简介：Ascientificdreamproposedsome20yearsagohasbeenrealized-thecompletionoftheDNAsequencefortheHumanGenomeProject(HGP)in2004.Asaresult,anentirelynewfieldofbiologicalresearchhasarisen:genomebiologyorgenomicsiscelebratedforitsunprecedentedscale,intrinsicallydigitaloutput,andsystematicapproachtogettingallthedata.Itssequel,theHapMapProject,willreachfruitionlaterthisyear.Theseprojectsestablishednewprecedentsforinternationalcollaborationsandopendataaccess.

简介：AnnotationofthegenomesequenceoftheSARS-CoV(severeacuterespiratorysyndrome-associatedcoronavirus)isindispensabletounderstanditsevolutionandpathogenesis.WehaveperformedafullannotationoftheSARS-CoVgenomesequencesbyusingannotationprogramspubliclyavailableordevelopedbyourselves.Totally,21openreadingframes(ORFs)ofgenesorputativeuncharacterizedproteins(PUPs)werepredicted.SevenPUPshadnotbeenreportedpreviously,andtwoofthemwerepredictedtocontaintransmembraneregions.EightORFspartiallyoverlappedwithorembeddedintothoseofknowngenes,revealingthattheSARS-CoVgenomeisasmallandcompactonewithoverlappedcodingregions.ThemoststrikingdiscoveryisthatanORFlocatesontheminusstrand.Wehavealsoannotatednon-codingregionsandidentifiedthetranscriptionregulatingsequences(TRS)intheintergenicregions.TheanalysisofTRSsupportstheminusstrandextendingtranscriptionmechanismofcoronavirus.TheSNPanalysisofdifferentisolatesrevealsthatmutationsofthesequencesdonotaffectthepredictionresultsofORFs.

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简介：Knowledgeoftheevolutionofpathogensisofgreatmedicalandbiologicalsignificancetotheprevention,diagnosis,andtherapyofinfectiousdiseases.InordertounderstandtheoriginandevolutionoftheSARS-CoV(severeacuterespiratorysyndrome-associatedcoronavirus),wecollectedcompletegenomesequencesofallvirusesavailableinGenBank,andmadecomparativeanalyseswiththeSARSCoV.GenomicsignatureanalysisdemonstratesthatthecoronavirusesalltaketheTGTTastheirrichesttetranucleotideexcepttheSARS-CoV.Adetailedanalysisoftheforty-twocompleteSARS-CoVgenomesequencesrevealedtheexistenceoftwodistinctgenotypes,andshowedthattheseisolatescouldbeclassifiedintofourgroups.OurmanualanalysisoftheBLASTNresultsdemonstratesthattheHE(hemagglutinin-esterase)geneexistsintheSARS-CoV,andmanymutationsmadeitunfamiliartous.

简介：Adatasetof103SARS-CoVisolates(101humanpatientsand2palmcivets)wasinvestigatedondifferentaspectsofgenomepolymorphismandisolateclassification.Thenumberandthedistributionofsinglenucleotidevariations(SNVs)andinsertionsanddeletions,withrespecttoa"profile",weredeterminedanddiscussed("profile"beingasequencecontainingthemostrepresentedletterperposition).Distributionofsubstitutioncategoriespercodonpositions,aswellassynonymousandnon-synonymoussubstitutionsincodingregionsofannotatedisolates,wasdetermined,alongwithaminoacid(a.a.)propertychanges.Similaranalysiswasperformedforthespike(S)proteininalltheisolates(55ofthembeingpredictedforthefirsttime).TheratioKa/KsconfirmedthattheSgenewassubjectedtotheDarwinianselectionduringvirustransmissionfromanimalstohumans.Isolatesfromthedatasetwereclassifiedaccordingtogenomepolymorphismandgenotypes.Genomepolymorphismyieldstotwogroups,onewithasmallnumberofSNVsandanotherwithalargenumberofSNVs,withuptofoursubgroupswithrespecttoinsertionsanddeletions.Weidentifiedthreebasicnine-locusgenotypes:TTTT/TTCGG,CGCC/TTCAT,andTGCC/TTCGT,withfoursubgenotypes.Bothclassificationsproposedareinaccordancewiththenewinsightsintopossibleepidemiologicalspread,bothinspaceandtime.

