ライフサイエンスコーパス: duplicate gene

1 le to uniquely amplify a specific variant or duplicate gene.

2 The eel, however, contains a duplicate gene.

3 arking may facilitate long-term retention of duplicate genes.

4 ts for the retention of almost two-thirds of duplicate genes.

5 n, and specialization in the preservation of duplicate genes.

6 n and is among the most fixed human-specific duplicate genes.

7 bs as well as insights into the evolution of duplicate genes.

8 utionary trajectories of partially redundant duplicate genes.

9 als for sequence and expression evolution of duplicate genes.

10 rstanding the mutational processes affecting duplicate genes.

11 tion and potential functional innovations of duplicate genes.

12 evolutionary processes for Arabidopsis young duplicate genes.

13 ausative factor for functional divergence of duplicate genes.

14 and is restricted to the nucleus having the duplicated gene.

15 acts are more likely to contain a completely duplicated gene.

16 to the selective constraints on a completely duplicated gene.

17 tional fate of a set of approximately 18 000 duplicated genes.

18 ession and may be related to survivorship of duplicated genes.

19 he evolution of specialized enzymes coded by duplicated genes.

20 oduced by immigrants when there are multiple duplicated genes.

21 on fitness of specific substitutions between duplicated genes.

22 liced isoforms and transcripts from recently duplicated genes.

23 are multiple possible evolutionary fates of duplicated genes.

24 in fact, contains seven distinctly evolving duplicated genes.

25 w contexts, and cooperative functions of the duplicated genes.

26 is poorly understood, as is the fate of most duplicated genes.

27 ing set of principles governing the fates of duplicated genes.

28 ich results in a higher rate of evolution in duplicated genes.

29 genes with new functions by modification of duplicated genes.

30 ivergence is a previously unreported fate of duplicated genes.

31 h are then combined in order to disambiguate duplicated genes.

32 element evolution and network divergence in duplicated genes.

33 n through the adaptive recruitment of tandem duplicated genes.

34 chromosome-internal locus comprising tandem-duplicated genes.

35 leading to this transcription pattern of RNA-duplicated genes.

36 t conservation is substantially weaker among duplicated genes.

37 parent low number of paralogous (ancestrally duplicated) genes.

38 itioning of ancestral splice forms among the duplicate genes - a form of subfunctionalization.

39 However, the paths by which duplicated genes acquire distinct functions are not well

40 Duplicate genes act as a source of genetic material from

41 tion analysis indicated that single-copy and duplicate genes after WGD were well preserved in A. thal

42 processes that have driven the retention of duplicated genes after recurrent WGDs.

43 emonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale.

44 ence divergence all increase with the age of duplicate genes, although their exact interrelationships

45 ogous FLC loci, which determines the fate of duplicate genes and adaptation of allopolyploids during

46 tioning alternatively spliced isoforms among duplicate genes and as such highlight the relationship b

47 ing additional insight into the evolution of duplicate genes and benefiting future genome annotation.

48 similar fitness effects of deleting pairs of duplicate genes and deleting individual singleton genes

49 Numbers of duplicate genes and plastid-derived tRNAs vary among cyt

50 udy highlights the importance of the cost of duplicate genes and the quantitative nature of the trade

51 patterns of genetic variation between these duplicated genes and between different extracellular dom

52 xpected functional differences between these duplicated genes and calling into question the practice

53 DNA methylation and expression divergence of duplicated genes and suggested a role of epigenetic mech

54 nt increases in the expression levels of the duplicated genes and that these duplications are more li

55 d insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait varia

56 te diverse processes, including silencing of duplicated genes and transposons and chromosome segregat

57 The enrichment of duplicate genes, and therefore paralogs (proteins coded

58 tified as part of an array of eight tandemly duplicated genes, and AcTPS1 expression and terpene prod

59 individuals possessed 0.81 deleted and 1.75 duplicated genes, and most (70%) carried at least one ra

60 ys) genome, in which only about one-third of duplicated genes appear to have been retained over a sim

61 A comparative study of two highly conserved duplicated genes, ARABIDOPSIS TRITHORAX-LIKE PROTEIN1 (A

62 ary processes and functionalization of plant duplicate genes are associated with their ancestral func

63 Moreover, we show that young duplicate genes are expressed primarily in testes and th

64 We first demonstrate that duplicate genes are initially heavily methylated, before

65 chanisms underlying functional divergence of duplicate genes are not well understood.

