ライフサイエンスコーパス: synteny

1 of S. parvula and Arabidopsis show extensive synteny.

2 ment, gene family evolution, and chromosomal synteny.

3 ith Drosophila without significantly reduced synteny.

4 ve analysis of rye/barley/model grass genome synteny.

5 rred as inferred from tree tests and genomic synteny.

6 nd allowed genome-wide analysis of conserved synteny.

7 ce to a new genome on the basis of conserved synteny.

8 ese genes there is limited evidence of local synteny.

9 ned functions based on database searching or synteny.

10 ic basidiomycete, share extensive regions of synteny.

11 ffold two other crocodilian genomes based on synteny.

12 lows the user to interrogate the evidence of synteny.

13 ,910 to 24,970 bp with highly conserved gene synteny.

14 for user-friendly tools capable of assessing synteny.

15 that were organized using wheat-Brachypodium synteny.

16 ome size in the 20 Gbp range, and show broad synteny.

17 rall their genomes displayed a high level of synteny.

18 Based on sequence similarity and synteny, 10,516 putative orthologs have been identified

19 gene encoding interleukin 26 and disrupting synteny 57 kilobases upstream of Ifng.

20 methods are currently available to visualize synteny across any number of annotated genomes.

21 These two genes show shared synteny across species from humans to sponges.

22 s developed two web-based tools to visualize synteny across whole genomes.

23 d Rearrangements In Multiple Mammals (DRIMM)-Synteny algorithm to address this bottleneck and apply i

24 The filtered hits are input to the synteny algorithm, which was designed to discover duplic

25 ighted the conservation of gene arrangement (synteny) along chromosomal regions.

26 etraodon nigroviridis reveals ALG2/GGAZ/HSAX syntenies among three pairs of ancestral chromosome dupl

27 lying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integ

28 Synteny among filamentous cyanobacteria and the similar

29 e of several other nematodes, we demonstrate synteny among filariae but not with nonparasitic nematod

30 Common chromosome maps identify major synteny among species.

31 We find little synteny among the 256 Hodgkinia circles analyzed except

32 he 5' untranslated region as well as a micro-synteny among the cereals.

33 Synteny among the three sequenced genomes can be viewed

34 Phylogenetic tree and synteny analyses of trout and other fish species suggest

35 enome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the B

36 Our new database is capable of systematic synteny analysis across M. truncatula, G. max, L. japoni

37 Synteny analysis between the grape and Arabidopsis genom

38 rease in numbers of sequenced plant genomes, synteny analysis can provide new insights into gene fami

39 On the other hand, synteny analysis lends support to the notion that the ab

40 this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are

41 Genome-wide synteny analysis reveals multiple other loci conserved b

42 Synteny analysis showed that zebrafish mate genes are or

43 Moreover, integrated synteny analysis suggested that the large-scale expansio

44 ene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe

45 Synteny analysis uncovered localized but scrambled block

46 Using phylogenetic and gene synteny analysis we identified an angiosperm PIN clade s

47 set of species on the basis of whole-genome synteny analysis, which are found to be higher than thos

48 ed against Rosaceae genomes to perform micro-synteny analysis.

49 and estimation of genome structure based on synteny analysis.

50 rat pre-miRNAs using bidirectional BLAST and synteny analysis.

51 ter in Photorhabdus luminescens using genome synteny analysis.

52 he persistence of large blocks of homologous synteny and a high frequency of breakpoint reuse are dis

53 Using synteny and a large number of F2 gametes, Iw1 was fine-m

54 nomes exhibit essentially no conservation of synteny and are highly repetitive, with evidence of reci

55 The genomes display extensive synteny and are similar in size ( approximately 3.27 Mb)

56 n adjusted MCScan algorithm for detection of synteny and collinearity that extends the original softw

57 it-associated lincRNAs, we also investigated synteny and conservation relative to mouse, expression p

58 However, operon structure in terms of synteny and gene content is not tightly conserved betwee

59 sed transposase frequency and decreased gene synteny and gene density in the distal semigenome.

60 The PhiHAP-1 genome shares synteny and gene similarity with coliphage N15 and vibri

61 In addition, a separate locus sharing synteny and hence homology with human Hox loci exists in

62 e only option for establishing the extent of synteny and homology with the X chromosome.