简介：Eelfamilyisahugeone,inwhichmanykindsofeelsespeciallysomemigratoryeels,bearstrongresemblancetoeachother,andarethereforedifficulttobeidentified.Inthisstudy29randomprimerswereusedtomakeRAPDanalysisforJapaneseseel(Anguillajaponica),Europeaneel(Anguillaanguilla)andPikeeel(Muraenesoxcinereus).Andtotally299fragmentswerecounted.Sharedorspecificfragmentswerecountedandgeneticsimilarityorgeneticdistancewerecalculated.ThegeneticsimilaritybetweenJapaneseeelandPikeeelis0.68andthegeneticdistancebetweenthemis0.32;thosebetweenEuropeaneelandPikeeelare0.72and0.28respectively,andbetweenJapaneseeelandEuropeaneelare0.74and0.25respectively.Themethodhasbeenshowntobesuitabletomolecularidentificationofeels.Itprovidesanalternativeapproachtodeterminetherelationshipbetweenspecies.

简介：ToinvestigategeneticmechanismsofhighaltitudeadaptationsofnativemammalsontheTibetanPlateau,wecomparedmitochondrialsequencesoftheendangeredPantholopshodgsoniiwithitslowlanddistantrelativesOvisariesandCaprahircus,aswellasothermammals.ThecompletemitochondrialgenomeofP.hodgsonii(16,498bp)revealedasimilargeneorderasofothermammals.Becauseoftandemduplications,thecontrolregionofP.hodgsoniimitochondrialgenomeisshorterthanthoseofO.ariesandC.hircus,butlongerthanthoseofBosspecies.PhylogeneticanalysisbasedonalignmentsoftheentirecytochromebgenessuggestedthatP.hodgsoniiismorecloselyrelatedtoO.ariesandC.hircus,ratherthantospeciesoftheAntilopinaesubfamily.TheestimateddivergencetimebetweenP.hodgsoniiandO.ariesisabout2.25millionyearsago.FurtheranalysisonnaturalselectionindicatedthattheCOXI(cytochromecoxidasesubunitI)genewasunderpositiveselectioninP.hodgsoniiandBosgrunniens.Consideringthesameclimatesandenvironmentssharedbythesetwomammalianspecies,weproposedthatthemitochondrialCOXIgeneisprobablyrelevantforthesenativemammalstoadaptthehighaltitudeenvironmentuniquetotheTibetanPlateau.

简介：WedescribedtheconstructionofBACcontigsofthegenomeofaindicavarietyofOryzasativa.GuangLuAi4.Anentirerepresentative(Sixfoldcoverageofricechromosomes)andgeneticallystableBAClibraryofricegenomeconstructedinthislabhasbeensystematicallyanalysedbyrestrictionenzymefragmentationandpolyacrylamidegelelectrophoresis.Andalltheimagesthusobtainedweresubjecttoimage-processing,whichconsistedofpreliminarylocationofbands,cooperativetrackingoflanesbycorrelationofadjacentbads.aprecisedensitometricpass,alignmentatthemarkerbandswiththestandard,optionalinteractiveediting,andnormalizationoftheacceptedbands.ThecontigsweregeneratedbasedontheComputerSoftwarespeciallydesignedforgenomemapping.Thenumberofcontigswith600kbinlengthonaveragewas464.ofcontigswith1000kbinlengthonaveragewas107;ofcontigswith1500kbinlengthonaveragewasConstructionofOryzaSativagenomecontigs.23.Therefor,allthecontigswehaveobtainedampuntedupto420megabasesinlength.Consideringthesizeofricegenome(430megabased),thecontigsgeneratedinthislabhavecoverednearly98%ofthericegenome.Wearenowintheprocessofmappingthecontigstochromosomes.

简介：高产量的genotyping芯片为极大地作出贡献到为复杂疾病发现危险性基因的染色体宽的协会研究(GWAS)生产了巨大的数据集。为为GWAS执行数据分析有二策略。一策略是使用为GWAS被设计的公开源码或商业的包裹。其它将与特定的功能利用经典基因程序，例如连接不平衡印射，haplotype推理和传播不平衡测试。然而，可得到的很经典的程序不对直接分析芯片数据合适并且要求定做的输入，它导致把未加工的genotyping文件变换成各种各样的数据格式的不方便。我们开发了一个强大的、用户友好的、小节目为包括五个主要模块(变压器，操作员，预览器，编码者和模拟器)的GWAS的命名SNPTransformer。为把genotyping文件转变成十输入的工作不仅与经典遗传包裹为使用格式化，而且执行的工具箱有用函数象标志上的关系操作那样，预览数据文件，重新代码数据格式和模仿的标记文件，在另外的函数之中。它为人的遗传学者作为一个在里面手工具箱用下游地基因的节目，和罐头行为衔接在上游的未加工的genotyping数据，特别为非程序员。SNPTransformer在http://snptransformer.sourceforge.net是自由地可得到的。

