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Mao B, Yin R, Li X, Cui S, Zhang H, Zhao J, Chen W. Comparative Genomic Analysis of Lactiplantibacillus plantarum Isolated from Different Niches. Genes (Basel) 2021; 12:genes12020241. [PMID: 33567604 PMCID: PMC7914981 DOI: 10.3390/genes12020241] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 11/16/2022] Open
Abstract
Lactiplantibacillus plantarum can adapt to a variety of niches and is widely distributed in many sources. We used comparative genomics to explore the differences in the genome and in the physiological characteristics of L. plantarum isolated from pickles, fermented sauce, and human feces. The relationships between genotypes and phenotypes were analyzed to address the effects of isolation source on the genetic variation of L. plantarum. The comparative genomic results indicate that the numbers of unique genes in the different strains were niche-dependent. L. plantarum isolated from fecal sources generally had more strain-specific genes than L. plantarum isolated from pickles. The phylogenetic tree and average nucleotide identity (ANI) results indicate that L. plantarum in pickles and fermented sauce clustered independently, whereas the fecal L. plantarum was distributed more uniformly in the phylogenetic tree. The pan-genome curve indicated that the L. plantarum exhibited high genomic diversity. Based on the analysis of the carbohydrate active enzyme and carbohydrate-use abilities, we found that L. plantarum strains isolated from different sources exhibited different expression of the Glycoside Hydrolases (GH) and Glycosyl Transferases (GT) families and that the expression patterns of carbohydrate active enzymes were consistent with the evolution relationships of the strains. L. plantarum strains exhibited niche-specific characteristicsand the results provided better understating on genetics of this species.
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Affiliation(s)
- Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ruimin Yin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaoshu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-510-8591-2155
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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Forsdyke DR. Homostability. Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Vlasschaert C, Xia X, Coulombe J, Gray DA. Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11. BMC Evol Biol 2015; 15:230. [PMID: 26503449 PMCID: PMC4624187 DOI: 10.1186/s12862-015-0511-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/17/2015] [Indexed: 12/19/2022] Open
Abstract
Background USP4, USP15 and USP11 are paralogous deubiquitinating enzymes as evidenced by structural organization and sequence similarity. Based on known interactions and substrates it would appear that they have partially redundant roles in pathways vital to cell proliferation, development and innate immunity, and elevated expression of all three has been reported in various human malignancies. The nature and order of duplication events that gave rise to these extant genes has not been determined, nor has their functional redundancy been established experimentally at the organismal level. Methods We have employed phylogenetic and syntenic reconstruction methods to determine the chronology of the duplication events that generated the three paralogs and have performed genetic crosses to evaluate redundancy in mice. Results Our analyses indicate that USP4 and USP15 arose from whole genome duplication prior to the emergence of jawed vertebrates. Despite having lower sequence identity USP11 was generated later in vertebrate evolution by small-scale duplication of the USP4-encoding region. While USP11 was subsequently lost in many vertebrate species, all available genomes retain a functional copy of either USP4 or USP15, and through genetic crosses of mice with inactivating mutations we have confirmed that viability is contingent on a functional copy of USP4 or USP15. Loss of ubiquitin-exchange regulation, constitutive skipping of the seventh exon and neural-specific expression patterns are derived states of USP11. Post-translational modification sites differ between USP4, USP15 and USP11 throughout evolution. Conclusions In isolation sequence alignments can generate erroneous USP gene phylogenies. Through a combination of methodologies the gene duplication events that gave rise to USP4, USP15, and USP11 have been established. Although it operates in the same molecular pathways as the other USPs, the rapid divergence of the more recently generated USP11 enzyme precludes its functional interchangeability with USP4 and USP15. Given their multiplicity of substrates the emergence (and in some cases subsequent loss) of these USP paralogs would be expected to alter the dynamics of the networks in which they are embedded. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0511-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caitlyn Vlasschaert
- Department of Biology, University of Ottawa, Ottawa, Canada. .,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada. .,The Ottawa Hospital Research Institute, Ottawa, Canada.