66 Tandemly arrayed duplicate genes are prevalent.

67 Most duplicate genes are removed after tetraploidy.

68 The question of how duplicate genes are retained in a population remains con

69 er studies have shown that a large number of duplicate genes are retained over a long evolutionary ti

70 andem duplication and random inactivation of duplicate genes are the major factors of gene number cha

71 Duplicated genes are a major contributor to genome evolu

72 Duplicated genes are also affected by epigenetic changes

73 d that most protein levels change little and duplicated genes are expressed similarly.

74 Surprisingly, the results show that duplicated genes are maintained because each copy carrie

75 (NCCs), in which neofunctionalization of the duplicated genes are thought to have facilitated develop

76 Recently duplicated genes are utilized at later stages of placent

77 In flowering plants, duplicated genes are widely observed, and functional red

78 hip that may be typical of the divergence of duplicate genes as one or both duplicates evolve a new f

79 It has been proposed that many of these duplicate genes became indispensable because the ancestr

80 esults indicate that divergent resolution of duplicate genes between lineages acts to reinforce repro

81 he greatest DNA similarity between surviving duplicated genes but also with the highest concentration

82 kelihood of pseudogenization than completely duplicated genes, but no single factor significantly con

83 Maintaining a duplicated gene by selection for the original function w

84 lso know that functional differences between duplicate genes can originate in several different ways,

85 ese findings evidence that in organisms with duplicated genes, cells can orchestrate the assemblage o

86 found, decreases rapidly with the number of duplicated genes, complicating the application of such a

87 lack any identifiable genes or contain only duplicate gene copies.

88 ence of large syntenic regions consisting of duplicated gene copies implies that small-scale duplicat

89 The two duplicated gene copies, y1 and y2 are separated by a 9.0

90 process, mutations in three or more tandemly duplicated genes could be generated.

91 rules govern the preservation or loss of the duplicated genes created by WGD?

92 For pairs of duplicated genes, divergence in body methylation levels

93 he molecular basis of genetic redundancy and duplicate gene diversification at the level of a specifi

94 tive selection in humans has largely ignored duplicated genes due to complications in orthology assig

95 s to examine the functional bias of retained duplicate genes during vascular plant evolution.

96 l mechanism for functional specialization of duplicated genes during evolution.

97 olving deeply conserved clusters of tandemly duplicated genes (e.g., Hox genes and histones).

98 l coalescent process, for the case where the duplicate gene either has fixed recently in the populati

99 Preferential retention of duplicated genes encoding long complex proteins and thei

100 yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins.

101 Duplicated genes escape gene loss by conferring a dosage

102 function, providing intriguing insights into duplicate gene evolution as well as sunflower domesticat

103 , such as DNA methylation, may contribute to duplicate gene evolution by facilitating tissue-specific

104 owever, the role of epigenetic divergence on duplicate gene evolution remains little understood.

105 d rapidly, and illustrates multiple modes of duplicate gene evolution.

106 interaction between genome and epigenome, on duplicate gene evolution.

107 n plays critical roles in several aspects of duplicate gene evolution.

108 g that local chromatin constraints influence duplicated gene evolution.

109 How these duplicated genes evolve and acquire the ability to speci

110 Following WGD, many of these duplicated genes evolved separate functions through subf

111 massive tandem array containing hundreds of duplicated genes expressed in testes.

112 sults indicate a significant partitioning of duplicate gene expression at the protein level, but an a

113 ome-wide gene-body CG methylation (BCGM) and duplicate gene expression between a rice mutant null for

114 Comparisons of duplicate gene expression patterns across a wide range o

115 s, indicating that significant alteration in duplicated gene expression is fairly frequent even at th

116 Here, we survey duplicate gene families and identify converted tracts in

117 model for coordinate regulation of tandemly duplicated gene families that are commonly found in high

118 d content of specific paralogs within highly duplicated gene families.

119 kinase kinase and is a member of a tandemly duplicated gene family with MEKK2 and MEKK3.

120 or further understanding factors controlling duplicate gene fate.

121 ce may represent extremes in the spectrum of duplicated gene fates.

122 se three possible paths for the evolution of duplicated genes following WGD.

123 s and 'unlocks' many previously inaccessible duplicated genes for association with human traits.

124 have analyzed Cyp12d1 and Cyp12d3, a pair of duplicated genes found in the sequenced Drosophila genom

125 owed by sequential insertions of segmentally duplicated gene fragments, with final exonization of its

126 noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy.