简介：Genomeassemblyisaprerequisitestepforanalyzingnextgenerationsequencingdataandalsofarfrombeingsolved.Manyassemblytoolshavebeenproposedandusedextensively.Majorityofthemaimtoassemblesequencingreadsintocontigs;however,wefocusontheassemblyofcontigsintoscaffoldsinthispaper.Thisiscalledscaffolding,whichestimatestherelativeorderofthecontigsaswellasthesizeofthegapsbetweenthesecontigs.Pheromonetrail-basedgeneticalgorithm(PGA)waspreviouslyproposedandhaddecentperformanceaccordingtotheirpaper.Fromourpreviousstudy,wefoundthatfamilycompetitionmechanismingeneticalgorithmisabletofurtherimprovetheresults.Therefore,weproposefamilycompetitionpheromonegeneticalgorithm(FCPGA)anddemonstratetheimprovementoverPGA.

简介：DNAcompositiondynamicsacrossgenomesofdiversetaxonomyisamajorsubjectofgenomeanalyses.DNAcompositionchangesarecharacteristicsofbothreplicationandrepairmachineries.Weinvestigated3,611,007singlenucleotidepolymorphisms(SNPs)generatedbycomparingtwosequencedricegenomesfromdistantinbredlines(subspecies),includingthosefrom242,811intronsand45,462protein-codingsequences(CDSs).Neighboring-nucleotideeffects(NNEs)oftheseSNPsarediverse,dependingonstructuralcontent-basedclassifications(genomewide,intronic,andCDS)andsequencecontext-basedcategories(A/C,A/G,A/T,C/G,C/T,andG/Tsubstitutions)oftheanalyzedSNPs.StrongandevidentNNEsandnucleotideproportionbiasessurroundingtheanalyzedSNPswereobservedin1-3bpsequencesonbothsidesofanSNP.Strongbiaseswereobservedaroundneighboringnucleotidesofprotein-codingSNPs,whichexhibitaperiodicityofthreeinnucleotidecontent,constrainedbyacombinedeffectofcodon-relatedrulesandDNArepairmechanisms.Unlikeapreviousfindinginthehumangenome,wefoundnegativecorrelationbetweenGCcontentsofchromosomesandthemagnitudeofcorrespondingbiasofnucleotideCat-1siteandGat+1site.Theseresultswillfurtherourunderstandingofthemutationmechanisminriceaswellasitsevolutionaryimplications.

简介：AbstractGenome editing serves as a powerful approach to interrogate the functions of both coding and noncoding sequences. In particular, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR associated protein 9 (Cas9) system-based editing tools have revolutionized the way we study genome function in mammalian cells, and are being widely used for interrogating critical genes and DNA elements essential for many biological processes. Here, we review CRISPR/Cas9-based genetic tools with an emphasis on CRISPR-mediated high throughput genetic screens in the mammalian genome.

简介：Withseveralricegenomeprojectsapproachingcompletiongeneprediction/findingbycomputeralgorithmshasbecomeanurgenttask.Twotestsetswereconstructedbymappingthenewlypublished28,469full-lengthKOMEricecDNAtotheRGPBACclonesequencesofOryzasativassp.japonica:asingle-genesetof550sequencesandamulti-genesetof62sequenceswith271genes.Thesedatasetswereusedtoevaluatefiveabinitiogenepredictionprograms:RiceHMM,GlimmerR,GeneMark,FGENSHandBGF.Thepredictionswerecomparedonnucleotide,exonandwholegenestructurelevelsusingcommonlyacceptedmeasuresandseveralnewmeasures.Thetestresultsshowaprogressinperformanceinchronologicalorder.Atthesametimecomplementarityoftheprogramshintsonthepossibilityoffurtherimprovementandonthefeasibilityofreachingbetterperformancebycombiningseveralgene-finders.

