ライフサイエンスコーパス: synteny

1 that were organized using wheat-Brachypodium synteny.

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

3 rall their genomes displayed a high level of synteny.

4 of S. parvula and Arabidopsis show extensive synteny.

5 ment, gene family evolution, and chromosomal synteny.

6 ith Drosophila without significantly reduced synteny.

7 s based on patterns of chromosomal conserved synteny.

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

9 idues and distinct genomic patterns of micro-synteny.

10 rred as inferred from tree tests and genomic synteny.

11 nd allowed genome-wide analysis of conserved synteny.

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

13 ese genes there is limited evidence of local synteny.

14 ned functions based on database searching or synteny.

15 ic basidiomycete, share extensive regions of synteny.

16 homolog because of local indels or scrambled synteny.

17 nteritis across the globe revealed extensive synteny.

18 ffold two other crocodilian genomes based on synteny.

19 ,910 to 24,970 bp with highly conserved gene synteny.

20 for user-friendly tools capable of assessing synteny.

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

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

23 Analyses of synteny across genomes of bioluminescent species resolve

24 ical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to t

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

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

27 ecies have maintained a complete chromosomal synteny after more than 9 million years of divergence.

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

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

30 genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint

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

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

33 Synteny among filamentous cyanobacteria and the similar

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

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

36 ough the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight sp

37 Synteny among the three sequenced genomes can be viewed

38 Phylogeny and synteny analyses allowed us to infer that they originate

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

40 Macro-synteny analyses revealed highly conserved genomic block

41 Synteny analyses suggest that the gamma event, resulting

42 our phylogenetic analysis complemented with synteny analyses suggests that Bmp2, -4 and -16 are remn

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

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

45 Synteny analysis between the grape and Arabidopsis genom

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

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

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

49 We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall p

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

51 Synteny analysis showed that zebrafish mate genes are or

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

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

54 Synteny analysis uncovered localized but scrambled block

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

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

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

58 and estimation of genome structure based on synteny analysis.

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

60 ter in Photorhabdus luminescens using genome synteny analysis.

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

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

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

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

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

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

67 is the foundation for comparative chromosome synteny and evolutionary studies.

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

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

70 Phylogenetics, synteny and gene structure analyses of H3.3 genes from 3

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

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

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

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

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

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

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

78 haracterized millipede sequences in terms of synteny and length.

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

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

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

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

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

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

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

86 Synteny and sequence alignments indicate that this gene

87 Synteny and sequence conservation, as well as deletions

88 A. thaliana genes by sequence similarity and synteny and sequenced candidate genes in the A. alpina m

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

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

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

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

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

94 luding genome metadata, RNA-seq, proteomics, synteny, and large-scale diversity.

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

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

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

98 mergence of BAT, the phylogeny of CHKB-CPT1B synteny, and the insufficiency of UCP1 to account for eu

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

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

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

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

103 Synteny-based annotation of hypothetical proteins highli

104 nd excluding paralogs by combining tree- and synteny-based approaches.

105 Synteny-based comparison of mouse and human tumours narr

106 sed on evolutionary constraint supported the synteny-based findings.

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

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

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

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

111 By comparing synteny-based phylostrata to standard phylostrata, fagin

112 ents standard phylostratigraphy, and extends synteny-based phylostratigraphy with an automated, custo

113 the age inference methods revealed that the synteny-based pipeline (SBP) is most suited for recently

114 We have developed a synteny-based pipeline in the R framework.

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

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

117 Conserved syntenies between seabass LG2 and five other teleosts we

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

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

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

121 e database, a 'SyntenyViewer' to view genome synteny between different cucurbit species and an 'RNA-S

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

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

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

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

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

127 The strong conserved synteny between mouse chromosome 12aF1 and human chromos

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

129 ready visualization of regions of conserved synteny between species.

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

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

132 n the Schizophora, and show that patterns of synteny between the Hox2 and Hox3 orthologs in Arthropod

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

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

135 ovel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and

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

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

138 We further combine synteny block generation with rearrangement analysis to

139 Most synteny block reconstruction algorithms use genes shared

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

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

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

143 comparative genomic analysis results such as synteny blocks and homologous gene pairs between differe

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

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

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

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

148 The synteny blocks from multiple chromosomes may be displaye

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

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

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

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

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

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

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

156 A Genomicus synteny browser explores the conservation of local gene

157 eight species can be viewed through the new synteny browser, SynView.

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

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

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

161 Synteny comparison with RPP1 loci involved in hybrid inc

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

163 Analysis of synteny conservation across centromeres with newly gener

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

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

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

167 The Synteny Database is optimized for the investigation of i

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

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

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

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

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

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

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

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

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

177 High levels of gene synteny exist among Saccharibacteria species.

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

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

180 Comparison of gene synteny from known crustacean-infecting nudiviruses reve

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

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

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

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

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

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

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

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

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

190 Thus, the chromosomal synteny in Populus has been remarkably maintained after

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

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

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

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

195 Evaluation of synteny indicated that segmental and tandem duplications

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

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

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

199 The syntenies involving LWS, SWS2 and Rh2 underwent complex

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

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

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

203 Synteny is maintained with distantly related blood fluke

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

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

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

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

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

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

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

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

212 Synteny mapping identified three pairs of B. betularia L

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

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

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

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

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

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

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

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

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

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

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

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

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

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

227 3D allow researchers to explore whole genome synteny patterns (across two or three genomes, respectiv

228 underpinning the investigation of conserved synteny patterns.

229 y of the SHMT gene family members, including synteny, phylogeny, subcellular localizations, haplotype

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

231 Using pipelines examining the synteny relationship between genomes and reciprocal-best

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

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

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

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

236 areas of conserved gene order, with overall synteny strongest with coffee.

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

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

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

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

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

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

243 id genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon

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

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

246 arness the special circumstance of conserved synteny to estimate the contribution of complete diverge

247 Here, using shared synteny to guide loss-of-function analysis of homologues

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

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

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

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

252 Toolboxes for search, Blast, synteny view, enrichment analysis, metabolic pathway ana

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

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

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

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

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

258 Ortholog prediction and synteny visualization across whole genomes are valuable

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

260 Current synteny visualization tools either focus on small region

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

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

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

264 Synteny was not detected between the two species' candid

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

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

267 Although synteny was typically conserved for those genes with try

268 Guided by synteny, we identified a highly divergent basalin orthol

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

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

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

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

273 The green ash map shows stronger synteny with coffee than tomato.

274 been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris).

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

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

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

278 Synteny with M. fijiensis implied that the nontelomeric

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

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

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

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

283 lion years ago, both of which exhibit strong synteny with other grass species.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 (