127 Duplicate genes from the whole-genome duplication (WGD)

128 enome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus

129 In this study, we analyzed duplicated genes from three WGD events in the Arabidopsi

130 s of gene expression microarrays showed that duplicate genes generally had higher levels of expressio

131 xpression patterns of 286 Arabidopsis lyrata duplicated gene groups and compared them with the respec

132 Particularly in plants, a high abundance of duplicate genes has been maintained for significantly lo

133 Gene conversion between duplicated genes has been implicated in homogenization o

134 Historically, duplicate genes have been regarded as a major source of

135 the vertebrate lineage, a high proportion of duplicate genes have been retained after whole genome du

136 a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of dupl

137 We found that duplicate genes have more similar sequences than expecte

138 Although most of the duplicate genes have since been deleted, many remain, an

139 Partially duplicated genes have a higher likelihood of pseudogeniz

140 t at least 5.5% and 4.1% of rice and sorghum duplicated genes have been affected by nonreciprocal rec

141 revealed that only a small proportion of the duplicated genes have been neo-functionalized or non-fun

142 0 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome.

143 ible for chromosomal rearrangements and some duplicated genes have overlapping processes.

144 se involved in signal transduction, and that duplicated genes have specialized, as evidenced by diffe

145 ever, we also present evidence that recently duplicated genes have variable probability of locus fixa

146 neofunctionalization and pseudogenization of duplicated genes, have all played a role in the dynamic

147 genome reduction appear to have occurred via duplicated gene (homeolog) loss in divergent species fol

148 valence of these events, the extent to which duplicated genes (homeolog gene pairs) functionally dive

149 d long-term alterations in the expression of duplicate genes ("homeologs").

150 chromosome shifts in expression bias between duplicated genes (homoeologs), and reduces transcription

151 d-like state, through downsizing and loss of duplicated genes (homoeologues), but relatively little i

152 ction, stipulates a higher retention rate of duplicate genes in a small population than in a large on

153 We examined the evolution of expression of duplicate genes in Arabidopsis thaliana, by analyzing 51

154 stigated the evolutionary processes of young duplicate genes in Arabidopsis.

155 d tempo of expression divergence between WGD duplicate genes in closely related species and recurrent

156 mate the exposed fitness contribution of WGD duplicate genes in metabolism and bound the importance o

157 The data suggest an important role of WGD duplicate genes in modulating diverse and novel gene exp

158 Duplicate genes in mouse are widely thought to have func

159 nto the dynamic retention processes of young duplicate genes in plant genomes.

160 te genes have contributed to an abundance of duplicate genes in plant genomes.

161 iderably more retentions and fewer losses of duplicate genes in the mouse genome than in the human ge

162 In contrast, two other duplicate genes in the region, CG33221 and GP-CG32779, a

163 We analyzed the surviving WGD-produced duplicate genes in this network, finding evidence that t

164 I observed one duplicated gene in the D. pseudoobscura genome that appe

165 cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign the

166 applications, such as the identification of duplicated genes in fragmented assemblies, although refi

167 enes suggests an analogous regulation of RNA-duplicated genes in plants and animals.

168 that govern the divergence and retention of duplicated genes in polyploids are poorly understood.

169 The expression levels of duplicated genes in polyploids can show deviation from p

170 the highly conserved sequences on the three duplicated genes in primates have been achieved essentia

171 gements and higher frequency of retention of duplicated genes in soybean than in maize.

172 evolutionary fates of a set of four recently duplicated genes in soybean: FT2a, FT2b, FT2c and FT2d t

173 ined the mechanisms responsible for recently duplicated genes in the D. pseudoobscura genome, and I o

174 amined the evolutionary dynamics of recently duplicated genes in the Drosophila pseudoobscura genome

175 egulatory complexity, is needed to stabilize duplicated genes in the genome.

176 hole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus tricho

177 y the cause of the variation, we analyzed of duplicated genes in yeast that originate from a whole ge

178 s, and therefore paralogs (proteins coded by duplicate genes), in multicellular versus unicellular or

179 tages may be conferred by the maintenance of duplicate genes, including environmental adaptation resu

180 table system for testing the hypothesis that duplicate genes increase expression diversity and regula

181 t was recently proposed that the fixation of duplicate genes is frequently driven by positive selecti

182 extent of functional differentiation between duplicate genes is reflected in the difference in evolut

183 m of duplication indirectly affect whether a duplicated gene is retained or pseudogenized.

