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1.
Richard P. Meisel 《Journal of molecular evolution》2009,69(1):81-93
Duplicated genes produce genetic variation that can influence the evolution of genomes and phenotypes. In most cases, for
a duplicated gene to contribute to evolutionary novelty it must survive the early stages of divergence from its paralog without
becoming a pseudogene. I examined the evolutionary dynamics of recently duplicated genes in the Drosophila pseudoobscura genome to understand the factors affecting these early stages of evolution. Paralogs located in closer proximity have higher
sequence identity. This suggests that gene conversion occurs more often between duplications in close proximity or that there
is more genetic independence between distant paralogs. Partially duplicated genes have a higher likelihood of pseudogenization
than completely duplicated genes, but no single factor significantly contributes to the selective constraints on a completely
duplicated gene. However, DNA-based duplications and duplications within chromosome arms tend to produce longer duplication
tracts than retroposed and inter-arm duplications, and longer duplication tracts are more likely to contain a completely duplicated
gene. Therefore, the relative position of paralogs and the mechanism of duplication indirectly affect whether a duplicated
gene is retained or pseudogenized.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
2.
In this paper we have analyzed 49 vertebrate gene families that were generated in the early stage of vertebrates and/or shortly
before the origin of vertebrates, each of which consists of three or four member genes. We have dated the first (T1) and second (T2) gene duplications of 26 gene families with 3 member genes. The means of T1 (594 mya) and T2 (488 mya) are largely consistent to a well-cited version of two-round (2R) genome duplication theory. Moreover, in most cases,
the time interval between two successive gene duplications is large enough that the fate of duplicate genes generated by the
first gene duplication was likely to be determined before the second one took place. However, the phylogenetic pattern of
23 gene families with 4 members is complicated; only 5 of them are predicted by 2R model, but 11 families require an additional
gene (or genome) duplication. For the rest (7 families), at least one gene duplication event had occurred before the divergence
between vertebrate and Drosophila, indicating a possible misleading of the 4:1 rule (member gene ratio between vertebrates and invertebrates). Our results show
that Ohno's 2R conjecture is valid as a working hypothesis for providing a most parsimonious explanation. Although for some
gene families, additional gene duplication is needed, the credibility of the third genome duplication (3R) remains to be investigated.
Received: 13 December 1999 / Accepted: 7 April 2000 相似文献
3.
Yongxiang Lin Ying Cheng Jing Jin Xiaolei Jin Haiyang Jiang Hanwei Yan Beijiu Cheng 《PloS one》2014,9(7)
Whole-genome duplication events (polyploidy events) and gene loss events have played important roles in the evolution of legumes. Here we show that the vast majority of Hsf gene duplications resulted from whole genome duplication events rather than tandem duplication, and significant differences in gene retention exist between species. By searching for intraspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found that genome duplications accounted for 42 of 46 Hsf-containing segments in Glycine max, while paired segments were rarely identified in Lotus japonicas, Medicago truncatula and Cajanus cajan. However, by comparing interspecies microsynteny, we determined that the great majority of Hsf-containing segments in Lotus japonicas, Medicago truncatula and Cajanus cajan show extensive conservation with the duplicated regions of Glycine max. These segments formed 17 groups of orthologous segments. These results suggest that these regions shared ancient genome duplication with Hsf genes in Glycine max, but more than half of the copies of these genes were lost. On the other hand, the Glycine max Hsf gene family retained approximately 75% and 84% of duplicated genes produced from the ancient genome duplication and recent Glycine-specific genome duplication, respectively. Continuous purifying selection has played a key role in the maintenance of Hsf genes in Glycine max. Expression analysis of the Hsf genes in Lotus japonicus revealed their putative involvement in multiple tissue-/developmental stages and responses to various abiotic stimuli. This study traces the evolution of Hsf genes in legume species and demonstrates that the rates of gene gain and loss are far from equilibrium in different species. 相似文献
4.