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, Canada. .,Ottawa Institute of Systems Biology, Ottawa, Canada.
| | | | - Douglas A Gray
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada. .,The Ottawa Hospital Research Institute, Ottawa, Canada. .,Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.
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Huang J, Pang C, Fan S, Song M, Yu J, Wei H, Ma Q, Li L, Zhang C, Yu S. Genome-wide analysis of the family 1 glycosyltransferases in cotton. Mol Genet Genomics 2015; 290:1805-18. [PMID: 25851236 DOI: 10.1007/s00438-015-1040-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 03/27/2015] [Indexed: 12/25/2022]
Abstract
Family 1 GT, designated as UGT, is the largest and most functionally important multigene family in the plant kingdom. In this study, we carried out a genome-wide identification, analysis, and comparison of 142, 146, and 196 putative UGTs from Gossypium raimondii, Gossypium arboreum, and Gossypium hirsutum, respectively. All members present the 44 amino-acid conserved consensus sequence termed the plant secondary product glycosyltransferase motif. According to the phylogenetic relationship among the cotton UGT proteins and those from other species, GrUGTs and GaUGTs could be classified into 16 major phylogenetic groups (A-P), whereas GhUGTs are classified into 15 major phylogenetic groups with a lack of group C. All cotton UGTs are dispersed throughout the chromosomes and are displayed in clusters with the same open reading frame orientation. The expansion of them appears to result from genome duplication and rearrangement. Two conserved introns, A and B, are detected in most of the intron-containing-UGTs in G. raimondii and G. arboreum, whereas only intron A is detected in the intron-containing-UGTs in G. hirsutum. Furthermore, expression patterns of the UGT genes in G. hirsutum wild type and its near isogenic fuzzless-lintless mutant at the stage of fiber initiation were analyzed using the RNA-seq data. Overall, this study not only deepens our understanding of the structure, phylogeny, evolution, and expression of cotton UGT genes, but also provides a solid foundation for further cloning and functional studies of the UGT family genes.
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Affiliation(s)
- Juan Huang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China.
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China
| | - Qifeng Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China
| | - Libei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China
| | - Chi Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, People's Republic of China.
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Zou Y, Su Z, Huang W, Gu X. Histone modification pattern evolution after yeast gene duplication. BMC Evol Biol 2012; 12:111. [PMID: 22776110 PMCID: PMC3495647 DOI: 10.1186/1471-2148-12-111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 07/09/2012] [Indexed: 12/17/2022] Open
Abstract
Background Gene duplication and subsequent functional divergence especially expression divergence have been widely considered as main sources for evolutionary innovations. Many studies evidenced that genetic regulatory network evolved rapidly shortly after gene duplication, thus leading to accelerated expression divergence and diversification. However, little is known whether epigenetic factors have mediated the evolution of expression regulation since gene duplication. In this study, we conducted detailed analyses on yeast histone modification (HM), the major epigenetics type in this organism, as well as other available functional genomics data to address this issue. Results Duplicate genes, on average, share more common HM-code patterns than random singleton pairs in their promoters and open reading frames (ORF). Though HM-code divergence between duplicates in both promoter and ORF regions increase with their sequence divergence, the HM-code in ORF region evolves slower than that in promoter region, probably owing to the functional constraints imposed on protein sequences. After excluding the confounding effect of sequence divergence (or evolutionary time), we found the evidence supporting the notion that in yeast, the HM-code may co-evolve with cis- and trans-regulatory factors. Moreover, we observed that deletion of some yeast HM-related enzymes increases the expression divergence between duplicate genes, yet the effect is lower than the case of transcription factor (TF) deletion or environmental stresses. Conclusions Our analyses demonstrate that after gene duplication, yeast histone modification profile between duplicates diverged with evolutionary time, similar to genetic regulatory elements. Moreover, we found the evidence of the co-evolution between genetic and epigenetic elements since gene duplication, together contributing to the expression divergence between duplicate genes.