184 ion in spatiotemporal expression between the duplicated genes is more likely to be the outcome of neu

185 ic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene

186 er polyploid formation, retention or loss of duplicated genes is not random.

187 ary process leading to the fixation of newly duplicated genes is not well understood.

188 The fate of duplicated genes is poorly understood, both functionally

189 The functional divergence of duplicated genes is thought to play an important role in

190 ired (Upd) family, encoded by three tandemly duplicated genes, is the only class of ligands associate

191 For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnolo

192 Many duplicated genes lack signatures of either retroposition

193 nd under models of molecular evolution where duplicated genes lose duplicated expression patterns in

194 The evolutionary mechanisms underlying duplicate gene maintenance and divergence remain highly

195 eories predict functional divergence between duplicate genes, many old duplicates still maintain a hi

196 Eighty percent of the BAC clones containing duplicate genes mapped to a single chromosomal location,

197 These clusters of duplicate genes may help explain the evolutionary origin

198 Contrary to classical predictions that duplicated genes may be relatively free to acquire uniqu

199 plication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retent

200 that a transcript, derived from a rearranged duplicated gene, must have to give rise to functional tR

201 ppreciated mechanism for the preservation of duplicate genes, namely preservation to limit expression

202 urther investigate whether and how these new duplicate genes (NDGs) play a functional role in the evo

203 In Drosophila, duplicated genes near inversion breakpoints can arise vi

204 ssess factors related to the preservation of duplicate genes of both types.

205 trate that adaptive evolutionary change in a duplicated gene of the anthocyanin biosynthetic pathway

206 The functional divergence of duplicate genes (ohnologues) retained from whole genome

207 n in closely spaced repeats, often result in duplicated genes or pseudogenes, and affect highly studi

208 nalization is the process by which a pair of duplicated genes, or paralogs, experiences a reduction o

209 pt levels of Plp1 and four of the five other duplicated genes over wild-type levels in the brain begi

210 We discover that simultaneously deleting a duplicate gene pair in S. cerevisiae reduces fitness sig

211 After duplication, one copy of each duplicate gene pair tends to be lost (fractionate).

212 e for the majority of total expression for a duplicate gene pair.

213 ancy has been selectively maintained in this duplicate gene pair.

214 ated evolution occurred to one member of the duplicated gene pair.

215 Remarkably, many duplicate gene pairs exhibit consistent division of DNA

216 Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes du

217 divergent tissues: For the majority (73%) of duplicate gene pairs, one partner is always hypermethyla

218 gene expression microarrays and 2022 recent duplicate gene pairs.

219 we survey tissue-specific expression of 144 duplicated gene pairs derived from different parental sp

220 Due to recent genome duplication, duplicated gene pairs have been identified for all genes

221 re binding sites and network connectivity in duplicated gene pairs in Arabidopsis (Arabidopsis thalia

222 ith antiquity of duplication: 24.1% of alpha-duplicated gene pairs in Arabidopsis remain in dosage ba

223 We found that duplicated gene pairs vary greatly in their cis-regulato

224 functional separation of autosomal/X-linked duplicated gene pairs.

225 dundancy, which is frequently observed among duplicated genes (paralogs) with overlapping functions.

226 shots of different evolutionary stages, with duplicated genes preceding recombinatorial events genera

227 We hypothesize that duplicate gene preservation in Populus is driven by a co

228 uent polyploidization and a higher degree of duplicate gene preservation than other paleopolyploids,

229 ities (low sequence divergence between paleo-duplicated genes) preserved in parallel for millions of

230 number of alternatively spliced transcripts duplicate genes produce.

231 Duplicated genes produce genetic variation that can infl

232 are frequent among flowering plants, and the duplicate genes produced via such events contribute sign

233 We also show that these duplicate gene products have qualitatively different pro

234 rgence of sequence and expression pattern of duplicated genes provides a means for genetic innovation

235 PTM3 (Populus tremuloides MADS-box 3), and a duplicate gene PTM4, are related to the SEPALLATA1-and 2

236 etween the expression patterns of ostensibly duplicated genes raise the possibility that subtle diffe

237 ctional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemi

238 Duplicate genes related to environmental stresses tended

239 However, the evolutionary fate of duplicated genes remains largely unresolved.

240 subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant ge

241 urther analyses suggest that this paucity of duplicated genes results from operon organization hinder

242 as been invoked to explain these patterns of duplicate gene retention and loss.