简介：Cervaphisquercus的mitochondrial染色体被定序并且注解。15272 bp的全部染色体编码二ribosomalRNA基因(rrnL和rrnS)，22转移RNA(tRNA)基因，13编码蛋白质的基因和控制区域。染色体作为在推断的祖先的昆虫发现了那有一样的基因顺序。核苷酸作文是高度，A+T偏导。所有编码蛋白质的基因使用标准mitochondrial开始codons。C的二ribosomalRNA基因的第二等的结构模型。quercus类似于为另外的昆虫建议的那些。所有tRNAs有经典四叶苜蓿形的立体道路交叉点结构，trnS(AGN)除了dihydrouridine(DHU)武装，它形成一个简单的环。在控制区域的结构的元素的存在也被讨论，与复制或抄写的可能的规定上的一个重音。有另外的蚜虫种类的mitochondrial染色体的比较证明他们的基因安排被保存；然而，在从一个不同蚜虫亚科的种类的重复区域的变化，Aphidinae，建议他们源于独立进化事件。

简介：Apicomplexa是感染人和另外的动物的单细胞的有机体的一个极其多样的组。尽管有在在过去的世纪与传染疾病作斗争的大进展，这些寄生虫仍然在人的社会上有巨大的社会、经济的负担，特别地在世界的热带、副热带的区域。从apicomplexa的朊酶在分子、细胞的层次被描绘了，并且中央角色在多样的过程为朊酶被建议了。在这个工作，为胰岛素朊酶编码的16新基因被染色体宽的调查在8个apicomplexan染色体识别。种系发生的分析建议这些基因通过两细胞内部的基因转移和垂直基因转移被获得。调停朊酶的过程的进化起源的鉴定，描述和理解是关键的增加知识并且为新奇化学疗法的代理人和疫苗的发展改进策略。

简介：在Poaceae的钙举起，translocation和累积的机制充分还没被理解。处理这个问题，我们在钙(Ca2+)的silico分析进行了染色体宽的比较级二庄稼种，米饭和蜀黍的transporter基因家庭。基因注解，在上游的行动cis元素的鉴定，种系发生的树构造和基因家庭印射的syntenic用几个生物信息学工具被执行。31Ca2+transporters的一个总数，从12个染色体在9上散布了，从米饭染色体被预言，当除了染色体10，从蜀黍预言的28Ca2+transporters在所有染色体上是分布式的时(Chr10)。有趣地，大多数Chr1和Chr3上的基因显示出在米饭和蜀黍之间的一种反的syntenic关系。这些transporter蛋白质的多重顺序排列和主题分析揭示了在二种之间的高保存。种系发生的树能很好在基因家庭之中识别隧道，ATPases和exchangers的子类。在里面silicocis规章的元素分析建议了与光，应力和荷尔蒙应答以及内乳特定、分裂组织特定的基因表示联系的多样的功能。进一步的实验被保证验证在里面预言的transporter基因家庭的silico分析并且阐明在各种各样的生物进程的Ca2+transporters的函数。

简介：Precisebaseeditingishighlydesiredinplantfunctionalgenomicresearchandcropmolecularbreeding.Inthisstudy,weconstructedarice-codonoptimizedadeninebaseeditor(ABE)-nCas9toolthatinducedtargetedA·TtoG·Cpointmutationofakeysinglenucleotidepolymorphismsiteinanimportantagriculturalgene.Combinedwiththemodifiedsingle-guideRNAvariant,ourplantABEtoolcanefficientlyachieveadeninebaseeditinginthericegenome.

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简介：Genesarecontinuallybeingcreatedbytheprocessesofgenomeduplication(ohnolog)andgeneduplication(paralog)Whole-genomeduplicationshavebeenfoundtobewidespreadinplantspeciesandplayanimportantroleinplantevolution.Clearlyun-overlappingduplicatedblocksofwhole-genomeduplicationscanbedetectedinthegenomeofsequencedrice(Oryzasativa).Syntenicohnologpairs(ohnologues)ofthewhole-genomeduplicationsinricewereidentifiedbasedontheirsyntenicduplicatelines.Theparalogsofohnologueswerefurtherscannedusingmulti-roundreciprocalBLASTbest-hitsearching(E＜e-14).Theresultsindicatedthatanaverageof0.55sisterparalogscouldbefoundforeveryohnologueinrice.Theseresultssuggestthatsmall-scaleduplications,aswellaswhole-genomeduplications,playasignificantroleinthetwoduplicatedricegenomes.

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