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Affiliation(s)
- Yangyun Zou
- Ministry of Education Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
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Ezawa K, Ikeo K, Gojobori T, Saitou N. Evolutionary patterns of recently emerged animal duplogs. Genome Biol Evol 2011; 3:1119-35. [PMID: 21859807 PMCID: PMC3194840 DOI: 10.1093/gbe/evr074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Duplogs, or intraspecies paralogs, constitute the important portion of eukaryote genomes and serve as a major source of functional innovation. We conducted detailed analyses of recently emerged animal duplogs. Genome data of three vertebrate species (Homo sapiens, Mus musculus, and Danio rerio), Caenorhabditis elegans, and two Drosophila species (Drosophila melanogaster and D. pseudoobscura) were used. Duplication events were divided into six age-groups according to the synonymous distance (dS) up to 0.6. Duplogs were classified into four equal-sized classes on physical distances and into three classes on relative orientations. We observed the following shared characteristics among intrachromosomal multiexon duplogs: 1) inverted duplogs account for 20-50%, and about a half of the physically most distant 25%; 2) except for C. elegans, the composition of physical distances, that of relative orientations, and the proportion of inverted duplogs in each physical distance category are more or less uniform; 3) except for C. elegans, the characteristics of the youngest (dS < 0.01) duplogs are similar to the overall characteristics of the entire set. These results suggest that intrachromosomal duplogs with fairly long physical distances were generated at once, rather than resulting from tandem duplications and subsequent genomic rearrangements. This is different from the three well-known modes of gene duplication: tandem duplication, retrotransposition, and genome duplication. We termed this new mode as "drift" duplication. The drift duplication has been producing duplicate copies at paces comparable with tandem duplications since the common ancestor of vertebrates, and it may have already operated in the common ancestor of bilateral animals.
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Affiliation(s)
- Kiyoshi Ezawa
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
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Chang AYF, Liao BY. DNA methylation rebalances gene dosage after mammalian gene duplications. Mol Biol Evol 2011; 29:133-44. [PMID: 21821837 DOI: 10.1093/molbev/msr174] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although gene duplication plays a major role in organismal evolution, it may also lead to gene dosage imbalance, thereby having an immediate adverse effect on an organism's fitness. Investigating the evolution of the expression patterns of genes that duplicated after the divergence of rodents and primates, we confirm that adaptive evolution has been involved in dosage rebalance after gene duplication. To understand mechanisms underlying this process, we examined 1) microRNA (miRNA)-mediated gene regulation, 2) cis-regulatory sequence modifications, and 3) DNA methylation. Neither miRNA-mediated regulation nor cis-regulatory changes was found to be associated with expression reduction of duplicate genes. By contrast, duplicate genes, especially lowly expressed copies, were heavily methylated in the upstream region. However, for duplicate genes encoding proteins that are members of macromolecular complexes, heavy methylation in the genic region was not consistently observed. This result held after controlling potential confounding factors, such as enrichment in functional categories. Our results suggest that during mammalian evolution, DNA methylation plays a dominant role in dosage rebalance after gene duplication by inhibiting transcription initiation of duplicate genes.
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Affiliation(s)
- Andrew Ying-Fei Chang
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
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Adaptive Evolution Hotspots at the GC-Extremes of the Human Genome: Evidence for Two Functionally Distinct Pathways of Positive Selection. Adv Bioinformatics 2010:856825. [PMID: 20454629 PMCID: PMC2862947 DOI: 10.1155/2010/856825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 12/31/2009] [Accepted: 02/10/2010] [Indexed: 11/21/2022] Open
Abstract
We recently reported that the human genome is ‘‘splitting” into two gene subgroups characterised by polarised GC content (Tang et al, 2007), and that such evolutionary change may be accelerated by programmed genetic instability (Zhao et al, 2008). Here we extend this work by mapping the presence of two separate high-evolutionary-rate (Ka/Ks) hotspots in the human genome—one characterized by low GC content, high intron length, and low gene expression, and the other by high GC content, high exon number, and high gene expression. This finding suggests that at least two different mechanisms mediate adaptive genetic evolution in higher organisms: (1) intron lengthening and reduced repair in hypermethylated lowly-transcribed genes, and (2) duplication and/or insertion events affecting highly-transcribed genes, creating low-essentiality satellite daughter genes in nearby regions of active chromatin. Since the latter mechanism is expected to be far more efficient than the former in generating variant genes that increase fitnesss, these results also provide a potential explanation for the controversial value of sequence analysis in defining positively selected genes.
