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Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus)

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Abstract

We have assessed the distribution and diversity of members of the Tc1/mariner superfamily of transposable elements in the channel catfish (Ictalurus punctatus) genome as well as evaluating the extent of transcription of Tc1 transposases in the species. Through use of PCR amplification and sequencing, assessment of random BAC end sequences (BES) equivalent to 1.2% genome coverage, and screening of over 45,000 catfish ESTs, a significant proportion of Tc1-like elements and their associated transcripts were captured. Up to 4.2% of the catfish genome in base pairs appears to be composed of Tc1-like transposon-related sequences and a significant fraction of the catfish cellular mRNA, approximately 0.6%, was transcribed from transposon-related sequences in both sense and antisense orientations. Based on results of repeat-masking, as much as 10% of BAC end sequences from catfish, which is a random survey of the genome, contain some remnant of Tc1 elements, suggesting that these elements are present in the catfish genome as numerous, small remnants of the transposons. Phylogenetic analysis allowed comparison of catfish Tc1 transposase types with those found in other vertebrate and invertebrate species. In spite of the existence of many types of Tc1-like sequences that are not yet able to be placed in clades with strong statistical support, it is clear that multiple families of Tc1-like elements exist in channel catfish.

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Abbreviations

BES:

BAC end sequences

Bp:

base pair

dNTP:

Deoxynucleotide triphosphate

E:

Expectation value

EST:

Expressed sequence tag

IR:

Inverted repeat

ORF:

Open reading frame

PCR:

Polymerase chain reaction

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Acknowledgements

This project was supported by National Research Initiative Grant No. # 2006-35616-16685 from the USDA Cooperative State Research, Education, and Extension Service under the Animal Genome Basic Genome Reagents and Tools Program, and in part by a Specific Cooperative Agreement with USDA ARS Aquatic Animal Health Laboratory under the Contract Number 58-6420-5-030. Samiran Nandi was supported by a fellowship from the Department of Biotechnology of the Government of India.

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Authors and Affiliations

  1. Department of Fisheries and Allied Aquacultures, The Fish Molecular Genetics and Biotechnology Laboratory, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA

    Samiran Nandi, Eric Peatman, Peng Xu, Shaolin Wang, Ping Li & Zhanjiang Liu

  2. Central Institute of Freshwater Aquaculture, ICAR, Bhubaneswar, India

    Samiran Nandi

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  1. Samiran Nandi
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  2. Eric Peatman
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  3. Peng Xu
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  4. Shaolin Wang
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  5. Ping Li
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  6. Zhanjiang Liu
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Correspondence to Zhanjiang Liu.

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Nandi, S., Peatman, E., Xu, P. et al. Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus) . Genetica 131, 81–90 (2007). https://doi.org/10.1007/s10709-006-9115-4

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  • DOI: https://doi.org/10.1007/s10709-006-9115-4

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