Evolution of Duplicated <Emphasis Type="BoldItalic">reggie</Emphasis> Genes in Zebrafish and Goldfish 总被引:1,自引:0,他引:1
Málaga-Trillo E Laessing U Lang DM Meyer A Stuermer CA 《Journal of molecular evolution》2002,54(2):235-245
Invertebrates, tetrapod vertebrates, and fish might be expected to differ in their number of gene copies, possibly due the
occurrence of genome duplication events during animal evolution. Reggie (flotillin) genes code for membrane-associated proteins involved in growth signaling in developing and regenerating axons. Until now,
there appeared to be only two reggie genes in fruitflies, mammals, and fish. The aim of this research was to search for additional copies of reggie genes in fishes, since a genome duplication might have increased the gene copy number in this group. We report the presence
of up to four distinct reggie genes (two reggie-1 and two reggie-2 genes) in the genomes of zebrafish and goldfish. Phylogenetic analyses show that the zebrafish and goldfish sequence pairs
are orthologous, and that the additional copies could have arisen through a genome duplication in a common ancestor of bony
fish. The presence of novel reggie mRNAs in fish embryos indicates that the newly discovered gene copies are transcribed and possibly expressed in the developing
and regenerating nervous system. The intron/exon boundaries of the new fish genes characterized here correspond with those
of human genes, both in location and phase. An evolutionary scenario for the evolution of reggie intron-exon structure, where loss of introns appears to be a distinctive trait in invertebrate reggie genes, is presented.
Received: 24 January 2001 / Accepted: 27 July 2001 相似文献
5.
Birgit Drabent Jae-Sun Kim Werner Albig Eva Prats Luis Cornudella Detlef Doenecke 《Journal of molecular evolution》1999,49(5):645-655
We isolated five different phage clones containing histone gene clusters with up to five H1 genes per phage clone from a
Mytilus edulis genomic library. Among these H1 genes, nine gene types coding for five different H1 proteins have been identified. All H1
histone genes were located on repetitive restriction fragments with only slightly different sizes. The H1 coding regions show
highly related sequences, suggesting that the multitude of H1 genes has evolved by gene duplication events. Core histone genes
could not be found on these five Mytilus edulis genome fragments.
Received: 28 July 1998 / Accepted: 17 May 1999 相似文献
6.
Jerzy K. Kulski Silvana Gaudieri Annalise Martin Roger L. Dawkins 《Journal of molecular evolution》1999,49(1):84-97
The recent availability of genomic sequence information for the class I region of the MHC has provided an opportunity to
examine the genomic organization of HLA class I (HLAcI) and PERB11/MIC genes with a view to explaining their evolution from
the perspective of extended genomic duplications rather than by simple gene duplications and/or gene conversion events. Analysis
of genomic sequence from two regions of the MHC (the alpha- and beta-blocks) revealed that at least 6 PERB11 and 14 HLAcI
genes, pseudogenes, and gene fragments are contained within extended duplicated segments. Each segment was searched for the
presence of shared (paralogous) retroelements by RepeatMasker in order to use them as markers of evolution, genetic rearrangements,
and evidence of segmental duplications. Shared Alu elements and other retroelements allowed the duplicated segments to be
classified into five distinct groups (A to E) that could be further distilled down to an ancient preduplication segment containing
a HLA and PERB11 gene, an endogenous retrovirus (HERV-16), and distinctive retroelements. The breakpoints within and between
the different HLAcI segments were found mainly within the PERB11 and HLA genes, HERV-16, and other retroelements, suggesting
that the latter have played a major role in duplication and indel events leading to the present organization of PERB11 and
HLAcI genes. On the basis of the features contained within the segments, a coevolutionary model premised on tandem duplication
of single and multipartite genomic segments is proposed. The model is used to explain the origins and genomic organization
of retroelements, HERV-16, DNA transposons, PERB11, and HLAcI genes as distinct segmental combinations within the alpha- and
beta-blocks of the human MHC.
Received: 5 December 1998 / Accepted: 27 January 1999 相似文献
7.