63 d coding sequences (CDSs) in all 15 loci for synteny and homology.

64 shmania major reveals marked conservation of synteny and identifies only approximately 200 genes with

65 Homologs of SgrR were analyzed for gene synteny and inter-homolog identity to identify those tha

66 Here we describe the synteny and isochore structure of P. vivax chromosomes,

67 in one or both strains based on analysis of synteny and lack of statistical support for acquisition

68 haracterized millipede sequences in terms of synteny and length.

69 ic skin development and a striking degree of synteny and linearity in the EDC locus across a wide ran

70 This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to a

71 Here we use genomic synteny and Monte Carlo-based simulations to resolve Hox

72 M7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have oc

73 tive trait locus mapping, analysis of genome synteny and other genomic data analyses.

74 of gene gain and losses, gene architectures, synteny and other genomic features can not be addressed

75 eries based on gene annotation, gene family, synteny and relative gene expression.

76 Synteny and sequence alignments indicate that this gene

77 Synteny and sequence conservation, as well as deletions

78 Brucella bacteria in terms of extensive gene synteny and the requirements for intracellular survival

79 iteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions

80 nferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic bran

81 s at the levels of nucleotide sequence, gene synteny, and chromosomal structure.

82 ne and MCH2 peptide share genomic structure, synteny, and high peptide sequence homology with mammali

83 e analyzed protein sequence, gene structure, synteny, and phylogenetics to identify GAD3 as a homolog

84 ata including genome-based phylogeny, genome synteny, and sequence alignments of orthologous genes an

85 Analyses based on gene tree, genome synteny, and structural models revealed rapid adaptive e

86 false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplica

87 are not evident, significant levels of local synteny are detected at a fine scale covering segments o

88 We also examined synteny around plant LysM kinase genes to help reconstru

89 Overreliance on synteny as a means of confirming and ordering contigs wi

90 ete mating-type switching, and panascomycete synteny at the MAT locus.

91 Meta-analysis linked to synteny-based and expression-based information provides

92 Synteny-based annotation of hypothetical proteins highli

93 Synteny-based comparison of mouse and human tumours narr

94 cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes.

95 The consensus map constitutes a platform for synteny-based gene cloning approaches and can support th

96 teny within the grass family, to establish a synteny-based linear gene order.

97 hese lineages were reconstructed using a new synteny-based method.

98 rn was weak overall, with colocalization and synteny being relatively rare.

99 We further show that conserved syntenies between ALG2 and amniote chromosomes are ident

100 Putative conserved syntenies between catfish and zebrafish, medaka, and Tet

101 hypothesis is primarily based upon conserved syntenies between in-group taxa (birds and mammals).

102 Conserved syntenies between seabass LG2 and five other teleosts we

103 Because of the conserved syntenies between the dog and human, this approach would

104 ynteny index' (SI) that measures the average synteny between a pair of genomes, we developed the phyl

105 We show extensive conservation of synteny between Ambystoma, chicken, and human, and a pos

106 orrelated, which provides support for strong synteny between bread wheat accessions.

107 Nevertheless, synteny between divergent taxa in several lineages has b

108 e inserts show high levels of similarity and synteny between each other, indicating that they are clo

109 While the phages do show synteny between each other, the nucleotide identity betw

110 thologs and paralogs, and viewing regions of synteny between genomes, and discuss how these can and a

111 isolate (HhCatGer041) and found the genomic synteny between H. hammondi and T. gondii to be >95%.

112 We observed strong segmental synteny between M. lewisii and M. guttatus maps, with es

113 RH mapping data indicate the conservation of synteny between macaque chromosome 5 and human chromosom

114 It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced m

115 ready visualization of regions of conserved synteny between species.

116 n of these molecules or to analyze conserved synteny between teleost and mammalian CC chemokines.

117 Phylogenomic analysis shows conservation of synteny between teleosts and tetrapods and suggests a mu

118 nd their respective centromeres show overall synteny between the 2 genomes, both MAT loci exhibit gen

119 is stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L.