243 The evolutionary mechanisms leading to duplicate gene retention are well understood, but the lo

244 The likelihood of duplicate gene retention following polyploidy varies by

245 fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguis

246 Levels of duplicate-gene retention from the recent WGD differ by >

247 However, the large number of duplicated gene sequences in the human genome implies th

248 ion approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-

249 bsence of phenotypes in mice deficient for a duplicate gene should not be automatically attributed to

250 gous mutations in human SMN1 Expression of a duplicate gene (SMN2) primarily results in skipping of e

251 r neurons 1 (SMN1) gene deletions, leaving a duplicate gene, SMN2, as the sole source of SMN protein.

252 al without the presence of a quasi-identical duplicated gene, SMN2, specific to humans.

253 sms, but other features of these ambiguously duplicated genes suggest that most were generated via re

254 ndem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvul

255 y true of only one RPL paralog of apparently duplicate genes, suggesting functional specialization be

256 Furthermore, duplicate genes tend to be initially expressed in pollen

257 Compared with single-copy genes, duplicate genes tended to contain TATA boxes and less DN

258 expression profile becomes partitioned among duplicated genes (termed homoeologs).

259 hii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its ch

260 an efficient method for making mutations in duplicate genes that are otherwise difficult to study du

261 Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-

262 The proportion of the progenitors' duplicate genes that were nonadditively expressed in the

263 y correlates with the copy number of SMN2, a duplicated gene that is nearly identical to SMN1.

264 The analysis found nine duplicated genes that are significantly associated with

265 Plant genomes contain large numbers of duplicated genes that contribute to the evolution of new

266 sis thaliana) and categorized them either as duplicated genes that have all introns lost or as duplic

267 cated genes that have all introns lost or as duplicated genes that have at least lost one and retaine

268 We also find that newly duplicated genes that have been transposed to new chromo

269 px2 genes of maize are a singular example of duplicated genes that have diverged by deletion and crea

270 Most duplicated genes that have survived from the most recent

271 his article, I consider families of tandemly duplicated genes that show 'microfunctionalization' - ge

272 We identified a group of alpha-duplicated genes that show higher than average single-nu

273 e detected accelerated sequence evolution in duplicated genes that transposed when compared to the pa

274 of the 78 ribosomal proteins are encoded by duplicated genes that, in most cases, encode identical o

275 ry interval of synonymous divergence between duplicate genes, the number of gene retentions in mouse

276 ses can result in the long-term retention of duplicate genes, their relative contributions in nature

277 ect other aspects of plant metabolism; these duplicated genes then diverge from each other over time.

278 subfunctionalization is common, one expects duplicate genes to diverge in expression; recent microar

279 To compare the contribution of chimeric and duplicate genes to genome evolution, we measured their p

280 ves rise to dynamical phenotypes that enable duplicate genes to spread in a population.

281 In most cases, for a duplicated gene to contribute to evolutionary novelty it

282 f common antibiotic classes and many sets of duplicated genes to support its saprophytic lifestyle.

283 for rapid and high-throughput genotyping of duplicated genes using molecular inversion probes design

284 ution rates indicated that divergence of the duplicated genes was driven by positive selection.

285 By characterizing the functional fate of duplicate genes we show that duplicated genes rarely div

286 Duplicate genes were almost always found at a similar lo

287 To address the manner in which young duplicate genes were derived primarily from small-scale

288 o be differentially expressed, and multicopy duplicate genes were likely to diverge expression betwee

289 d in collinear blocks, and several blocks of duplicated genes were co-regulated, suggesting some type

290 nal divergence, approximately 92.7% of alpha-duplicated genes were diverged in function from one anot

291 In addition, duplicated genes were often found in collinear blocks, a

292 mportant causes for decelerated evolution of duplicate genes, whereas gene conversion is effective on

293 introns in the same locations in the IR-type duplicate genes, which directly support our hypothesis.

294 le of concerted divergence of simultaneously duplicated genes whose products function in the same com

295 ting a potential preference for retention of duplicate genes with these functions.

296 Because RPS17 is a duplicated gene with 4 copies in a diploid genome, we de

297 rpl23 is the most highly duplicated gene, with portions of this gene duplicated s

298 identified a suite of 47 genes, enriched for duplicated genes, with variants associated with spatial

299 paint a dynamic picture of both chimeras and duplicate genes within the genome and suggest that chime

300 tide polymorphism chromosomal microarray and duplicated genes within the segment where determined by