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

Your Location：

Home >

Browse articles >

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

OriginalPaper | Updated：2023-05-16

- BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp
- BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp
- 海洋湖沼学报（英文） 2012年30卷第3期页码：456-470
- 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：
  
  Supported by the National Natural Science Foundation of China (Nos. 30972245, 30730071), and the National Basic Research Program of China (973 Program) (No. 2012CB114403)
- DOI：10.1007/s00343-012-1159-y
  中图分类号：
- 网络首发：2011-11-10，
  
  纸质出版：2012
- Accepted：
Scan QR Code
BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp[J]. 海洋湖沼学报（英文）, 2012,30(3):456-470.

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
BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp[J]. 海洋湖沼学报（英文）, 2012,30(3):456-470. DOI： 10.1007/s00343-012-1159-y.

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.

关键词

Keywords

references

Alcivar-Warren A, Dunham R, Gaffney P et al. 1997. First aquaculture species genome mapping workshop. Anim. Genet., 28(6): 451–452.

Alcivar-Warren A, Meehan-Meola D, Park S W et al. 2007. ShrimpMap: A low-density, microsatellite-based linkage map of the pacific whiteleg shrimp, Litopenaeus vannamei: identification of sex-linked markers in linkage group 4. J. Shellfish Res., 26(4): 1 259–1 277.

Budiman M A, Mao L, Wood T C et al. 2000. A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res., 10(1): 129–136.

Cheng W, Liu C H, Tsai C H et al. 2005. Molecular cloning and characterisation of a pattern recognition molecule, lipopolysaccharide- and beta-1,3-glucan binding protein (LGBP) from the white shrimp Litopenaeus vannamei. Fish Shellfish Immunol., 18(4): 297–310.

Cheung F, Town C. 2007. A BAC end view of the Musa acuminata genome. BMC Plant Biology, 7(1): 29.

Christopher A Saski R H, Robert W Chapman, John A Benzie. 2009. Advancing Shrimp Genomics (abstract). Plant & Animal Genomes XVII Conference: W021.

Ciobanu D C, Bastiaansen J W M, Magrin J et al. 2010. A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Anim. Genet., 41(1): 39–47.

Colbourne J K, Pfrender M E, Gilbert D et al. 2011. The ecoresponsive genome of Daphnia pulex. Science, 331(6017): 555–561.

Dalloul R A, Long J A, Zimin A V et al. 2010. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol., 8(9): e1000475, doi:10.1371/journal. pbio.1000475.

Dan N V, Ramchiary N, Choi S R et al. 2010. Development and characterization of new microsatellite markers in Panax ginseng (CA Meyer) from BAC end sequences. Conserv. Genet., 11(3): 1 223–1 225.

Du Z Q, Ciobanu D C, Onteru S K et al. 2010. A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. Anim. Genet., 41(3): 286–294.

Gao H, Kong J. 2005. The microsatellites and minisatellites in the genome of Fenneropenaeus chinensis. DNA Seq., 16(6): 426–436.

Garcia D K, Alcivar-Warren A. 2007. Characterization of 35 new microsatellite genetic markers for the pacific whiteleg shrimp, Litopenaeus vannamei: their usefulness for studying genetic diversity of wild and cultured stocks, tracing pedigree in breeding programs, and linkage mapping. J. Shellfish Res., 26(4): 1 203–1 216.

Gregory T R. 2005. Synergy between sequence and size in large-scale genomics. Nat. Rev. Genet., 6(9): 699–708.

Gross P S, Bartlett T C, Browdy C L et al. 2001. Immune gene discovery by expressed sequence tag analysis of hemocytes and hepatopancreas in the Pacific White Shrimp, Litopenaeus vannamei, and the Atlantic White Shrimp, L. setiferus. Dev. Comp. Immunol., 25(7): 565–577.

Han Y, Korban S. 2008. An overview of the apple genome through BAC end sequence analysis. Plant Mol. Biol., 67(6): 581–588.

Holt R A, Subramanian G M, Halpern A et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science, 298(5591): 129–149.

Hong C, Plaha P, Koo D et al. 2006. A survey of the Brassica rapa genome by BAC-End sequence analysis and comparison with Arabidopsis thaliana. Mol. Cells, 22: 300–307.

Hou Y B, Lin S J. 2009. Distinct gene number-genome size relationships for Eukaryotes and Non-Eukaryotes: gene content estimation for dinoflagellate genomes. PLoS ONE, 4(9): e6978.

Huan P, Zhang X, Li F et al. 2010. Chromosomal localization of 5S rDNA in Chinese shrimp (Fenneropenaeus chinensis): a chromosome-specific marker for chromosome identification. Chin. J. Oceanol. Limnol., 28(2): 233–238.

Huang S W, Lin Y Y, You E M et al. 2011. Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon. BMC Genomics, 12: 242.

Kaminker J S, Bergman C M, Kronmiller B et al. 2002. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol., 3(12): RESEARCH0084.

Kawakami T, Dhakal P, Katterhenry A N et al. 2011. Transposable element proliferation and genome expansion are rare in contemporary sunflower hybrid populations despite widespread transcriptional activity of LTR retrotransposons. Genome Biol. Evol., 3: 156–167.

