The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

LETTERS The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

The French–Italian Public Consortium for Grapevine Genome Characterization*

The analysis of the first plant genomes provided unexpected evid-ence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics1–3. These polyploidization events may have had important conse-quences in plant evolution,in particular for species radiation and adaptation and for the modulation of functional capacities4–10.Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera)obtained from a highly homozygous genotype.The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants,the second for a woody species and the first for a fruit crop(cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cul-tural heritage of humanity beginning during the Neolithic period11. Several large expansions of gene families with roles in aromatic features are observed.The grapevine genome has not undergone recent genome duplication,thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content.This ancestral arrangement is com-mon to many dicotyledonous plants but is absent from the genome of rice,which is a monocotyledon.Furthermore,we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

All grapevine varieties are highly heterozygous;preliminary data showed that there was as much as13%sequence divergence between alleles,which would hinder reliable contig assembly when a whole-genome shotgun strategy was used for sequencing.Our consortium therefore selected the grapevine PN40024genotype for sequencing. This line,originally derived from Pinot Noir,has been bred close to full homozygosity(estimated at about93%)by successive selfings, permitting a high-quality whole-genome shotgun assembly.

A total of6.2million end-reads were produced by our consortium, representing an8.4-fold coverage of the genome.Within the assem-bly,performed with Arachne12,316supercontigs represent putative allelic haplotypes that constitute11.6million bases(Mb).These values are in good fit with the7%residual heterozygosity of PN40024assessed by using genetic markers.When considering only one of the haplotypes in each heterozygous region,the assembly (Table1a)consists of19,577contigs(N50565.9kilobases(kb), where N50corresponds to the size of the shorter supercontig or contig in a subset representing half of the assembly size)and3,514 supercontigs(N5052.07Mb)totalling487Mb.This value is close to the475Mb previously reported for the grapevine genome size13.

Using a set of409molecular markers from the reference grapevine map14,69%of the assembled487Mb,arranged into45ultracontigs

Table1|Global statistics on the genome of Vitis vinifera

(a)Assembly

Status Number N50(kb)Longest(kb)Size(Mb)Percentage of the

assembly Contigs All19,57765.9557467.5–Supercontigs All3,5142,06512,675487.1100 Anchored on chromosomes1913,18912,675335.668.9

Anchored on chromosomes

and oriented

1433,82712,675296.960.9

(b)Annotation

Number Median size(bp)Total length(Mb)Percentage of the genome%GC

Gene30,4343,399225.646.336.2

Exons CDS149,35113033.66.944.5

Introns CDS118,917213178.636.734.7

Intergenic30,4533,544261.534.733.0

tRNA*600730.04NS43.0

miRNA{164103.50.002NS35.9

(c)Orthology

Number of orthologous proteins Mean identity(%)

P.trichocarpa12,99672.7

A.thaliana11,40465.5

O.sativa9,73159.8

Common to eudicotyledons{10,547

Common to Magnoliophyta18,121

*Transfer RNA(tRNA)values were computed on exons.

{Micro RNAs(miRNAs)are members of known conserved miRNA families.

{Eudicotyledons are represented by P.trichocarpa and A.thaliana.

1Magnoliophyta(most flowering plants)are represented by P.trichocarpa,A.thaliana and O.sativa.

*A list of participants and their affiliations appears at the end of the paper.

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and51single supercontigs,were anchored along the19linkage groups.Thirty-seven ultracontigs and22single supercontigs were oriented,representing61%of the genome assembly(Supplemen-tary Tables2and3).

This assembly has been annotated by using a combination of evid-ence.The major features of the genome annotation are presented in Table1b.The8.4-fold draft sequence of the grapevine genome con-tains a set of30,434protein-coding genes(an average of372codons and5exons per gene).This value is considerably lower than the 45,555protein-coding genes reported for the poplar(Populus tricho-carpa)genome,which has a similar size,at485Mb(ref.1),and even lower than the37,544protein-coding genes identified in the389Mb of the rice genome2.

Three different approaches revealed that41.4%(average value)of the grapevine genome is composed of repetitive/transposable ele-ments(TEs),a slightly higher proportion than that identified in the rice genome,which has a somewhat smaller size2.The distribution of repeats and TEs along the chromosomes is quite uneven(see below). All classes and superfamilies of TEs are represented in the grapevine genome,with a large prevalence of class I elements over class II and helitrons(rolling-circle transposons)(Supplementary Table7).An analysis of the distribution of the repetitive elements in the different fractions of the grapevine genome based on the current annotation shows that introns are quite rich in repeats and TEs(data not shown). In addition,12.4%of the intron sequence contains transposons as determined using our set of manually annotated elements,most of which(75%)correspond to LINE(long interspersed element)retro-transposons,which therefore seem to have contributed specifically to the intron size observed in grapevine(Supplementary Table8).

In eukaryotes with large genomes,the coding and repeated ele-ments are distributed over the chromosomes and may be more or less interlaced,hence defining gene-poor and gene-rich regions.It has previously been noticed that the distribution of the genes along the chromosomes of rice and Arabidopsis thaliana is fairly homo-geneous2,3.In contrast,we observe large regions that alternate between high and low gene density in V.vinifera(Supplementary Figs2and3).As expected,the density of TEs reflects a pattern substantially complementary to gene density.We observe a similar characteristic in the genome sequence of poplar,therefore indicating a dynamic for the invasion of TEs that is shared with the grapevine (Supplementary Fig.3).