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Comparison of pig, sheep and chicken SCD5 homologs: Evidence for an early gene duplication event. Comp Biochem Physiol B Biochem Mol Biol 2008; 150:440-6. [PMID: 18556229 DOI: 10.1016/j.cbpb.2008.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 05/02/2008] [Accepted: 05/02/2008] [Indexed: 11/21/2022]
Abstract
Stearoyl-CoA desaturase (SCD) catalyzes the desaturation of saturated fatty acyl-CoA substrates at the delta-9 position. Multiple SCD isoforms are well characterized in rodents, especially in mice, where four isoforms have been described. In humans and cows, two SCD isoforms have been described: SCD1, which is a homolog of murine SCD1, and SCD5, which appears to be a distinct SCD gene rather than an ortholog of any of the four murine isoforms. In this paper, we describe for the first time SCD5 homologs in sheep, pigs and chickens. The SCD5 nucleotide sequences have notably higher GC content than SCD1 sequences, and the predicted protein sequences lack N-terminal PEST sequences typically found in SCD1 proteins. Similar to humans and bovines, the mRNA expression of sheep and pig SCD5 is greatest in the brain, and the mRNA expression of chicken SCD5 is greatest in the pancreas and brain. In contrast, SCD1 expression was found to be highest in adipose tissue in pigs and sheep, and liver in the chicken. This is the first report of an SCD5 homolog in a non-mammalian species, and suggests that SCD5 may be the result of an early gene duplication event that occurred before the divergence of mammals.
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Clément Y, Tavares R, Marais GAB. Does lack of recombination enhance asymmetric evolution among duplicate genes? Insights from the Drosophila melanogaster genome. Gene 2006; 385:89-95. [PMID: 17049187 DOI: 10.1016/j.gene.2006.05.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 05/09/2006] [Accepted: 05/19/2006] [Indexed: 10/24/2022]
Abstract
Gene duplication has different outcomes: pseudogenization (death of one of the two copies), gene amplification (both copies remain the same), sub-functionalization (both copies are required to perform the ancestral function) and neo-functionalization (one copy acquires a new function). Asymmetric evolution (one copy evolves faster than the other) is usually seen as a signature of neo-functionalization. However, it has been proposed that sub-functionalization could also generate asymmetric evolution among duplicate genes when they experience different local recombination rates. Indeed, the low recombination copy is expected to evolve faster because of Hill-Robertson effects. Here we tested this idea with about 100 pairs of young duplicates from the Drosophila melanogaster genome. Looking only at young duplicates allowed us to compare recombination rates and evolutionary rates on a similar time-scale contrary to previous work. We found that dispersed pairs tend to evolve more asymmetrically than tandem ones. Among dispersed copies, the low recombination copy tends to be the fast-evolving one. We also tested the possibility that all this was explained by a confounding factor (expression level) but found no evidence for it. In conclusion, our results do support the idea that asymmetric evolution among duplicates is enhanced by restricted recombination. However, further work is needed to clearly distinguish between sub-functionalization and neo-functionalization for the asymmetrically-evolving duplicate pairs that we found.