Kocher T D, Kole C. 2008. Genome mapping and genomics in fishes and aquatic animals. In: Kole C ed. Genome Mapping and Genomics in Animals v. 2. Springer, Berlin. xxiii. 180p.

Konstantinidis K T, Tiedje J M. 2004. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc. Natl. Acad. Sci. U. S. A., 101(9): 3 160–3 165.

Koyama T, Asakawa S, Katagiri T et al. 2010. Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus. BMC Genomics, 11: 141.

Kremer H, Hennig W. 1990. Isolation and characterization of a Drosophila hydei histone DNA repeat unit. Nucleic Acids Res, 18(6): 1 573–1 580.

Lai C W, Yu Q, Hou S et al. 2006. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol. Genet. Genomics, 276(1): 1–12.

Larsen N J, Hayes H, Bishop M et al. 1999. A comparative linkage and physical map of bovine chromosome 24 with human chromosome 18. Mamm. Genome, 10(5): 482–487.

Liu H, Jiang Y L, Wang S L et al. 2009. Comparative analysis of catfish BAC end sequences with the zebrafish genome. BMC Genomics, 10: 592.

Luo T, Li F, Lei K et al. 2007. Genomic organization, promoter characterization and expression profiles of an antiviral gene PmAV from the shrimp Penaeus monodon. Mol. Immunol., 44(7): 1 516–1 523.

Lynch M, Conery J S. 2003. The origins of genome complexity. Science, 302(5649): 1 401–1 404.

Maxson R, Cohn R, Kedes L et al. 1983. Expression and organization of histone genes. Annu. Rev. Genet., 17: 239–277.

Meehan D, Xu Z K, Zuniga G et al. 2003. High frequency and large number of polymorphic Microsatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei [Crustacea: Decapoda]. Mar. Biotechnol., 5(4): 311–330.

Mishra A K, Agarwal S, Jain C K et al. 2009. High GC content: critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana. Bioinformation, 4(4): 151–154.

Naylor R L, Goldburg R J, Primavera J H et al. 2000. Effect of aquaculture on world fish supplies. Nature, 405(6790): 1 017–1 024.

Ohyama A, Asamizu E, Negoro S et al. 2009. Characterization of tomato SSR markers developed using BAC-end and cDNA sequences from genome databases. Mol. Breed., 23(4): 685–691.

Panaud O, Chen X, McCouch S R. 1996. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol. Gen. Genet., 252(5): 597–607.

Perez F, Erazo C, Zhinaula M et al. 2004. A sex-specific linkage map of the white shrimp Penaeus (Litopenaeus) vannamei based on AFLP markers. Aquaculture, 242(1–4): 105–118.

Perez F, Ortiz J, Zhinaula M et al. 2005. Development of ESTSSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Mar. Biotechnol., 7(5): 554–569.

Pritham E J. 2009. Transposable elements and factors influencing their success in eukaryotes. J. Hered., 100(5): 648–655.

Ren C, Lee M K, Yan B et al. 2003. A BAC-based physical map of the chicken genome. Genome Res., 13(12): 2 754–2 758.

Sambrook J, Russell D W. 2001. Molecular cloning: a laboratory manual. 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

Seinen Chow W J D a P A S. 1990. Meiotic chromosome complements and nuclear DNA contents of four species of shrimps of the genus Penaeus. J. Crustac. Biol., 10(1): 29–36.

Stein N, Feuillet C, Wicker T et al. 2000. Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). Proc. Natl. Acad. Sci. U. S. A., 97(24): 13 436–13 441.

Wessler S R. 2006. Transposable elements and the evolution of eukaryotic genomes. Proc. Natl. Acad. Sci. USA, 103(47): 17 600–17 601.

Xu L, Chen H, Hu X H et al. 2006. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms. Mol. Biol. Evol., 23(6): 1 107–1 108.

Xu P, Wang S, Liu L et al. 2006. Channel catfish BAC-end sequences for marker development and assessment of syntenic conservation with other fish species. Anim. Genet., 37(4): 321–326.

Xu P, Wang S, Liu Z. 2007. Physical characterization of genomes through BAC end sequencing. In: Liu Z ed. Aquaculture Genome Technologies. Blackwell Publishing Ltd 261–274.

Zhang L S, Yang C J, Zhang Y et al. 2007. A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates. Genetica, 131(1): 37–49.

Zhang X J, Zhang Y, Scheuring C et al. 2010. Construction and characterization of a bacterial artificial chromosome (BAC) library of Pacific white shrimp, Litopenaeus vannamei. Mar. Biotechnol., 12(2): 141–149.

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

Peritrophin-like protein from Litopenaeus vannamei (LvPT) involved in white spot syndrome virus (WSSV) infection in digestive tract challenged with reverse gavage

EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)

Effects of water temperature and dietary carbohydrate levels on growth and energy budget of juvenileLitopenaeus vannamei

Closed recirculating system for shrimp-mollusk polyculture

Regulation of water quality and growth characteristics of indoor raceway culture of Litopenaeus vannamei