BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

Cui Zhao; Xiaojun Zhang; Chengzhang Liu; Pin Huan; Fuhua Li; Jianhai Xiang; Chao Huang

doi:10.1007/s00343-012-1159-y

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BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

Updated：2023-05-16

- BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp
- Journal of Oceanology and Limnology Vol. 30, Issue 3, Pages: 456-470(2012)
- Affiliations：
  
  1. Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences
  2. Graduate University of Chinese Academy of Sciences
- Author bio：
- Funds：
- DOI：10.1007/s00343-012-1159-y
  CLC：
- Online First：10 November 2011，
  
  Published：2012
- Accepted：
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Zhao, C., Zhang, X., Liu, C. et al. BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp., Chin. J. Ocean. Limnol. 30, 456–470 (2012). https://doi.org/10.1007/s00343-012-1159-y
DOI：

Zhao, C., Zhang, X., Liu, C. et al. BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp., Chin. J. Ocean. Limnol. 30, 456–470 (2012). https://doi.org/10.1007/s00343-012-1159-y DOI：

摘要

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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references

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