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Affiliation(s)
- Yves Clément
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS, Univ. Lyon 1, Villeurbanne Cedex, France
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Rodin SN, Parkhomchuk DV, Rodin AS, Holmquist GP, Riggs AD. Repositioning-dependent fate of duplicate genes. DNA Cell Biol 2006; 24:529-42. [PMID: 16153154 DOI: 10.1089/dna.2005.24.529] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Gene duplication is the main source of evolutionary novelties. However, the problem with duplicates is that the purifying selection overlooks deleterious mutations in the redundant sequence, which therefore, instead of gaining a new function, often degrades into a functionless pseudogene. This risk of functional loss instead of gain is much higher for small populations of higher organisms with a slow and complex development. We propose that it is the epigenetic tissue/stage-complementary silencing of duplicates that makes them exposable to the purifying selection, thus saving them from pseudogenization and opening the way towards new function(s). Our genome-wide analyses of gene duplicates in several eukaryotic species combined with the phylogenetic comparison of vertebrate alpha- and beta-globin gene clusters strongly support this epigenetic complementation (EC) model. The distinctive condition for a new duplicate to survive by the EC mechanism seems to be its repositioning to an ectopic site, which is accompanied by changes in the rate and direction of mutagenesis. The most distinguished in this respect is the human genome. In this review, we extend and discuss the data on the EC- and repositioning-dependent fate of gene duplicates with the special emphasis on the problem of detecting brief postduplication period of adaptive evolution driven by positive selection. Accordingly, we propose a new CpG-focused measure of selection that is insensitive to translocation-caused biases in mutagenesis.
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Affiliation(s)
- Sergei N Rodin
- Theoretical Biology Department, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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Rayko E, Jabbari K, Bernardi G. The evolution of introns in human duplicated genes. Gene 2006; 365:41-7. [PMID: 16356663 DOI: 10.1016/j.gene.2005.09.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 07/07/2005] [Accepted: 09/07/2005] [Indexed: 11/17/2022]
Abstract
In previous work [Jabbari, K., Rayko, E., Bernardi, G., 2003. The major shifts of human duplicated genes. Gene 317, 203-208], we investigated the fate of ancient duplicated genes after the compositional transitions that occurred between the genomes of cold- and warm-blooded vertebrates. We found that the majority of duplicated copies were transposed to the "ancestral genome core", the gene-dense genome compartment that underwent a GC enrichment at the compositional transitions. Here, we studied the consequences of the events just outlined on the introns of duplicated genes. We found that, while intron number was highly conserved, total intron size (the sum of intron sizes within any given gene) was smaller in the GC-rich copies compared to the GC-poor copies, especially in dispersed copies (i.e., copies located on different chromosomes or chromosome arms). GC-rich copies also showed higher densities of CpG islands and Alus, whereas GC-poor copies were characterized by higher densities of LINEs. The features of the copies that underwent the compositional transition and became GC-richer are suggestive of, or related to, functional changes.
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Affiliation(s)
- Edda Rayko
- Laboratoire de Génétique Moléculaire, Institut Jacques Monod, 2 Place Jussieu, F-75005 Paris, France.
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Rodin SN, Parkhomchuk DV, Riggs AD. Epigenetic changes and repositioning determine the evolutionary fate of duplicated genes. BIOCHEMISTRY (MOSCOW) 2005; 70:559-67. [PMID: 15948709 DOI: 10.1007/s10541-005-0149-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Consideration of epigenetic silencing, perhaps by DNA methylation, led to an epigenetic complementation (EC) model for evolution by gene duplication (Rodin and Riggs (2003) J. Mol. Evol., 56, 718-729). This and subsequent work on genome-wide analyses of gene duplicates in several eukaryotic species pointed to a fundamental link between localization in the genome, epigenetic regulation of expression, and the evolutionary fate of new redundant gene copies, which can be either non- or neo-functionalization. Our main message in this report is that repositioning of a new duplicate to an ectopic site epigenetically alters its expression pattern, and concomitantly the rate and direction of mutations. Furthermore, comparison of syntenic vs. non-syntenic pairs of gene duplicates of different age unambiguously indicates that repositioning saves redundant gene duplicates from pseudogenization and hastens their evolution towards a new development-time and tissue-specific pattern of function.
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Affiliation(s)
- S N Rodin
- Department of Theoretical Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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