COMPLETE SEQUENCE OF A 93.4-KB CONTIG FROM CHROMOSOME-3 OF TRYPANOSOMA-CRUZI CONTAINING A STRAND-SWITCH REGION

We have initiated large-scale sequencing of the third smallest chromos ome of the CL Brener strain of Trypanosoma cruzi and we report here th e complete sequence of a contig consisting of three cosmids. This cont ig covers 93.4 kb and has been found to contain 20-30 novel genes and several repeat elements, including a novel chromosome 3-specific 400-b p repeat sequence. The intergenic sequences were found to be rich in d i- and trinucleotide repeats of varying lengths and also contained sev eral known T. cruzi repeat elements. The sequence contains 29 open rea ding frames (ORFs) longer than 700 bp, the longest being 5157 bp, and a large number of shorter ORFs. Of the long ORFs, seven show homology to known genes in parasites and other organisms, whereas four ORFs wer e confirmed by sequencing of cDNA clones. Two shorter ORFs were confir med by a database homology and a cDNA clone, respectively, and one RNA gene was identified. The identified genes include two copies of the g ene for alanine-aminotransferase as well as genes for glucose-6-phosph ate isomerase, protein kinases and phosphatases, and an ATP synthase s ubunit. An interesting feature of the sequence was that the genes appe ar to be organized in two long clusters containing multiple genes on t he same strand. The two clusters are transcribed in opposite direction s and they are separated by an similar to 20-kb long, relatively GC-ri ch sequence, that contains two large repetitive elements as well as a pseudogene for cruzipain and a gene for U2snRNA. It is likely that thi s strand switch region contains one or more regulatory and promoter re gions. The reported sequence provides the first insight into the genom e organization of T. cruzi and shows the potential of this approach fo r rapid identification of novel genes.