title: Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon.
abstract: BACKGROUND
  The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses.
  
  
  RESULTS
  We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome.
  
  
  CONCLUSIONS
  The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.
authors.affiliation: Institute of Zoology and Department of Life Science, National Taiwan University, Taipei, ROC.
authors.forename: Shiao-Wei
authors.initials: SW
authors.lastname: Huang
authors.forename: You-Yu
authors.initials: YY
authors.lastname: Lin
authors.forename: En-Min
authors.initials: EM
authors.lastname: You
authors.forename: Tze-Tze
authors.initials: TT
authors.lastname: Liu
authors.forename: Hung-Yu
authors.initials: HY
authors.lastname: Shu
authors.forename: Keh-Ming
authors.initials: KM
authors.lastname: Wu
authors.forename: Shih-Feng
authors.initials: SF
authors.lastname: Tsai
authors.forename: Chu-Fang
authors.initials: CF
authors.lastname: Lo
authors.forename: Guang-Hsiung
authors.initials: GH
authors.lastname: Kou
authors.forename: Gwo-Chin
authors.initials: GC
authors.lastname: Ma
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.forename: Dongying
authors.initials: D
authors.lastname: Wu
authors.forename: Takashi
authors.initials: T
authors.lastname: Aoki
authors.forename: Ikuo
authors.initials: I
authors.lastname: Hirono
authors.forename: Hon-Tsen
authors.initials: HT
authors.lastname: Yu
mesh_terms: D000818:Animals; D001483:Base Sequence; D005260:Female; D015698:Genomic Library; D023281:Genomics; D018895:Microsatellite Repeats / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D033561:Penaeidae / Q000235:genetics*; D010957:Plasmids / Q000235:genetics*; D017422:Sequence Analysis, DNA