Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus).
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.
Nandi
Samiran
S
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.
Peatman
Eric
E
Xu
Peng
P
Wang
Shaolin
S
Li
Ping
P
Liu
Zhanjiang
Z
D000818:Animals; D001483:Base Sequence; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation; D016678:Genome; D007059:Ictaluridae / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012091:Repetitive Sequences, Nucleic Acid; D014158:Transcription, Genetic; D019895:Transposases / Q000235:genetics* / Q000378:metabolism
D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; C081454:Tc1 transposase; D019895:Transposases