CARE1, a TY3-gypsy like LTR-retrotransposon in the food legume chickpea (Cicer arietinum L.)

We report a Ty3-gypsy like retrotransposon CARE1 (Cicer arietinum retro-element 1) in chickpea (Accession no. DQ239702). This 5,920-bp AT-rich (63%) element carries 723-bp 5′-LTR and 897-bp 3′-LTR flanking to an internal region of 4,300-bp. The LTRs of CARE1 show 93.9% nucleotide identity to each other and have 4-bp (ACTA) terminal inverted repeats. A 17-bp potential tRNAmet primer binding site downstream to 5′-LTR and a 13-bp polypurine tract upstream to 3′-LTR have been identified. The order of characteristic domains (Gag-proteinase-reverse transcriptase-RNaseH-integrase) in the deduced amino acid sequence and its phylogenetic analysis with other retrotransposons, places CARE1 in the gypsy group of retrotransposons. Homologues of a number of cis-elements including CCAAT, TATA and GT-1 have been detected in the regulatory region or the 5′-LTR of CARE1. Transgenic tobacco plants containing 5′-LTR:GUS construct showed that its 5′-LTR is inactive in a heterologous system under normal as well as tissue culture conditions. Genomic Southern blot experiments using 5′-LTR of the element as a probe showed that CARE1 or its related elements are present in the genomes of various chickpea accessions from various geographic regions.