کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
5911687 | 1161368 | 2011 | 11 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Identification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0
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کلمات کلیدی
موضوعات مرتبط
علوم زیستی و بیوفناوری
علوم کشاورزی و بیولوژیک
بوم شناسی، تکامل، رفتار و سامانه شناسی
پیش نمایش صفحه اول مقاله
![عکس صفحه اول مقاله: Identification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0 Identification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0](/preview/png/5911687.png)
چکیده انگلیسی
The pan-genome of a taxonomic group consists of evolutionarily conserved core genes shared by all members and accessory genes that are present only in some members of the group. Group- and subgroup-specific core genes are thought to contribute to shared phenotypes such as virulence and niche specificity. In this study we analyzed 39 Salmonella enterica genomes (16 closed, 23 draft), a species that contains two human-specific serovars that cause typhoid fever, as well as a large number of zoonotic serovars that cause gastroenteritis in humans. Panseq 2.0 was used to define the pan-genome by adjusting the threshold at which group-specific “core” loci are defined. We found the pan-genome to be 9.03Â Mbp in size, and that the core genome size decreased, while the number of SNPs/100Â bp increased, as the number of strains used to define the core genome increased, suggesting substantial divergence among S. enterica subgroups. Subgroup-specific “core” genes, in contrast, had fewer SNPs/100Â bp, likely reflecting their more recent acquisition. Phylogenetic trees were created from the concatenated and aligned pan-genome, the core genome, and multi-locus-sequence typing (MLST) loci. Branch support increased among the trees, and strains of the same serovar grouped closer together as the number of loci used to create the tree increased. Further, high levels of discrimination were achieved even amongst the most closely related strains of S. enterica Typhi, suggesting that the data generated by Panseq may also be of value in short-term epidemiological studies. Panseq provides an easy and fast way of performing pan-genomic analyses, which can include the identification of group-dominant as well as group-specific loci and is available as a web-server and a standalone version at http://lfz.corefacility.ca/panseq/.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Infection, Genetics and Evolution - Volume 11, Issue 8, December 2011, Pages 2151-2161
Journal: Infection, Genetics and Evolution - Volume 11, Issue 8, December 2011, Pages 2151-2161
نویسندگان
Chad Laing, Andre Villegas, Eduardo N. Taboada, Andrew Kropinski, James E. Thomas, Victor P.J. Gannon,