120 We have examined the level of synteny between the model species Arabidopsis thaliana a

121 quences suggested a high degree of conserved synteny between the two avian genomes.

122 The high level of synteny between these oomycete genomes extends to the AB

123 enes genetically map to chromosome MGA2 with synteny between turkey and human alpha-class GSTs and fl

124 ma should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.

125 We further combine synteny block generation with rearrangement analysis to

126 of genes syntenic and collinear within each synteny block is relatively homogeneous.

127 Most synteny block reconstruction algorithms use genes shared

128 when reconstructing mammalian genomes at the synteny-block level, although the relative positions of

129 Homologous synteny blocks (HSBs; N = 2233) and chromosome evolution

130 The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized

131 rogram), consists of an algorithm to compute synteny blocks and Web-based graphics to visualize the r

132 Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map,

133 rders with duplications guided by homologous synteny blocks for a set of related descendant genomes.

134 Neighboring chains are merged into synteny blocks for display.

135 We found multiple synteny blocks for morphological, life history, and phys

136 nes shared over all genomes to construct the synteny blocks for multiple genomes.

137 The synteny blocks from multiple chromosomes may be displaye

138 me 5M(g) with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza s

139 highlights the importance of identifying the synteny blocks in multiple and/or highly duplicated geno

140 gout uses the assembly graph and multi-scale synteny blocks to reduce assembly gaps caused by small c

141 istent with regions of conserved gene order (synteny blocks).

142 go genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and f

143 about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome r

144 ver duplicated regions and form larger-scale synteny blocks, where intervening micro-rearrangements a

145 ify 152 cat-human and 134 cat-dog homologous synteny blocks.

146 these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (

147 enome, and they are nearly always located at synteny breakpoints.

148 ular human pathogens that share near genomic synteny but have distinct infection and disease organotr

149 d by almost complete conservation of genomic synteny, but against this strikingly conserved backgroun

150 etailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finne

151 e, comparative gene structure, and conserved synteny, chicken DNase II appears to represent a member

152 d at http://try-gobe.appspot.com/ and http://synteny.cnr.berkeley.edu/gobe-app/.

153 her grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manif

154 Synteny comparison with RPP1 loci involved in hybrid inc

155 Here we report synteny comparisons between these species, including det

156 tion of which requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and non

157 g fossil' coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a

158 alysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene

159 ization of tps26 and confirm by homology and synteny criteria that it is the ortholog of stc1.

160 The Synteny Database is optimized for the investigation of i

161 The product of this automated analysis, the Synteny Database, allows a user to examine fully or part

162 d observation that gene order conservation ('synteny') decreases in time as a result of gene mobility

163 Conservation of synteny demonstrates that, despite changes in its gene c

164 ing was observed across regions of conserved synteny, despite considerable species variation in the a

165 of gene family members as frequent causes of synteny disruption.

166 ving maintained little conservation of local synteny during approximately 350 million years of evolut

167 romosomes, suggesting that the dependence of synteny erosion on gene location along the centromere-te

168 ation of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detecti

169 Through phylogenetic analyses and synteny evidence, we show that gene conversion has playe

170 icient on short evolutionary distances where synteny footprints remain detectable, whereas the nucleo

171 tive genomic analysis demonstrated conserved syntenies for all FA genes.

172 ether, our results support a conservation of synteny for NB-LRR genes and further show that their dis

173 However, no obvious synteny gaps were observed across the centromeric region

174 ated to actinobacterial homologues, although synteny has not been maintained.

175 The conserved syntenies identified here between the catfish and the th

176 Here, I present a Synteny Imaging tool (Synima) written in Perl, which use

177 evious studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the

178 We submit that the structure of synteny in metabolic pathways of fungi is a signature of

179 The use of conserved genome synteny in orthology detection has been relatively under

180 iner, and outputs an overview of genome-wide synteny in PDF.

181 d evidence of multi-domain var structure and synteny in Plasmodium gaboni, one of the ape Laverania s

182 s conserved gene content, gene structure and synteny in relation to the human and other complex eumet

183 There is a high degree of conserved synteny in the genomic regions encoding the conventional

184 entified the opsin genes and adjacent genes (syntenies) in each genome.