A striking feature of the grapevine proteome lies in the existence of large families related to wine characteristics,which have a higher gene copy number than in the other sequenced plants.Stilbene synthases (STSs)drive the synthesis of resveratrol,the grapevine phytoalexin that has been associated with the health benefits associated with moderate consumption of red wine15,16.The family of genes encoding STSs has a noticeable expansion:43genes have been identified.Of these,20have previously been shown to be expressed after infection by Plasmopara viticola,thus confirming that they are likely to be functional.The terpene synthases(TPSs)drive the synthesis of terpenoids;these secondary metabolites are major components of resins,essential oils and aromas(their relative abundance is directly correlated with the aromatic features of wines17)and are involved in plant–environment interactions.In comparison with the30–40 genes of this family in Arabidopsis,rice and poplar,the grapevine TPS family is more than twice as large,with89functional genes and 27pseudogenes.Classification based on known plant homologues reveals that the subclass of putative monoterpene synthases repre-sents only15%of the Arabidopsis TPS family18whereas this subclass represents40%of the grapevine TPS family.This result suggests a high diversification of grapevine monoterpene synthases that specif-ically produce C10terpenoids present in aroma(such as geraniol, linalool,cineole and a-terpineol).Furthermore,the grapevine gen-ome annotation has also revealed genes encoding homologues to the two forms of geranyl diphosphate synthases(GPPSs),the enzymes that produce the substrate for monoterpene synthases:both the homodimeric GPPS and the heterodimeric form are present;the latter is present only in plants such as Mentha piperita and Clarkia breweri,which produce large quantities of monoterpenes19.Most of the STS and TPS genes occur as20clusters,including up to33para-logous genes located in a680-kb stretch.

Because global duplication events seem to be a frequent event in plant evolution20,we searched the genome of V.vinifera for paralo-gous regions by using protein sequence similarity.Paralogous regions are defined as chromosome fragments in which homologous genes are present in clusters.Statistical analysis21of these clusters reveals that94.5%have high probability of being paralogous(P,1024; Supplementary Table11).Most Vitis gene regions have two different paralogous regions,which we have grouped together as triplets (Supplementary Fig.5;coverage details in Supplementary Table 10).We conclude that the present-day grapevine haploid genome originated from the contribution of three ancestral genomes.It is yet to be demonstrated whether this content came from a true hex-aploidization event or through successive genome duplications.The resulting plant had a diploid content that corresponds to the three full diploid contents of the three ancestors;it may therefore be described as a‘palaeo-hexaploid’organism.A number of rearrange-ments have affected the original three complements after the forma-tion of the palaeo-hexaploid state.However,the gene order has been sufficiently conserved to permit the alignment of most regions with their two siblings.

We explored the time of formation of the palaeo-hexaploid arrangement by comparing grapevine gene regions with those of other completely sequenced plant genomes.If the palaeo-hexaploid complement is present in another species,it should result in a one-for-one pairing of gene regions between the two species considered. In contrast,if another species’s genome evolved before palaeo-hexaploid formation,it should result in a one-to-three relationship between the other species and the grapevine genome.The available genome sequences were those of poplar1,Arabidopsis3and rice(Oryza sativa2),of which poplar is considered to be most closely related to grapevine.All clusters constructed between the orthologues in the three comparisons have P,1024(Table1c).When the gene order in poplar is compared with that in grapevine,there are two clear dis-tributions.First,the grapevine regions align with two poplar seg-ments,as would be expected from a recent whole-genome duplication(WGD)in the poplar lineage1.Second,each of the three grapevine regions that form a homologous triplet recognizes differ-ent pairs of poplar segments(Fig.1a and Supplementary Fig.6).This shows that the palaeo-hexaploidy observed in grapevine was already present in its common ancestor with poplar.

Poplar belongs to the Eurosid I clade.The sister clade to Eurosid I is that of Eurosid II,which contains the model species Arabidopsis.Its gene order was compared with that in the grapevine genome.Two distributions appear:first,most grapevine regions correspond to four Arabidopsis segments(Supplementary Fig.7);second,each compon-ent of a triplicated group in grapevine recognizes four different regions in Arabidopsis(Fig.1b).This shows that the grapevine palaeo-hexaploidy was present in the common ancestor to Arabidopsis and grapevine,and therefore that it is a trait common to all Eurosids.This is confirmed by the homology level distribution between paralogues of the grapevine,indicating a lower conservation than between Vitis/Arabidopsis orthologues(Supplementary Fig.4). The Eurosid group contains many economically important flowering plants such as legumes,cotton and Brassicaceae.Our present results establish these species as having a palaeo-hexaploid common ancestor.The grapevine/Arabidopsis comparison also reveals that the Arabidopsis lineage underwent two WGDs after its separation from the Eurosid I clade21–24.This contradicts some models based on more indirect evidence that placed the most ancient of these two duplications at the base of the Eurosid group,or even earlier4,20–22. Some studies had also suggested a possible third duplication event in the distant past of the Arabidopsis lineage,potentially at the base of

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the angiosperm radiation.The controversy about this third event is now resolved by the Vitis genome comparisons:this event corre-sponds to the palaeo-hexaploidy formation that remains evident in the grapevine genome but has been difficult to characterize in Arabidopsis and poplar because of the more recent WGDs.In par-ticular,the Arabidopsis genome lineage has undergone many rear-rangements and chromosome fusions such that the ancestral gene order is particularly difficult to deduce from this species (Fig.2).Grapevines,like Arabidopsis and poplar,are dicotyledonous plants that diverged from monocotyledons about 130–240Myr ago 25,26.

