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Assis R, Conant G, Holland B, Liberles DA, O'Reilly MM, Wilson AE. Models for the retention of duplicate genes and their biological underpinnings. F1000Res 2024; 12:1400. [PMID: 38173826 PMCID: PMC10762295 DOI: 10.12688/f1000research.141786.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2024] [Indexed: 01/05/2024] Open
Abstract
Gene content in genomes changes through several different processes, with gene duplication being an important contributor to such changes. Gene duplication occurs over a range of scales from individual genes to whole genomes, and the dynamics of this process can be context dependent. Still, there are rules by which genes are retained or lost from genomes after duplication, and probabilistic modeling has enabled characterization of these rules, including their context-dependence. Here, we describe the biology and corresponding mathematical models that are used to understand duplicate gene retention and its contribution to the set of biochemical functions encoded in a genome.
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Affiliation(s)
- Raquel Assis
- Florida Atlantic University, Boca Raton, Florida, USA
| | - Gavin Conant
- North Carolina State University, Raleigh, North Carolina, USA
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2
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Wilson AE, Liberles DA. Expectations of duplicate gene retention under the gene duplicability hypothesis. BMC Ecol Evol 2023; 23:76. [PMID: 38097959 PMCID: PMC10720195 DOI: 10.1186/s12862-023-02174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Gene duplication is an important process in evolution. What causes some genes to be retained after duplication and others to be lost is a process not well understood. The most prevalent theory is the gene duplicability hypothesis, that something about the function and number of interacting partners (number of subunits of protein complex, etc.), determines whether copies have more opportunity to be retained for long evolutionary periods. Some genes are also more susceptible to dosage balance effects following WGD events, making them more likely to be retained for longer periods of time. One would expect these processes that affect the retention of duplicate copies to affect the conditional probability ratio after consecutive whole genome duplication events. The probability that a gene will be retained after a second whole genome duplication event (WGD2), given that it was retained after the first whole genome duplication event (WGD1) versus the probability a gene will be retained after WGD2, given it was lost after WGD1 defines the probability ratio that is calculated. RESULTS Since duplicate gene retention is a time heterogeneous process, the time between the events (t1) and the time since the most recent event (t2) are relevant factors in calculating the expectation for observation in any genome. Here, we use a survival analysis framework to predict the probability ratio for genomes with different values of t1 and t2 under the gene duplicability hypothesis, that some genes are more susceptible to selectable functional shifts, some more susceptible to dosage compensation, and others only drifting. We also predict the probability ratio with different values of t1 and t2 under the mutational opportunity hypothesis, that probability of retention for certain genes changes in subsequent events depending upon how they were previously retained. These models are nested such that the mutational opportunity model encompasses the gene duplicability model with shifting duplicability over time. Here we present a formalization of the gene duplicability and mutational opportunity hypotheses to characterize evolutionary dynamics and explanatory power in a recently developed statistical framework. CONCLUSIONS This work presents expectations of the gene duplicability and mutational opportunity hypotheses over time under different sets of assumptions. This expectation will enable formal testing of processes leading to duplicate gene retention.
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Affiliation(s)
- Amanda E Wilson
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA.
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3
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Roberts M, Josephs EB. Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana. Genetics 2023; 224:iyad074. [PMID: 37094602 PMCID: PMC10484170 DOI: 10.1093/genetics/iyad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/06/2023] [Accepted: 04/07/2023] [Indexed: 04/26/2023] Open
Abstract
Differential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data on Arabidopsis thaliana from over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a gene's expression and the strength of selection on said gene in A. thaliana. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.
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Affiliation(s)
- Miles Roberts
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI 48824, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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4
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Wilson AE, Liberles DA. Dosage balance acts as a time-dependent selective barrier to subfunctionalization. BMC Ecol Evol 2023; 23:14. [PMID: 37138246 PMCID: PMC10155369 DOI: 10.1186/s12862-023-02116-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Gene duplication is an important process for genome expansion, sometimes allowing for new gene functions to develop. Duplicate genes can be retained through multiple processes, either for intermediate periods of time through processes such as dosage balance, or over extended periods of time through processes such as subfunctionalization and neofunctionalization. RESULTS Here, we built upon an existing subfunctionalization Markov model by incorporating dosage balance to describe the interplay between subfunctionalization and dosage balance to explore selective pressures on duplicate copies. Our model incorporates dosage balance using a biophysical framework that penalizes the fitness of genetic states with stoichiometrically imbalanced proteins. These imbalanced states cause increased concentrations of exposed hydrophobic surface areas, which cause deleterious mis-interactions. We draw comparison between our Subfunctionalization + Dosage-Balance Model (Sub + Dos) and the previous Subfunctionalization-Only (Sub-Only) Model. This comparison includes how the retention probabilities change over time, dependent upon the effective population size and the selective cost associated with spurious interaction of dosage-imbalanced partners. We show comparison between Sub-Only and Sub + Dos models for both whole-genome duplication and small-scale duplication events. CONCLUSION These comparisons show that following whole-genome duplication, dosage balance serves as a time-dependent selective barrier to the subfunctionalization process, by causing an overall delay but ultimately leading to a larger portion of the genome retained through subfunctionalization. This higher percentage of the genome that is ultimately retained is caused by the alternative competing process, nonfunctionalization, being selectively blocked to a greater extent. In small-scale duplication, the reverse pattern is seen, where dosage balance drives faster rates of subfunctionalization, but ultimately leads to a smaller portion of the genome retained as duplicates. This faster rate of subfunctionalization is because the dosage balance of interacting gene products is negatively affected immediately after duplication and the loss of a duplicate restores the stoichiometric balance. Our findings provide support that the subfunctionalization of genes that are susceptible to dosage balance effects, such as proteins involved in complexes, is not a purely neutral process. With stronger selection against stoichiometrically imbalanced gene partners, the rates of subfunctionalization and nonfunctionalization slow; however, this ultimately leads to a greater proportion of subfunctionalized gene pairs.