185 Using a 'synteny index' (SI) that measures the average synteny be

186 Evaluation of synteny indicated that segmental and tandem duplications

187 uplication Database, a web service providing synteny information in terms of colinearity between chro

188 vey sequencing, and integration of conserved synteny information of three sequenced model grass genom

189 gnments of closely related species that uses synteny information to remove misassembled and misaligne

190 The syntenies involving LWS, SWS2 and Rh2 underwent complex

191 fish-human comparisons demonstrate conserved synteny involving nrf2 and hox genes, indicating that nr

192 ESM) to identify regions of the genome where synteny is broken.

193 two genome sequences are highly similar and synteny is conserved throughout, 168 species-specific ge

194 Nonetheless, chromosomal synteny is generally maintained among all three insects,

195 of genes included in an analysis, the use of synteny is likely to improve the quality of ortholog inf

196 Synteny is maintained with distantly related blood fluke

197 Furthermore, in cases where genomic synteny is sufficient to allow comparisons of relative g

198 r locus is linked to Ppu020, which, assuming synteny, is located on avian chromosome 11.

199 an diseases, such as cancer, are common, but synteny issues complicate modeling of these deletions in

200 This work demonstrates that the inclusion of synteny-level information can help us obtain better gene

201 The method uses a synteny-level reconstruction to break the gene-order pro

202 omes/subgenomes revealed almost perfect gene synteny, low sequence divergence and a high number of sh

203 nio, revealing numerous regions of conserved synteny, many of which are shared across critical region

204 thology assignments were used to construct a synteny map that illustrates the considerable fragmentat

205 SyMAP (Synteny Mapping and Analysis Program) was originally dev

206 The system, called SyMAP (Synteny Mapping and Analysis Program), consists of an al

207 Synteny mapping identified three pairs of B. betularia L

208 , LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and

209 High-resolution synteny maps identified many small disruptions to conser

210 y patterns were inferred and visualized from synteny network clusters.

211 Specifically, we analyzed synteny networks of the MADS-box transcription factor ge

212 nteny provides a pipeline for evaluating the synteny of a preselected set of gene targets across mult

213 The genetic synteny of aaPGS and ahyD is conserved in >60 different

214 This revealed that the organization and synteny of avian and mammalian SerpinA6 genes are conser

215 iversity that we observe in the sequence and synteny of genes.

216 ic analysis combined with an analysis of the synteny of Ls in several species strongly supported the

217 Second, we analyzed the gene content and synteny of morphogenesis and cell division genes and com

218 tribution, extent of colocalization, and the synteny of QTL for ecologically relevant traits, we used

219 o identified angiosperm-wide conservation of synteny of several other less studied clades.

220 e, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon.

221 e targeting to flank a region of orthologous synteny on mouse chromosome band 5A3 with loxP sites.

222 3D allow researchers to explore whole genome synteny patterns (across two or three genomes, respectiv

223 underpinning the investigation of conserved synteny patterns.

224 st majority of gene duplications (96.5%) and synteny rearrangements were found to occur, as expected,

225 nary forces that affect genome architecture, synteny relationships among 10 amniotes (human, chimp, m

226 respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chro

227 The conserved gene order (synteny) revealed by heterospecific SNP maps is in conco

228 We find the distribution of synteny segment sizes to be biased by a large number of

229 Phylogenetic analysis and synteny studies suggest that both carbonic anhydrase gen

230 Next, a synteny study was completed to determine the present loc

231 Colocalization and fine-scale synteny suggest genetic linkage between traits within sp

232 n an extended region of conserved fine-scale synteny, suggesting that avian and mammalian CYP1A paral

233 associated with the high degree of conserved synteny, suggesting that these are features of the Afrot

234 large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analy

235 etween wheat and rice, a far higher level of synteny than previously reported, and 6% were nonsynteni

236 gbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the abil

237 Conserved synteny-the tendency of neighboring genes to retain thei

238 ts: 53% of equine chromosomes show conserved synteny to a single human chromosome.

239 um perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass

240 tified a genomic region exhibiting conserved synteny to human chromosome 2, which included one of the

241 line chromosome A1q in a region of conserved synteny to human chromosome 5q15.