Because rice is a monocotyledon,we assessed the presence or absence of palaeo-hexaploidy in its genome sequence.The observed pattern is the opposite of that seen for Arabidopsis and poplar:constituents of a grapevine triplet are generally orthologous to the same group of rice regions (Fig.1c and Supplementary Fig.11).Because rice and grape-vine are phylogenetically distant,it is more difficult to detect rela-tions of orthology across the two whole genomes:rearrangements,duplication and gene loss have affected the gene orders differently in the two lineages (Supplementary Fig.10).Even with this limitation,we observed numerous cases of one-to-three relationships

between

c

a b

Figure 1|Comparison between three paralogous Vitis genomic regions and their orthologues in P.trichocarpa ,A.thaliana and O.sativa .Orthologous gene pairs are joined with a different colour for each of the three paralogous grapevine chromosomes 6(green),8(blue)and 13(red).a ,Orthologous regions in the poplar genome are different for each of the three Vitis chromosomes,showing that the triplication predates the poplar/Vitis separation.One Vitis region recognizes two poplar segments because of a WGD in the poplar lineage after the separation.b ,Orthologous regions with Arabidopsis are different for each of the three Vitis chromosomes.This

shows that the Arabidopsis /Vitis ancestor had the same palaeo-hexaploid content.One Vitis region corresponds to four Arabidopsis segments,indicating the presence of two WGDs in the Arabidopsis lineage after

separation from the Vitis lineage.c ,Orthologous regions in rice are the same for the three paralogous chromosomes.This indicates that the triplication was not present in the common ancestor of monocotyledons and

dicotyledons.The presence in rice of different homologous blocks is due to global duplications in the rice lineage after divergence from dicotyledons.

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rice and grapevine (Supplementary Figs 8,9and 11);23%of ortho-logous blocks include the paralogous regions that originate from the grapevine palaeo-hexaploidy.For Arabidopsis ,this number is as low as 1.4%(this difference is significant at 5%:x 258.9;Supplementary Table 12),despite the fact that the Arabidopsis genome has suffered many gene losses since its two WGDs.These gene losses would be expected to obscure the orthologous relations with the grapevine genome,but they are clearly insufficient to explain the high number of one-to-three relationships observed in the rice–grapevine com-parison.The most probable explanation for this excess is that the rice ancestor did not exhibit the palaeo-hexaploidy observed in the grape-vine,poplar and Arabidopsis .

These findings are summarized in Fig.3:the triplicated arrange-ment is apparent after the separation of the monocotyledons and dicotyledons and before the spread of the Eurosid clade.Future gen-ome sequencing projects for other clades of dicotyledons,such as Solanaceae or basal eudicots,will help in situating the triplication event more precisely,and eventually in establishing its precise nature (hexaploidization or genome duplications at distant times).

Public access to the grapevine genome sequence will help in the identification of genes underlying the agricultural characteristics of

this species,including domestication traits.A selective amplification of genes belonging to the metabolic pathways of terpenes and tannins has occurred in the grapevine genome,in contrast with other plant genomes.This suggests that it may become possible to trace the diversity of wine flavours down to the genome level.Grapevine is also a crop that is highly susceptible to a large diversity of pathogens including powdery mildew,oidium and Pierce disease.Other Vitis species such as V.riparia or V.cinerea ,which are known to be res-istant to several of these pathogens,are interfertile with V.vinifera and can be used for the introduction of resistance traits by advanced backcrosses 27or by gene transfer.Access to the Vitis sequence and the exploitation of synteny will speed up this process of introgression of pathogen resistance traits.As a consequence of this,it is hoped that it will also prompt a strong decrease in pesticide use.

The high quality of the assembly,due mainly to the highly homo-zygous nature of the PN40024line,enables the discovery of three ancestral genomes constituting the diploid content of grapevine.The Greek historian Thucydides wrote that Mediterranean people began to emerge from ignorance when they learnt to cultivate olives and grapes.This first characterization of the grapevine genome,with its indication of a palaeo-hexaploid ancestral genome for many dico-tyledonous plants,addresses fundamental questions related to the origin and importance of this event in the history of flowering plants.Future work may help in correlating the differential fates of the three gene complements with phenotypic traits of dicotyledonous species.METHODS SUMMARY

Gene annotation.Protein-coding genes were predicted by combining ab initio models,V.vinifera complementary DNA alignments,and alignments of proteins and genomic DNA from other species.The integration of the data was performed with GAZE 28.Details are given in Supplementary Information.

Paralogous and orthologous gene sets.Statistical testing of homologous regions was performed as described in ref.21.

