High-resolution physical map of the Sinorhizobium meliloti 1021 pSyma megaplasmid

Abstract

To facilitate sequencing of the Sinorhizobium meliloti 1021 pSyma megaplasmid, a high-resolution map was constructed by ordering 113 overlapping bacterial artificial chromosome clones with 192 markers. The 157 anonymous sequence tagged site markers (81,072 bases) reveal hypothetical functions encoded by the replicon.

FIG. 1

(A) High-resolution map of the pSyma megaplasmid of S. meliloti 1021. The map is presented in three linear and contiguous parts of approximately 500 kb for convenience. Identified S. meliloti genes (genetic database or BLASTX results) are indicated on the left side while anonymous STS markers are located on the right side. The positions of underlined genes were deduced from mapped genes in the operon; i.e., no PCR primers were designed. Some genes are listed more than once because several sets of primers were used. Black rectangles indicate pairwise invertable markers. ‡, partial similarity. The minimum set of BAC clones covering the replicon is also presented. (B) Simplified map oriented according to the Honeycutt et al. map (23) showing STS markers mentioned in the text, selected genes, and the minimum set of BAC clones. Lengths of BAC inserts are shown relative to the sizes determined by field inversion gel electrophoresis. Genes previously mapped by Honeycutt et al. are marked with asterisks. Corresponding BAC insert sizes are as follows: BAC01, 110 kb; BAC02, 75 kb; BAC03, 110 kb; BAC04, 75 kb; BAC05, 55 kb; BAC06, 85 kb; BAC07, 120 kb; BAC08, 65 kb; BAC09, 80 kb; BAC10, 75 kb; BAC11, 60 kb; BAC12, 110 kb; BAC13, 100 kb; BAC14, 140 kb; BAC15, 80 kb; BAC16, 25 kb; BAC17, 100 kb; BAC18, 80 kb; and BAC19, 60 kb.

FIG. 2

(A) Distribution of BLASTX results among four categories of significance. 1, strong similarity with S. meliloti proteins (E ≤ 1e⁻⁶; identity, ≥85%); 2, strong similarity with sequences available in the databases (E ≤ 1e⁻⁶); 3, local or weaker similarity with sequences available in the databases (1e⁻² ≤ E ≤ 1e⁻⁶); 4, no similarity with sequences available in the databases. (B) Classification of the most significant matches (E ≤ 1e⁻⁶) using Riley's classification (34, 35).