Isolation and sequence analysis of Caenorhabditis briggsae repetitive elements related to the Caenorhabditis elegans transposon Tc1

Abstract

We have identified two repetitive element families in the genome of the nematode Caenorhabditis briggsae with extensive sequence identity to the Caenorhabditis elegans transposable element Tc1. Five members each of the TCb1 (previously known as Barney) and TCb2 families were isolated by hybridization to a Tc1 probe. Tc1-hybridizing repetitive elements were grouped into either the TCb1 or TCb2 family based on cross-hybridization intensities among the C. briggsae elements. The genomic copy number of the TCb1 family is 15 and the TCb2 family copy number is 33 in the C. briggsae strain G16. The two transposable element families show numerous genomic hybridization pattern differences between two C. briggsae strains, suggestive of transpositional activity. Two members of the TCb1 family, TCb1#5 and TCb1#10, were sequenced. Each of these two elements had suffered an independent single large deletion. TCb1#5 had a 627-bp internal deletion and TCb1#10 had lost 316 bp of one end. The two sequenced TCb1 elements were highly conserved over the sequences they shared. A 1616-bp composite TCb1 element was constructed from TCb1#5 and TCb1#10. The composite TCb1 element has 80-bp terminal inverted repeats with three nucleotide mismatches and two open reading frames (ORFs) on opposite strands. TCb1 and the 1610-bp Tc1 share 58% overall nucleotide sequence identity, and the greatest similarity occurs in their ORF1 and inverted repeat termini.