Full Methods and any associated references are available in the online version of the paper at https://www.wendangku.net/doc/1417283618.html,/nature.Received 5April;accepted 7August 2007.Published online 26August 2007.

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Acknowledgements The sequencing of the grapevine genome was launched and carried out after a scientific cooperation agreement between the Ministry of Agriculture in France and the Ministry of Agriculture in Italy,involving l’Institut National de la Recherche Agronomique(INRA),Consiglio per la Ricerca e Sperimentazione in Agricoltura(CRA)and Friuli Venezia Giulia Region.This work was financially supported by Consortium National de Recherche en Ge′nomique, Agence Nationale de la Recherche,INRA,and by MiPAF(VIGNA-CRA),Friuli Innovazione,Universita`di Udine,Federazione BCC,Fondazione CRUP,Fondazione Carigo,Fondazione CRT,Vivai Cooperativi Rauscedo,Eurotech,Livio Felluga, Marco Felluga,Venica e Venica,Le Vigne di Zamo`(IGA).We thank S.Cure for correcting the manuscript;F.Ca?mara and R.Guigo for the calibration of the GeneID gene prediction software,and the Centre Informatique National de l’Enseignement Supe′rieur for computing resources.

Author Information The final assembly and annotation are deposited in the EMBL/ Genbank/DDBJ databases under accession numbers CU459218–CU462737(for all scaffolds)and CU462738–CU462772(for chromosome reconstitutions and unanchored scaffolds).An annotation browser and further information on the project are available from https://www.wendangku.net/doc/1417283618.html,s.fr/vitis,http://

www.vitisgenome.it/and https://www.wendangku.net/doc/1417283618.html,/.Reprints and permissions information is available at https://www.wendangku.net/doc/1417283618.html,/reprints.The authors declare no competing financial interests.Correspondence and requests for materials should be addressed to P.W.(pwincker@https://www.wendangku.net/doc/1417283618.html,s.fr).

The French-Italian Public Consortium for Grapevine Genome Characterization Olivier Jaillon1*,Jean-Marc Aury1*,Benjamin Noel1,Alberto Policriti2,3,Christian Clepet4,Alberto Casagrande2,5,Nathalie Choisne1,4,Se′bastien Aubourg4,Nicola Vitulo6,15,Claire Jubin1,Alessandro Vezzi6,15,Fabrice Legeai7,Philippe Hugueney8, Corinne Dasilva1,David Horner9,15,Erica Mica9,15,Delphine Jublot4,Julie Poulain1, Cle′mence Bruye`re4,Alain Billault1,Be′atrice Segurens1,Michel Gouyvenoux1,Edgardo Ugarte1,Federica Cattonaro2,Ve′ronique Anthouard1,Virginie Vico1,Cristian Del Fabbro2,3,Michae¨l Alaux7,Gabriele Di Gaspero2,5,Vincent Dumas8,Nicoletta Felice2,5, Sophie Paillard4,Irena Juman2,5,Marco Moroldo4,Simone Scalabrin2,3,Aure′lie Canaguier4,Isabelle Le Clainche4,Giorgio Malacrida6,15,Ele′onore Durand7,Graziano Pesole10,11,15,Vale′rie Laucou12,Philippe Chatelet13,Didier Merdinoglu8,Massimo Delledonne14,15,Mario Pezzotti15,16,Alain Lecharny4,Claude Scarpelli1,Franc?ois Artiguenave1,M.Enrico Pe`9,15,Giorgio Valle6,15,Michele Morgante2,5,Michel Caboche4,Anne-Franc?oise Adam-Blondon4,Jean Weissenbach1,Francis Que′tier1& Patrick Wincker1

*These authors contributed equally to this work.

Affiliations for participants:1Genoscope(CEA)and UMR8030

CNRS-Genoscope-Universite′d’Evry,2rue Gaston Cre′mieux,BP5706,91057Evry, France.2Istituto di Genomica Applicata,Parco Scientifico e Tecnologico di Udine,Via Linussio51,33100Udine,Italy.3Dipartimento di Matematica ed Informatica,Universita` degli Studi di Udine,via delle Scienze208,33100Udine,Italy.4URGV,UMR INRA1165, CNRS-Universite′d’Evry Genomique Ve′ge′tale,2rue Gaston Cre′mieux,BP5708,91057 Evry cedex,France.5Dipartimento di Scienze Agrarie ed Ambientali,Universita`degli Studi di Udine,via delle Scienze208,33100Udine,Italy.6CRIBI,Universita`degli Studi di Padova,viale G.Colombo3,35121Padova,Italy.7URGI,UR1164Ge′nomique Info,523, Place des Terrasses,91034Evry Cedex,France.8UMR INRA1131,Universite′de Strasbourg,Sante′de la Vigne et Qualite′du Vin,28rue de Herrlisheim,BP20507,68021 Colmar,France.9Dipartimento di Scienze Biomolecolari e Biotecnologie,Universita`degli Studi di Milano,via Celoria26,20133Milano,Italy.10Dipartimento di Biochimica e Biologia Molecolare,Universita`degli Studi di Bari,via Orabona4,70125Bari,Italy.