Linh M. Chau Michael A. D. Goodisman 《Evolution; international journal of organic evolution》2017,71(12):2871-2884
Gene duplication is an important evolutionary process thought to facilitate the evolution of phenotypic diversity. We investigated if gene duplication was associated with the evolution of phenotypic differences in a highly social insect, the honeybee Apis mellifera. We hypothesized that the genetic redundancy provided by gene duplication could promote the evolution of social and sexual phenotypes associated with advanced societies. We found a positive correlation between sociality and rate of gene duplications across the Apoidea, indicating that gene duplication may be associated with sociality. We also discovered that genes showing biased expression between A. mellifera alternative phenotypes tended to be found more frequently than expected among duplicated genes than singletons. Moreover, duplicated genes had higher levels of caste‐, sex‐, behavior‐, and tissue‐biased expression compared to singletons, as expected if gene duplication facilitated phenotypic differentiation. We also found that duplicated genes were maintained in the A. mellifera genome through the processes of conservation, neofunctionalization, and specialization, but not subfunctionalization. Overall, we conclude that gene duplication may have facilitated the evolution of social and sexual phenotypes, as well as tissue differentiation. Thus this study further supports the idea that gene duplication allows species to evolve an increased range of phenotypic diversity. 相似文献
8.
Yves Van de Peer John S. Taylor Ingo Braasch Axel Meyer 《Journal of molecular evolution》2001,53(4-5):436-446
The duplication of genes and even complete genomes may be a prerequisite for major evolutionary transitions and the origin
of evolutionary novelties. However, the evolutionary mechanisms of gene evolution and the origin of novel gene functions after
gene duplication have been a subject of many debates. Recently, we compiled 26 groups of orthologous genes, which included
one gene from human, mouse, and chicken, one or two genes from the tetraploid Xenopus and two genes from zebrafish. Comparative analysis and mapping data showed that these pairs of zebrafish genes were probably
produced during a fish-specific genome duplication that occurred between 300 and 450 Mya, before the teleost radiation (Taylor
et al. 2001). As discussed here, many of these retained duplicated genes code for DNA binding proteins. Different models have
been developed to explain the retention of duplicated genes and in particular the subfunctionalization model of Force et al.
(1999) could explain why so many developmental control genes have been retained. Other models are harder to reconcile with
this particular set of duplicated genes. Most genes seem to have been subjected to strong purifying selection, keeping properties
such as charge and polarity the same in both duplicates, although some evidence was found for positive Darwinian selection,
in particular for Hox genes. However, since only the cumulative pattern of nucleotide substitutions can be studied, clear indications of positive
Darwinian selection or neutrality may be hard to find for such anciently duplicated genes. Nevertheless, an increase in evolutionary
rate in about half of the duplicated genes seems to suggest that either positive Darwinian selection has occurred or that
functional constraints have been relaxed at one point in time during functional divergence.
Received: 4 January 2001 / Accepted: 29 March 2001 相似文献
9.
Spliced leader trans-splicing is an mRNA maturation process used by a small set of eukaryotes, including the nematode C. elegans, to cap the downstream genes of operons. We analyzed the frequency of duplication of operonic genes in C. elegans and confirmed that they are duplicated less often in the genome than monocistronic genes. Because operons account for about
15% of the genes in C. elegans, this lower duplication frequency might place a large constraint on the plasticity of the genome. Further analyses suggest
that this paucity of duplicated genes results from operon organization hindering specific types of gene duplication.
[Reviewing Editor: Dr. Yves van de Peer] 相似文献
10.
11.
Calpains, the Ca2+-dependent intracellular proteinases, are involved in the regulation of distinct cellular pathways including signal transduction
and processing, cytoskeleton dynamics, and muscle homeostasis. To investigate the evolutionary origin of diverse calpain subfamilies,
a phylogenetic study was carried out. The topology of the calpain phylogenetic tree has shown that some of the gene duplications
occurred before the divergence of the protostome and deuterostome lineages. Other gene doublings, leading to vertebrate-specific
calpain forms, took place during early chordate evolution and coincided with genome duplications as disclosed by the localization
of calpain genes to paralogous chromosome regions in the human genome. On the basis of the phylogenetic tree, the time of
gene duplications, and the localization of calpain genes, we propose a model of tandem and chromosome duplications for the
evolution of vertebrate-specific calpain forms. The data presented here are consistent with scenarios proposed for the evolution
of other multigene families.
Received: 17 November 1998 / Accepted: 30 April 1999 相似文献
12.