242 n mouse chromosome 6qA3 with conservation of synteny to human chromosome 7q32.2.

243 consensus map building, and determination of synteny to reference genomes.

244 cation of a maize progenitor from genes with synteny to sorghum (Sorghum bicolor) were highly overrep

245 salmoninarum genome has extended regions of synteny to the Arthrobacter sp. strain FB24 and Arthroba

246 ntains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-inf

247 We have developed a multi-Genome Synteny Viewer (mGSV).

248 nce data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wh

249 ar homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of ortholog

250 Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the a

251 otations, along with the barley-Ae. tauschii synteny viewer.

252 Ortholog prediction and synteny visualization across whole genomes are valuable

253 Web-based synteny visualization tools are important for sharing da

254 Current synteny visualization tools either focus on small region

255 while the evolution of the other opsin gene syntenies was much simpler.

256 ly reported interchromosomal conservation of synteny was confirmed, but a larger than expected number

257 Exceptional regions where synteny was disrupted probably are nonessential for expr

258 A high level of synteny was found with pine genetic maps, which should f

259 eriod of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae.

260 Synteny was reduced in the vicinity of the termini of mo

261 Although synteny was typically conserved for those genes with try

262 ion of phylogenetic analysis and analysis of synteny, we have determined that ten are likely ortholog

263 ure, and gene order although discordances in synteny were observed.

264 omes are identified as overlapping conserved syntenies when all available chicken (N = 3120) and huma

265 roughout the bird taxa show a much-conserved synteny, whereas at the single-base resolution there are

266 chordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply

267 Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversi

268 ements, and (4) does not exhibit large-scale synteny with either rice or sorghum genomes but does con

269 The SWS1 gene shows a conserved synteny with flanking genes.

270 physical map data exhibited a high level of synteny with homologous sequences on the wheat and/or ri

271 egion of CFA10 that exhibits conservation of synteny with HSA12q13.

272 The genome exhibits substantial shared synteny with human and chicken over major parts of large

273 Synteny with M. fijiensis implied that the nontelomeric

274 We observed large blocks of conserved synteny with Medicago truncatula and estimated that the

275 nts can be predicted through conservation of synteny with model cereal genomes, providing a route to

276 The region of synteny with mouse D14mit160 is the human 13q14 region,

277 H. akashiwo chloroplast genomes share little synteny with other algal chloroplast genomes sequenced t

278 sions about candidate genes, assuming shared synteny with other birds.

279 ments (MGEs), which contributes to a limited synteny with other Rickettsia genomes.

280 omly in clusters that lie between regions of synteny with other Sordariomycetes.

281 Following conserved synteny with other vertebrates, we also mapped five addi

282 Combining analysis of synteny with phylogenetics, gene expression and function

283 mosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like

284 Mvwf6 displays conservation of synteny with potential VWF modifier loci identified in h

285 Significant genome synteny with prototypic pre-seventh pandemic strains of

286 These genomes shared limited synteny with Rhodococcus equi phage ReqiDocB7 and Gordon

287 we report cloning of ZmNope1 on the basis of synteny with rice.

288 ified within a 0.2-Mb region in near-perfect synteny with that of the chicken MHC-B.

289 The genome shows extensive synteny with that of the closely related organism, Kocur

290 The apple has a higher degree of synteny with the closely related Populus than with the d

291 shares striking overall similarity and gene synteny with the M. mycoides subsp. mycoides SC genome.

292 Both these loci share synteny with the mammalian alpha-globin locus.

293 nto genomic clusters, which are in conserved synteny with the mammalian LRC.

294 id nucleotide composition and shared a large synteny with the other sequenced glass sponge mtDNAs.

295 cation and one of the class A locations show synteny with the rice (Oryza sativa) regions where ortho

296 Given its genomic synteny with the TH2-LCR, we refer to this lncRNA cluste

297 nt on scaffold 104, in a region of conserved synteny with zebrafish.

298 her gene clusters has now revealed conserved synteny with zygomycete fungi, indicating that microspor

299 y between perennial ryegrass and barley, and synteny within the grass family, to establish a synteny-

300 ene-based markers to reconstruct chromosomal synteny within the model flowering plant genus Mimulus (