11Istituto Tecnologie Biomediche,Consiglio Nazionale delle Ricerche,via Amendola122/ D,70125Bari,Italy.12UMR INRA1097,IRD-Montpellier SupAgro-Univ.Montpellier II, Diversite′et Adaptation des Plantes Cultive′es,2Place Pierre Viala,34060Montpellier Cedex1,France.13UMR INRA1098,IRD-Montpellier SupAgro-CIRAD,De′veloppement et Ame′lioration des Plantes,2Place Pierre Viala,34060Montpellier Cedex1,France. 14Dipartimento Scientifico e Tecnologico,Universita`degli Studi di Verona Strada Le Grazie15–Ca’Vignal,37134Verona,Italy.15Dipartimento di Scienze,Tecnologie e Mercati della Vite e del Vino,Universita`degli Studi di Verona,via della Pieve,7037029S. Floriano(VR),Italy.16VIGNA-CRA Initiative;Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante,c/o Universita`degli Studi di Siena,via Banchi di Sotto 55,53100Siena,Italy.

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METHODS

Genome sequencing.The V.vinifera PN40024genome was sequenced with the use of a whole-genome shotgun strategy.All data were generated by paired-end sequencing of cloned inserts using Sanger technology on ABI3730xl sequencers. Supplementary Table2gives the number of reads obtained per library. Genome assembly and chromosome anchoring.All reads were assembled with Arachne12.We obtained20,784contigs that were linked into3,830supercontigs of more than2kb.The contig N50was64kb,and the supercontig N50was1.9Mb. The total supercontig size was498Mb,remarkably close to the expected size of 475Mb.This indicates that the PN40024has retained few heterozygous regions. Remaining heterozygosity was assessed by aligning all supercontigs with each other.We first selected the supercontigs more than30kb in size that were covered over more than40%of their length by another supercontig with more than95%identity.After visual inspection of the alignments,we added to this list the supercontigs more than10kb in size that aligned at more than40%of their length with supercontigs identified previously.All potential cases were then inspected visually to discard potential heterozygous regions(aligning relatively homogeneously across their complete length)and retained repeated regions (with more heterogeneous alignments).This treatment identified11Mb of potentially allelic supercontigs.We confirmed that in most cases their coverage was about half the average of the homozygous supercontigs.Only one super-contig of each allelic pair was therefore conserved in the final assembly,which consists of3,514supercontigs(N5052Mb)containing19,577contigs (N50566kb),totalling487Mb.If the haploid genome size of475Mb is con-sidered correct,then our final assembly contains only about12Mb of remaining heterozygosity,or2.6%.

A set of30,151bacterial artificial chromosome(BAC)fingerprints of the BAC clones of a Cabernet–Sauvignon library29were assembled into1,763contigs with FPC30,v.8.In parallel,1,981markers were anchored on a subset of BAC clones31, among which388markers mapped onto the genetic map,and77,237BAC end sequences were obtained31.Blat32alignments(90%identity on80%of the length, fewer than five hits)were performed with BAC end sequences on the3,830 supercontigs of sequences with lengths over2kb.The results were then filtered with homemade Perl scripts to keep only the occurrences in which two paired ends were matching at a distance of less than300kb and with a consistent orientation.Two supercontigs were considered linked to each other if two BAC links could be found or one BAC link and a BAC contig link.A total number of111ultracontigs were constructed with this procedure.

Genome annotation.Several resources were used to build V.vinifera gene mod-els automatically with GAZE28.We used predictions of repetitive regions by repeatscout33,conserved coding regions predicted by the exofish method34,35, genewise36alignments of proteins from Uniprot37,Geneid38and Snap39ab initio gene predictions,and alignments of several cDNA resources(Supplementary Information).

A weight was assigned to each resource to further reflect its reliability and accuracy in predicting gene models.This weight acts as a multiplier for the score of each information source,before being processed by GAZE.When applied to the entire assembled sequence,GAZE predicted30,434gene models.Paralogous and orthologous gene sets.We identified orthologous genes in six pairs of genomes from four species:A.thaliana,O.sativa,P.trichocarpa and V.vinifera.Each pair of predicted gene sets was aligned with the Smith–Waterman algorithm,and alignments with a score higher than300(BLOSUM62; gapo510,gape51)were retained.Two genes,A from genome GA and

B from genome GB,were considered orthologues if B was the best match for gene A in GB and A was the best match for B in GA.

For each orthologous gene set with V.vinifera,clusters of orthologous genes were generated.A single linkage clustering with a euclidean distance was used to group genes.The distances were calculated with the gene index in each chro-mosome rather than the genomic position.The minimal distance between two orthologous genes was adapted in accordance with the selected genomes.Finally, we retained only clusters that were composed of at least six genes for Arabidopsis and O.sativa,and eight genes for P.trichocarpa(Supplementary Table10). To validate the clustering quality we used a method described previously21.For each cluster we computed the probability of finding this cluster in the gene homology matrix(Supplementary Table11).This matrix was constructed from two compared chromosomes with genes numbered according to their position on each chromosome,with no reference to physical distances.

Paralogous genes were computed by comparing all-against-all of V.vinifera proteins by using blastp,and alignments with an expected value of less than0.1 were retained and realigned with the Smith–Waterman algorithm40.Two genes A and B were considered paralogues if B was the best match for gene A and A was the best match for B.Moreover,clusters of paralogous genes were constructed in the same fashion as orthologous clusters(Supplementary Table10).

