Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome

The nucleotide sequence of 1.5 Mb of genomic DNA fromMycobacterium leprae was determined using computer-assisted multiplex sequencing technology. This brings the 2.8-Mb M. leprae genome sequence to ∼66% completion. The sequences, derived from 43 recombinant cosmids, contain 1046 putative protein-coding genes, 44 repetitive regions, 3 rRNAs, and 15 tRNAs. The gene density of one per 1.4 kb is slightly lower than that ofMycoplasma (1.2 kb). Of the protein coding genes, 44% have significant matches to genes with well-defined functions. Comparison of 1157 M. leprae and 1564 Mycobacterium tuberculosisproteins shows a complex mosaic of homologous genomic blocks with up to 22 adjacent proteins in conserved map order. Matches to known enzymatic, antigenic, membrane, cell wall, cell division, multidrug resistance, and virulence proteins suggest therapeutic and vaccine targets. Unusual features of the M. leprae genome include large polyketide synthase (pks) operons, inteins, and highly fragmented pseudogenes. [The sequence data described in this paper have been submitted to GenBank under accession nos. L78811 – L78829 , U00010 – U00023 , U15180 – U15184 , U15186 , U15187 , L01095 , L01536 , L04666 , and L01263 . On-line supplementary information for Table 1 is available at http://www.cshl.org/gr .]