In this paper we analyzed 49 lactate dehydrogenase (LDH) sequences, mostly from vertebrates. The amino acid sequence differences
were found to be larger for a human–killifish pair than a human–lamprey pair. This indicates that some protein sequence convergence
may occur and reduce the sequence differences in distantly related species. We also examined transitions and transversions
separately for several species pairs and found that the transitions tend to be saturated in the distantly related species
pair, while transversions are increasing. We conclude that transversions maintain a conservative rate through the evolutionary
time. Kimura's two-parameter model for multiple-hit correction on transversions only was used to derive a distance measure
and then construct a neighbor-joining (NJ) tree. Three findings were revealed from the NJ tree: (i) the branching order of
the tree is consistent with the common branch pattern of major vertebrates; (ii) Ldh-A and Ldh-B genes were duplicated near the origin of vertebrates; and (iii) Ldh-C and Ldh-A in mammals were produced by an independent gene duplication in early mammalian history. Furthermore, a relative rate test
showed that mammalian Ldh-C evolved more rapidly than mammalian Ldh-A. Under a two-rate model, this duplication event was calibrated to be approximately 247 million years ago (mya), dating back
to the Triassic period. Other gene duplication events were also discovered in Xenopus, the first duplication occurring approximately 60–70 mya in both Ldh-A and Ldh-B, followed by another recent gene duplication event, approximately 20 mya, in Ldh-B.
Received: 5 October 2001 / Accepted: 24 October 2001 相似文献
13.
Background
Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (i.e., the random duplication model). However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (i.e., the tandem duplication model). 相似文献14.
Suga H Koyanagi M Hoshiyama D Ono K Iwabe N Kuma K Miyata T 《Journal of molecular evolution》1999,48(6):646-653
To know whether genes involved in cell–cell communication typical of multicellular animals dramatically increased in concert
with the Cambrian explosion, the rapid evolutionary burst in the major groups of animals, and whether these genes exist in
the sponge lacking cell cohesiveness and coordination typical of eumetazoans, we have carried out cloning of the G-protein
α subunit (Gα) and the protein tyrosine kinase (PTK) cDNAs from Ephydatia fluviatilis (freshwater sponge) and Hydra magnipapillata strain 105 (hydra). We obtained 13 Gα and 20 PTK cDNAs. Generally animal gene families diverged first by gene duplication
(subtype duplication) that gave rise to diverse subtypes with different primary functions, followed by further gene duplication
in the same subtype (isoform duplication) that gave rise to isoform genes with virtually identical function. Phylogenetic
trees of Gα and PTK families including cDNAs from sponge and hydra revealed that most of the present-day subtypes had been
established in the very early evolution of animals before the parazoan–eumetazoan split, the earliest branching among the
extant animal phyla, by extensive subtype duplication: for PTK and Gα families, 23 and 9 subtype duplications were observed
in the early stage before the parazoan–eumetazoan split, respectively, and after that split, only 2 and 1 subtype duplications
were found, respectively. After the separation from arthropods, vertebrates underwent frequent isoform duplications before
the fish–tetrapod split. Furthermore, rapid amino acid changes appear to have occurred in concert with the extensive subtype
duplication and isoform duplication. Thus the pattern of gene diversification during animal evolution might be characterized
by bursts of gene duplication interrupted by considerably long periods of silence, instead of proceeding gradually, and there
might be no direct link between the Cambrian explosion and the extensive gene duplication that generated diverse functions
(subtypes) of these families.
Received: 4 November 1998 / Accepted: 17 November 1998 相似文献
15.
16.