29.Adam-Blondon,A.F.et al.Construction and characterization of BAC libraries

from major grapevine cultivars.Theor.Appl.Genet.110,1363–1371(2005). 30.Soderlund,C.,Humphray,S.,Dunham,A.&French,L.Contigs built with

fingerprints,markers,and FPC V4.7.Genome Res.10,1772–1787(2000).

https://www.wendangku.net/doc/1417283618.html,moureux,D.et al.Anchoring of a large set of markers onto a BAC library for the

development of a draft physical map of the grapevine genome.Theor.Appl.Genet.

113,344–356(2006).

32.Kent,W.J.BLAT—the BLAST-like alignment tool.Genome Res.12,656–664

(2002).

33.Price,A.L.,Jones,N.C.&Pevzner,P.A.De novo identification of repeat families in

large genomes.Bioinformatics21(Suppl.1),i351–i358(2005).

34.Roest Crollius,H.et al.Estimate of human gene number provided by genome-wide

analysis using Tetraodon nigroviridis DNA sequence.Nature Genet.25,235–238 (2000).

35.Jaillon,O.et al.Genome-wide analyses based on comparative genomics.Cold

Spring Harb.Symp.Quant.Biol.68,275–282(2003).

36.Birney,E.,Clamp,M.&Durbin,R.GeneWise and Genomewise.Genome Res.14,

988–995(2004).

37.Bairoch,A.et al.The Universal Protein Resource(UniProt).Nucleic Acids Res.33,

D154–D159(2005).

38.Parra,G.,Blanco,E.&Guigo,R.GeneID in Drosophila.Genome Res.10,511–515

(2000).

39.Korf,I.Gene finding in novel genomes.BMC Bioinformatics5,59(2004).

40.Smith,T.F.&Waterman,M.S.Identification of common molecular

subsequences.J.Mol.Biol.147,195–197(1981).

doi:10.1038/nature06148

数据库简答题 (2)

章一 1、简述数据库管理技术发展的三个阶段。各阶段的特点是什么？ 答：数据库管理技术经历了人工管理阶段、文件系统阶段和数据库系统阶段。 (1）、人工管理数据的特点： A、数据不保存。 B、系统没有专用的软件对数据进行管理。 C、数据不共享。 D、数据不具有独立性。 （2）、文件系统阶段的特点： A、数据以文件的形式长期保存。 B、由文件系统管理数据。 C、程序与数据之间有一定的独立性。 D、文件的形式已经多样化 E、数据具有一定的共享性 （3）、数据库系统管理阶段特点： A、数据结构化。 B、数据共享性高、冗余度底。 C、数据独立性高。 D、有统一的数据控制功能。 3、简述数据库、数据库管理系统、数据库系统三个概念的含义和联系。 答：数据库是指存储在计算机内、有组织的、可共享的数据集合。 数据库管理系统是软件系统的一个重要组成部分，它通过借助操作系统完成对硬件的访问，并对数据库的数据进行存取、维护和管理。 数据库系统是指计算机系统中引入数据库后的系统构成。它主要由数据库、数据库用户、计算机硬件系统和计算机软件系统几部分组成。 三者的联系是：数据库系统包括数据库和数据库管理系统。数据库系统主要通过数据库管理系统对数据库进行管理的。 4、数据库系统包括哪几个主要组成部分？各部分的功能是什么？画出整个数据库系统的层次结构图。 答：数据库系统包括：数据库、数据库用户、软件系统和硬件系统。 数据库主要是来保存数据的。 数据库用户是对数据库进行使用的人，主要对数据库进行存储、维护和检索等操作。 软件系统主要完成对数据库的资源管理、完成各种操作请求。 硬件系统主要完成数据库的一些物理上的操作，如物理存储、输入输出等。

sequence的用法

ORACLE SEQUENCE用法 在oracle中sequence就是序号，每次取的时候它会自动增加。sequence与表没有关系。 1、Create Sequence 首先要有CREATE SEQUENCE或者CREATE ANY SEQUENCE权限。 创建语句如下： CREATE SEQUENCE seqTest INCREMENT BY1-- 每次加几个 START WITH1-- 从1开始计数 NOMAXvalue -- 不设置最大值 NOCYCLE -- 一直累加，不循环 CACHE 10; --设置缓存cache个序列，如果系统down掉了或者其它情况将会导致序列不连续，也可以设置为---------NOCACHE 2、得到Sequence值 定义好sequence后，你就可以用currVal，nextVal取得值。 CurrVal：返回sequence的当前值 NextVal：增加sequence的值，然后返回增加后sequence值 得到值语句如下： SELECT Sequence名称.CurrVal FROM DUAL; 如得到上边创建Sequence值的语句为： select seqtest.currval from dual 在Sql语句中可以使用sequence的地方： - 不包含子查询、snapshot、VIEW的SELECT 语句 - INSERT语句的子查询中 - INSERT语句的values中 - UPDATE 的SET中 如在插入语句中 insert into表名(id,name)values(seqtest.Nextval,'sequence 插入测试'); 注：

