Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera 英文参考文献.docVIP

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Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera 英文参考文献.doc

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Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera 英文参考文献

SequenceConservationandFunctionalConstrainton IntergenicSpacersinReducedGenomesoftheObligate SymbiontBuchnera PatrickH.Degnan*,HowardOchman,NancyA.Moran DepartmentofEcologyandEvolutionaryBiology,YaleUniversity,NewHaven,Connecticut,UnitedStatesofAmerica Abstract Analyses of genome reduction in obligate bacterial symbionts typically focus on the removal and retention of protein- codingregions,whicharesubjecttoongoinginactivationanddeletion.However,thesesameforcesoperateonintergenic spacers (IGSs) and affect their contents, maintenance, and rates of evolution. IGSs comprise both non-coding, non- functional regions, including decaying pseudogenes at varying stages of recognizability, as well as functional elements, suchasgenesforsRNAsandregulatorycontrolelements.ThegenomesofBuchneraandothersmallgenomesymbionts display biased nucleotide compositions and high rates of sequence evolution and contain few recognizable regulatory elements. However, IGS lengths are highly correlated across divergent Buchnera genomes, suggesting the presence of functional elements. To identify functional regions within the IGSs, we sequenced two Buchnera genomes (from aphid speciesUroleuconambrosiaeandAcyrthosiphonkondoi)andappliedaphylogeneticfootprintingapproachtoalignmentsof orthologous IGSs from a total of eight Buchnera genomes corresponding to six aphid species. Inclusion of these new genomes allowed comparative analyses at intermediate levels of divergence, enabling the detection of both conserved elementsandpreviouslyunrecognizedpseudogenes.Analysesofthesegenomesrevealedthat232of336IGSalignments over50nucleotidesinlengthdisplayedsubstantialsequenceconservation.ConservedalignmentblockswithintheseIGSs encompassed88Shine-Dalgarnosequences,55transcriptionalterminators,5Sigma-32bindingsites,and12novelsmall RNAs. Although pseudogene formation, and thus IGS formation, are ongoing processes in these genomes, a large proportionofintergenicspacerscontainfunctionalsequences. Citation:DegnanPH,Ochm