zhao Email author" target="_blank">Xiaojun?ZhangEmail author Chengzhang?Liu Pin?Huan Fuhua?Li Jianhai?Xiang Chao?Huang |
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Institution: | 1, 2 1 Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China 2 Graduate University of Chinese Academy of Sciences, Beijing 100049, China |
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Abstract: | Little is known about the genome of Pacific white shrimp (Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing.
After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total
length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs
indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences.
Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element
was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our
results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly
for this species. |
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Keywords: | Litopenaeus vannamei BES repetitive sequences SSR genome survey |
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