Comparable Rates of Gene Loss and Functional Divergence after Genome Duplications Early in Vertebrate Evolution 总被引:20,自引:3,他引:17 下载免费PDF全文
Duplicated genes are an important source of new protein functions and novel developmental and physiological pathways. Whereas most models for fate of duplicated genes show that they tend to be rapidly lost, models for pathway evolution suggest that many duplicated genes rapidly acquire novel functions. Little empirical evidence is available, however, for the relative rates of gene loss vs. divergence to help resolve these contradictory expectations. Gene families resulting from genome duplications provide an opportunity to address this apparent contradiction. With genome duplication, the number of duplicated genes in a gene family is at most 2(n), where n is the number of duplications. The size of each gene family, e.g., 1, 2, 3, . . . , 2(n), reflects the patterns of gene loss vs. functional divergence after duplication. We focused on gene families in humans and mice that arose from genome duplications in early vertebrate evolution and we analyzed the frequency distribution of gene family size, i.e., the number of families with two, three or four members. All the models that we evaluated showed that duplicated genes are almost as likely to acquire a new and essential function as to be lost through acquisition of mutations that compromise protein function. An explanation for the unexpectedly high rate of functional divergence is that duplication allows genes to accumulate more neutral than disadvantageous mutations, thereby providing more opportunities to acquire diversified functions and pathways. 相似文献
17.
The temporal distribution of gene duplication events in a set of highly conserved human gene families 总被引:13,自引:0,他引:13
Using a data set of protein translations associated with map positions in the human genome, we identified 1520 mapped highly conserved gene families. By comparing sharing of families between genomic windows, we identified 92 potentially duplicated blocks in the human genome containing 422 duplicated members of these families. Using branching order in the phylogenetic trees, we timed gene duplication events in these families relative to the primate-rodent divergence, the amniote-amphibian divergence, and the deuterostome-protostome divergence. The results showed similar patterns of gene duplication times within duplicated blocks and outside duplicated blocks. Both within and outside duplicated blocks, numerous duplications were timed prior to the deuterostome-protostome divergence, whereas others occurred after the amniote-amphibian divergence. Thus, neither gene duplication in general nor duplication of genomic blocks could be attributed entirely to polyploidization early in vertebrate history. The strongest signal in the data was a tendency for intrachromosomal duplications to be more recent than interchromosomal duplications, consistent with a model whereby tandem duplication-whether of single genes or of genomic blocks-may be followed by eventual separation of duplicates due to chromosomal rearrangements. The rate of separation of tandemly duplicated gene pairs onto separated chromosomes in the human lineage was estimated at 1.7 x 10(-9) per gene-pair per year. 相似文献
18.
M. Stodolsky 《Genetics》1974,78(3):809-822
An Hfr13 Delta(proA-lac) deletion recipient, -Delta(proA-lac)-F-purE(+)-, has been utilized in a study of the origins of duplications formed during chromosome fragment integration. Among the Pro(-)Lac(+) transductants, some have duplications spanning the F locus. These transductants are, or segregate, strains with F' episomes carrying genes of the duplication. Some of the duplications include purE(+), a gene which is not coinherited with lac(+) during bacteriophage P1-mediated transduction. Thus recipient genes have been duplicated during recombinant formation. Crossing-over models including replication steps provide a basis for explaining the duplication process. 相似文献
19.
Singhania NA Dyer KD Zhang J Deming MS Bonville CA Domachowske JB Rosenberg HF 《Journal of molecular evolution》1999,49(6):721-728
The two eosinophil ribonucleases, eosinophil-derived neurotoxin (EDN/RNase 2) and eosinophil cationic protein (ECP/RNase
3), are among the most rapidly evolving coding sequences known among primates. The eight mouse genes identified as orthologs
of EDN and ECP form a highly divergent, species-limited cluster. We present here the rat ribonuclease cluster, a group of
eight distinct ribonuclease A superfamily genes that are more closely related to one another than they are to their murine
counterparts. The existence of independent gene clusters suggests that numerous duplications and diversification events have
occurred at these loci recently, sometime after the divergence of these two rodent species (∼10–15 million years ago). Nonsynonymous
substitutions per site (d
N) calculated for the 64 mouse/rat gene pairs indicate that these ribonucleases are incorporating nonsilent mutations at accelerated
rates, and comparisons of nonsynonymous to synonymous substitution (d
N / d
S) suggest that diversity in the mouse ribonuclease cluster is promoted by positive (Darwinian) selection. Although the pressures
promoting similar but clearly independent styles of rapid diversification among these primate and rodent genes remain uncertain,
our recent findings regarding the function of human EDN suggest a role for these ribonucleases in antiviral host defense.
Received: 8 April 1999 / Accepted: 22 June 1999 相似文献