数据库期末考试填空题及答案

1 .数据库数据具有__________、__________和__________三个基本特点。 2.数据库管理系统是数据库系统的一个重要组成部分，它的功能包括__________、__________、__________、__________。 3. 数据库系统是指在计算机系统中引入数据库后的系统，一般由__________、__________、__________和__________构成。 4. 数据库管理技术的发展是与计算机技术及其应用的发展联系在一起的，它经历了三个阶段：__________阶段，__________阶段和__________阶段。 5. 数据库具有数据结构化、最小的__________、较高的__________等特点。 6. DBMS还必须提供__________保护、__________检查、__________、__________等数据控制功能。 7. 模式（Schema）是数据库中全体数据的__________和__________的描述，它仅仅涉及到__________的描述，不涉及到具体的值。 8. 三级模式之间的两层映象保证了数据库系统中的数据能够具有较高的__________和__________。 9. 根据模型应用的不同目的，可以将这些模型划分为两类，它们分别属于两个不同的层次。第一类是__________，第二类是__________。 10. 数据模型的三要素是指__________，__________，__________。实际数据库系统中所支持的主要数据模型是__________，__________，__________。 11. 数据模型中的__________是对数据系统的静态特征描述，包括数据结构和数据间联系的描述，__________是对数据库系统的动态特征描述，是一组定义在数据上的操作，包括操作的涵义、操作符、运算规则及其语言等。 12. 用树型结构表示实体类型及实体间联系的数据模型称为__________模型，上一层的父结点和下一层的子结点之间的联系是的联系。 13. 用有向图结构表示实体类型及实体间联系的数据模型称为__________模型，数据之间的联系通常通过__________实现。 14. 关系的完整性约束条件包括三大类：__________、__________和__________。 15. 关系数据模型中，二维表的列称为________，二维表的行称为________。 16. 用户选作元组标识的一个候选码为________，其属性不能取________。 17. 关系代数运算中，传统的集合运算有_____，_____，_____，_____。 18. 关系代数运算中，基本的运算是________，________，________，________，________。 (问答题) 19. 关系代数运算中，专门的关系运算有________，________，________。 20. 关系数据库中基于数学上的两类运算是________和________。 21. 关系代数中，从两个关系中找出相同元组的运算称为________运算。 22. R S表示R与S的________。 23. 设有学生关系：S（XH，XM，XB，NL，DP）。在这个关系中，XH表示学号，XM表示姓名，XB表示性别，NL表示年龄，DP表示系部。查询学生姓名和所在系的投影操作的关系运算式是________________。 24. 在“学生-选课-课程”数据库中的3个关系如下：S（S#，SNAME，SEX，AGE）；SC（S#，C#，GRADE）; C（C#，CNAME，TEACHER），查找选修“数据库技术”这门课程学生的学生名和成绩，若用关系代数表达式来表示为________________。 25. 已知系（系编号，系名称，系主任，电话，地点）和学生（学号，姓名，性别，入学日期，专业，系编号）两个关系，系关系的主码是________，系关系的外码是________，学生关系的主码是________，学生关系的外码是________。

SQL数据库应用原理题库

D 1 逻辑模型不包括（），它是按计算机系统的观点对数据建模，主要用于DBMS 的实现。A、层次模型B、网状模型 C、关系模型 D、文件模型 D 2 数据模型的组成要素不包括（）。 A、数据结构 B、数据操作 C、完整性约束 D、数据定义 D 3 数据库管理系统的主要功能不包括（）。 A、数据定义功能 B、数据组织、存储和管理 C、数据操纵 D、数据结构C 4 人工管理数据的特点不包括（）。 A、数据不保存 B、应用程序管理数据 C、数据共享 D、数据不具有独立性A 5 文件系统管理数据的特点不包括（）。 A、数据不能长期保存 B、由文件系统管理数据 C、数据共享性差 D、数据独立性差 D 6 数据库系统的特点不包括（）。 A、数据结构化 B、数据共享性高 C、数据独立性高 D、数据由DBA统一管理 D 7 数据库系统的核心和基础是（）。 A、物理模型 B、逻辑模型 C、概念模型 D、数据模型 D 8 数据模型不包括（）。 A、数据结构 B、数据操作 C、完整性约束 D、数据应用 C 9 以下不是数据库领域中常用的逻辑数据模型的是（）。 A、层次模型 B、网状模型 C、物理模型 D、关系模型 C 10 位于用户和操作系统之间的数据管理软件称为（）。 A、数据库 B、数据库系统 C、数据库管理系统 D、DBA A 11 以下数据模型中是非关系模型的是（）。 A、层次模型 B、关系模型 C、面向对象模型 D、对象关系模型 A 12 有且只有一个结点没有双亲节点，这个节点称为（）。 A、根节点 B、兄弟节点 C、子节点 D、叶结点 A 13 一个数据库可以有多个（）。 A、外模式 B、模式 C、内模式 D、逻辑模式 C 14 数据库系统是采用了数据库技术的计算机系统，数据库系统由数据库、数据库管理系统、应用系统和（）组成。 A、系统分析员 B、程序员 C、数据库管理员 D、操作员 A 15 数据库（DB），数据库系统（DBS）和数据库管理系统（DBMS）之间的关系是（）。 A、DBS包括DB和DBMS B、DBMS包括DB和DBS C、DB包括DBS和DBMS D、DBS就是DB，也就是DBMS B 16 数据库系统的数据独立性体现在（）。 A、不会因为数据的变化而影响到应用程序 B、不会因为数据存储结构与数据逻辑结构的变化而影响应用程序 C、不会因为存储策略的变化而影响存储结构 D、不会因为某些存储结构的变化而影响其他的存储结构 A 17 描述数据库全体数据的全局逻辑结构和特性的是（）。 A、模式 B、外模式 C、内模式 D、子模式 C 18 要保证数据库的数据独立性，需要修改的是（） A、模式与外模式 B、模式与内模式 C、三级模式之间的两层映射 D、三层模式

