Open Access Highly Accessed Research article

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

Shiao-Wei Huang1, You-Yu Lin1, En-Min You1, Tze-Tze Liu2, Hung-Yu Shu2, Keh-Ming Wu3, Shih-Feng Tsai3, Chu-Fang Lo1, Guang-Hsiung Kou1, Gwo-Chin Ma4, Ming Chen145, Dongying Wu67, Takashi Aoki8, Ikuo Hirono8 and Hon-Tsen Yu1*

Author Affiliations

1 Institute of Zoology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan, ROC

2 Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan, ROC

3 Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County 350, Taiwan, ROC

4 Center for Medical Genetics, and Genetics Laboratory, Department of Medical Research, Changhua Christian Hospital, Changhua 500, Taiwan, ROC

5 Department of Obstertrics and Gynecology, College of Medicine, National Taiwan University, Taipei 106, Taiwan

6 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA

7 Department of Evolution and Ecology, University of California Davis Genome Center, University of California, Davis, California 95616, USA

8 Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7 Minato-ku, Tokyo 108-8477, Japan

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BMC Genomics 2011, 12:242  doi:10.1186/1471-2164-12-242

Published: 17 May 2011

Additional files

Additional file 1:

Estimates of the P. monodon genome size, as percentage of human DNA.

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Additional file 2:

Insert sizes of representative clones from the P. monodon fosmid library. The first and last lanes of each gel are 36 kb-size markers. The average insert size is 40.8 kb.

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Additional file 3:

Frequency and length distribution of the 20,926 Penaeus monodon fosmid end sequences.

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Additional file 4:

Examples of P. monodon ESTs found to contain a very long stretch of microsatellites (a). Some sets of ESTs derived from the same gene showed copy number variation in the microsatellites they contain (b). Dinucleotide repeats [(TC)50, (TA) 50, (TG)50, and (CG)50] were used as query sequences to search against the Penaeus Genome Database. Only top 10 hits were listed.

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Additional file 5:

Thirty-six PREs were found transcriptionally active via BlastN search against the P. monodon EST dataset (PmTwN) in the Penaeus Genome Database. Only top 3 hits are listed.

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