Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands 英文参考文献.docVIP

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Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands 英文参考文献.doc

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Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands 英文参考文献

EvidenceofaLargeNovelGenePool AssociatedwithProkaryoticGenomicIslands William W. L.Hsiao1,Korine Ung1,Dana Aeschliman2,Jenny Bryan2,B.Brett Finlay3,Fiona S.L.Brinkman1* 1DepartmentofMolecularBiologyandBiochemistry,SimonFraserUniversity,Burnaby,BritishColumbia,Canada,2DepartmentofStatistics,UniversityofBritishColumbia, Vancouver,BritishColumbia,Canada,3MichaelSmithLaboratory,UniversityofBritishColumbia,Vancouver,BritishColumbia,Canada Microbial genes that are ‘‘novel’’ (no detectable homologs in other species) have become of increasing interest as environmentalsamplingsuggeststhattherearemanymoresuchnovelgenesinyet-to-be-culturedmicroorganisms. Byanalyzingknownmicrobialgenomicislandsandprophages,wedevelopedcriteriaforsystematicidentificationof putativegenomicislands(clustersofgenesofprobablehorizontalorigininaprokaryoticgenome)in63prokaryotic genomes, and then characterized the distribution of novel genes and other features. All but a few of the genomes examinedcontainedsignificantlyhigherproportionsofnovelgenesintheirpredictedgenomicislandscomparedwith the rest of their genome (Paired t test ? 4.43E-14 to 1.27E-18, depending on method). Moreover, the reverse observation (i.e., higher proportions of novel genes outside of islands) never reached statistical significance in any organismexamined.Weshowthatthishigherproportionofnovelgenesinpredictedgenomicislandsisnotduetoless accurate gene prediction in genomic island regions, but likely reflects a genuine increase in novel genes in these regionsforbothbacteriaandarchaea.Thisrepresentsthefirstcomprehensiveanalysisofnovelgenesinprokaryotic genomic islands and provides clues regarding the origin of novel genes. Our collective results imply that there are different gene pools associated with recently horizontally transmitted genomic regions versus regions that are primarily vertically inherited. Moreover, there are more novel genes within the gene pool associated with genomic islands. Since genomic islands are frequent