DNAStar详细中文使用说明书

Sequence Analysis Software for Macintosh and Windows GETTING STARTED Introductory Tour of the LASERGENE System MAY 2001

DNASTAR, Inc. 1228 South Park Street Madison, Wisconsin 53715 (608) 258-7420 Copyright . 2001 by DNASTAR, Inc. All rights reserved. Reproduction, adaptation, or translation without prior written permission is prohibited,except as allowed under the copyright laws or with the permission of DNASTAR, Inc. Sixth Edition, May 2001 Printed in Madison, Wisconsin, USA Trademark Information DNASTAR, Lasergene, Lasergene99, SeqEasy, SeqMan, SeqMan II, EditSeq, MegAlign, GeneMan, Protean,MapDraw, PrimerSelect, GeneQuest, GeneFont , and the Method Curtain are trademarks or registered trademarks of DNASTAR, Inc. Macintosh is a trademark of Apple Computers, Inc. Windows is a trademark of Microsoft Corp. ABI Prism are registered trademarks of Pharmacopeia, Inc. Disclaimer & Liability DNASTAR, Inc. makes no warranties, expressed or implied, including without limitation the implied warranties of merchantability and fitness for a particular purpose, regarding the software. DNASTAR does not warrant, guaranty, or make any representation regarding the use or the results of the use of the software in terms of correctness, accuracy, reliability, currentness, or otherwise. The entire risk as to the results and performance of the software is assumed by you. The exclusion of implied warranties is not permitted by some states. The above exclusion may not apply to you. In no event will DNASTAR, Inc. and their directors, officers, employees, or agents (collectively DNASTAR) be liable to you for any consequential, incidental or indirect damages (including damages for loss of business profits, business interruption, loss of business information and the like) arising out of the use of, or the inability to use the software even if DNASTAR Inc. has been advised of the possibility of such damages. Because some states do not allow the exclusion or limitation of liability for consequential or incidental damages, the above limitations may not apply to you. DNASTAR, Inc. reserves the right to revise this publication and to make changes to it from time to time without obligation of DNASTAR, Inc. to notify any person or organization of such revision or changes. The screen and other illustrations in this publication are meant to be representative of those that appear on your monitor or printer.

数据库的基本原理和sql语言的主要特点

The basic principle of database is the professional basic course of Comeputer science and technology ,it mainly discuss the basic concept ,basic princple,basic methods and applications involved.Its main contents include the structure and characteristics of database,the composition of databse system and function of every parts,the relational database,the object-oriented database, SQL, design of database and protection of data,meanwhile it explain a kind of important application of database system.Students can learn a lot by studing the course such as understand basic concept of database system,master the query,update and relational technology of database,master the design method of database initially,and build new database and simple application with database system. SQL is a kind of coumputer language for database only,it can not only query database but selection also can be done on the database, add or delete, update, and jump and other various operations. SQL include DDL,DML,DCL,with the same language style and all of activities of life cycle of database can be done. Users dont have to know about access path,the selection of it and the operation of SQL are automatic done by system.It reduces users’pressure and improve the independence of data It adopt operation mode of collection ,it is a self-contained and embedded language,and supply two different operarion way with a same grammer structure,it makes users feel flexible and convenient. SQL is a language which is similar to oral English , it is easy to be studied and used.

血管内超声图像序列分割的研究进展

万方数据

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揭秘美国16大情报机构

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美国情报工作重地—国防部五角大楼 美国情报工作重地—美国国家安全局大楼

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（一）中央情报局（CIA） 中情局1947年经美国国会通过而成立。美国最大从事情报收集、分析的隐蔽行动机构，是美国情报体系中唯一一个独立的情报部门。中情局通过公开和秘密渠道收集、分析关于国外政府、公司和个人，以及政治、文化、科技等方面的情报；协调其他美国国内情报机构的活动。中情局没有国内任务，也没有逮捕权。

（二）联邦调查局 联邦调查局(FBI)创立于1908年7月26日，隶属于司法部(DOJ).是美国最大的反间谍机构和最重要的联邦执法部门，它与中情局并驾齐驱。FBI的任务是：调查违反美国联邦法律的内部犯罪行为，以及调查来自于外国的情报和恐怖活动等。其中，在反外国间谍活动、暴力犯罪和白领阶层犯罪等方面，FBI享有最高优先权。2002年10月22日, 美国驻华使馆设立了FBI北京办事处，这是美国FBI第45个海外专员办事处,配备特工2名，负责FBI在中国的事务。

(完整版)试述数据库系统的特点

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