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 ausative factor for functional divergence 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 er investigation of the dynamic evolution of duplicate genes.

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

12 rstanding the mutational processes affecting duplicate genes.

13 evolutionary processes for Arabidopsis young 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 chromosome-internal locus comprising tandem-duplicated genes.

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

19 t conservation is substantially weaker among duplicated genes.

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

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

22 he evolution of specialized enzymes coded by duplicated genes.

23 oduced by immigrants when there are multiple duplicated genes.

24 on fitness of specific substitutions between duplicated genes.

25 liced isoforms and transcripts from recently duplicated genes.

26 in fact, contains seven distinctly evolving duplicated genes.

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

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

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

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

31 ivergence is a previously unreported fate of duplicated genes.

32 are multiple possible evolutionary fates of duplicated genes.

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

34 element evolution and network divergence in duplicated genes.

35 n through the adaptive recruitment of tandem duplicated genes.

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

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

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

39 for the analysis of the expression ratios of duplicate genes across two conditions (e.g., tissues).

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

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

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

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

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

49 with a focus on cis-trans interactions among duplicated genes and alleles in hybrids and allopolyploi

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

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

52 ana) plastid preproteins encoded by recently duplicated genes and show that, within a duplicated prep

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

54 tablish a more complete understanding of how duplicated genes and TEs contribute in concert to chemic

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

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

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

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

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

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

61 to resolve the last gene-rich gaps, improve duplicate gene annotation, and better understand copy-nu

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

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

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

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

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

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

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

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

70 Duplicated genes are a major contributor to genome evolu

71 Duplicated genes are also affected by epigenetic changes

72 ng suggest that evolutionary trajectories of duplicated genes are dictated by combined functional and

73 Most duplicated genes are eliminated, and factors that influe

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

75 Therefore, it may be expected that duplicated genes are less likely to be critical for the

76 xpressed in early spermatocytes, while young duplicated genes are often bimodally expressed.

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

78 Recently duplicated genes are utilized at later stages of placent

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

80 However, it remains unclear how duplicated genes are wired into existing regulatory netw

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

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

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

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

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

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

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

88 In multicellular organisms, duplicated genes can diverge through tissue-specific gen

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

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

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

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

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

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

95 We show that the duplicated gene CYP82C2 has been recruited into the WRKY

96 n different plants, we constructed the Plant Duplicate Gene Database.

97 The number of WGD-derived duplicate genes decreases exponentially with increasing

98 Duplicate genes descending from polyploidy augmented the

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

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

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

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

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

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

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

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

107 Duplicated genes escape gene loss by conferring a dosage

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

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

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

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

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

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

114 g that local chromatin constraints influence duplicated gene evolution.

115 A primary way that duplicate genes evolve new functions is by altering thei

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

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

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

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

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

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

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

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

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

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

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

127 or further understanding factors controlling duplicate gene fate.

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

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

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

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

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

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

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

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

136 Comparing the expression patterns of duplicate genes gives clues as to whether any of these e

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

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

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

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

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

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

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

144 Partially duplicated genes have a higher likelihood of pseudogeniz

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

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

147 0 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome.

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

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

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

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

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

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

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

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

156 Duplicate genes (i.e., homeologs, in the case of a whole

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

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

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

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

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

162 Duplicate genes in mouse are widely thought to have func

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

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

165 nd phenotypes resulting from the knockout of duplicate genes in the mouse.

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

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

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

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

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

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

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

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

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

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

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

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

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

179 synthetic enzymes are present in clusters of duplicated genes in the M. truncatula genome.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

194 Many duplicated genes lack signatures of either retroposition

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

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

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

198 While duplicate genes may retain some functional redundancy, i

199 A duplicated gene may have a similar function to its ances

200 These duplicated genes may have been free to diverge in functi

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

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

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

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

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

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

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

208 Arabidopsis, CGL20 is encoded by segmentally duplicated genes of high sequence similarity (AtCGL20A a

209 We found that duplicated genes often accumulate more transcripts.

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

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

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

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

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

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

216 red the developmental expression patterns of duplicate gene pairs and the relationship between develo

217 We found that duplicate gene pairs comprised of two essential genes te

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

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

220 different stages of development, compared to duplicate gene pairs with at least one non-essential mem

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

222 gene expression microarrays and 2022 recent duplicate gene pairs.

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

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

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

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

227 To provide a platform for accessing duplicated gene pairs in different plants, we constructe

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

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

230 g on methods that allow for the inclusion of duplicated genes (paralogs).

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

232 Duplicated genes preferentially retained include photosy

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

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

235 number of alternatively spliced transcripts duplicate genes produce.

236 Duplicated genes produce genetic variation that can infl

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

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

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

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

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

242 Duplicate genes related to environmental stresses tended

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

244 affect functional features, and overlap more duplicated genes retained from an ancestral salmonid aut

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

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

247 The likelihood of duplicate gene retention following polyploidy varies by

248 following whole-genome duplication and that duplicate gene retention patterns are shaped by selectio

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

250 xa, and unravel common principles underlying duplicate gene retention.

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

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

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

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

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

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

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

258 Among the possible fates of duplicated genes, subfunctionalization refers to duplica

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

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

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

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

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

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

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

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

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

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

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

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

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

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

273 Most duplicated genes that have survived from the most recent

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

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

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

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

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

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 usive functional evidence linking new and/or duplicated genes to NCC evolution is lacking.

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

284 Although duplicated genes undoubtedly shape each other's evolutio

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

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

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

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

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

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

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

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

293 d pipeline (SBP) is most suited for recently duplicated genes, whereas the protein-family-based metho

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

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

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