Genomic analysis of multiple Roseophage SIO1 strains

被引:56
作者
Angly, Florent [1 ,3 ]
Youle, Merry [2 ]
Nosrat, Bahador [1 ,3 ]
Srinagesh, Shailaja [1 ]
Rodriguez-Brito, Beltran [1 ,3 ]
McNairnie, Patrick [1 ,3 ]
Deyanat-Yazdi, Gordafaried [1 ]
Breitbart, Mya [1 ,4 ]
Rohwer, Forest [1 ,5 ]
机构
[1] San Diego State Univ, Dept Biol, San Diego, CA 92182 USA
[2] Rainbow Rock, Ocean View, HI USA
[3] San Diego State Univ, Computat Sci Res Ctr, San Diego, CA 92182 USA
[4] Univ S Florida, Coll Marine Sci, St Petersburg, FL 33701 USA
[5] San Diego State Univ, Ctr Microbial Sci, San Diego, CA 92182 USA
基金
美国国家科学基金会;
关键词
MARINE-ENVIRONMENT; SEQUENCE ALIGNMENT; GENE-TRANSFER; BACTERIA; VIRUSES; PHAGE; BACTERIOPHAGES; DIVERSITY; DNA; VIRIOPLANKTON;
D O I
10.1111/j.1462-2920.2009.02021.x
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
P>Roseophage SIO1 is a lytic marine phage that infects Roseobacter SIO67, a member of the Roseobacter clade of near-shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re-sequenced and re-annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near-shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein-encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein-coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1-like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and similar to 50 km).
引用
收藏
页码:2863 / 2873
页数:11
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