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Divergence and Mosaicism among Virulent Soil Phages of the Burkholderia cepacia Complex

Elizabeth J. Summer,¹ Carlos F. Gonzalez,² Morgan Bomer,¹ Thomas Carlile,¹ Addie Embry,¹ Amalie M. Kucherka,¹ Jonte Lee,¹ Leslie Mebane,¹ William C. Morrison,¹ Louise Mark,³ Maria D. King,¹ John J. LiPuma,⁴ Anne K. Vidaver, and Ry Young^1*

Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128,¹ Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132,² Microbiology Department, BIOMERIT Research Centre, National University of Ireland, Cork, Ireland,³ Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109⁴

Received 20 June 2005/ Accepted 5 October 2005

We have determined the genomic sequences of four virulent myophages, Bcep1, Bcep43, BcepB1A, and Bcep781, whose hosts are soil isolates of the Burkholderia cepacia complex. Despite temporal and spatial separations between initial isolations, three of the phages (Bcep1, Bcep43, and Bcep781, designated the Bcep781 group) exhibit 87% to 99% sequence identity to one another and most coding region differences are due to synonymous nucleotide substitutions, a hallmark of neutral genetic drift. Phage BcepB1A has a very different genome organization but is clearly a mosaic with respect to many of the genes of the Bcep781 group, as is a defective prophage element in Photorhabdus luminescens. Functions were assigned to 27 out of 71 predicted genes of Bcep1 despite extreme sequence divergence. Using a lambda repressor fusion technique, 10 Bcep781-encoded proteins were identified for their ability to support homotypic interactions. While head and tail morphogenesis genes have retained canonical gene order despite extreme sequence divergence, genes involved in DNA metabolism and host lysis are not organized as in other phages. This unusual genome arrangement may contribute to the ability of the Bcep781-like phages to maintain a unified genomic type. However, the Bcep781 group phages can also engage in lateral gene transfer events with otherwise unrelated phages, a process that contributes to the broader-scale genomic mosaicism prevalent among the tailed phages.

Supplemental material for this article may be found at http://jb.asm.org/.

Present address: Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583.