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Affiliation(s)
- Amanda E Wilson
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
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5
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Overexpression of TgERF1, a Transcription Factor from Tectona grandis, Increases Tolerance to Drought and Salt Stress in Tobacco. Int J Mol Sci 2023; 24:ijms24044149. [PMID: 36835560 PMCID: PMC9961280 DOI: 10.3390/ijms24044149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Teak (Tectona grandis) is one of the most important wood sources, and it is cultivated in tropical regions with a significant market around the world. Abiotic stresses are an increasingly common and worrying environmental phenomenon because it causes production losses in both agriculture and forestry. Plants adapt to these stress conditions by activation or repression of specific genes, and they synthesize numerous stress proteins to maintain their cellular function. For example, APETALA2/ethylene response factor (AP2/ERF) was found to be involved in stress signal transduction. A search in the teak transcriptome database identified an AP2/ERF gene named TgERF1 with a key AP2/ERF domain. We then verified that the TgERF1 expression is rapidly induced by Polyethylene Glycol (PEG), NaCl, and exogenous phytohormone treatments, suggesting a potential role in drought and salt stress tolerance in teak. The full-length coding sequence of TgERF1 gene was isolated from teak young stems, characterized, cloned, and constitutively overexpressed in tobacco plants. In transgenic tobacco plants, the overexpressed TgERF1 protein was localized exclusively in the cell nucleus, as expected for a transcription factor. Furthermore, functional characterization of TgERF1 provided evidence that TgERF1 is a promising candidate gene to be used as selective marker on plant breeding intending to improve plant stress tolerance.
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Henry CN, Piper K, Wilson AE, Miraszek JL, Probst CS, Rong Y, Liberles DA. WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events. BMC Bioinformatics 2022; 23:505. [PMID: 36434497 PMCID: PMC9701042 DOI: 10.1186/s12859-022-05042-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 11/08/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Multiple processes impact the probability of retention of individual genes following whole genome duplication (WGD) events. In analyzing two consecutive whole genome duplication events that occurred in the lineage leading to Atlantic salmon, a new phylogenetic statistical analysis was developed to examine the contingency of retention in one event based upon retention in a previous event. This analysis is intended to evaluate mechanisms of duplicate gene retention and to provide software to generate the test statistic for any genome with pairs of WGDs in its history. RESULTS Here a software package written in Python, 'WGDTree' for the analysis of duplicate gene retention following whole genome duplication events is presented. Using gene tree-species tree reconciliation to label gene duplicate nodes and differentiate between WGD and SSD duplicates, the tool calculates a statistic based upon the conditional probability of a gene duplicate being retained after a second whole genome duplication dependent upon the retention status after the first event. The package also contains methods for the simulation of gene trees with WGD events. After running simulations, the accuracy of the placement of events has been determined to be high. The conditional probability statistic has been calculated for Phalaenopsis equestris on a monocot species tree with a pair of consecutive WGD events on its lineage, showing the applicability of the method. CONCLUSIONS A new software tool has been created for the analysis of duplicate genes in examination of retention mechanisms. The software tool has been made available on the Python package index and the source code can be found on GitHub here: https://github.com/cnickh/wgdtree .
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Affiliation(s)
- C. Nicholas Henry
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA
| | - Kathryn Piper
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA ,grid.265850.c0000 0001 2151 7947Present Address: Department of Biological Sciences, University at Albany, Albany, NY 12222 USA
| | - Amanda E. Wilson
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA
| | - John L. Miraszek
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA ,grid.134936.a0000 0001 2162 3504Present Address: Genetics Area Program, University of Missouri, Columbia, MO 65211 USA
| | - Claire S. Probst
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA
| | - Yuying Rong
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA ,grid.256868.70000 0001 2215 7365Department of Biology, Haverford College, Haverford, PA 19041 USA ,grid.4830.f0000 0004 0407 1981Present Address: Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
| | - David A. Liberles
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA
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Miao S, Li F, Han Y, Yao Z, Xu Z, Chen X, Liu J, Zhang Y, Wang A. Identification of OSCA gene family in Solanum habrochaites and its function analysis under stress. BMC Genomics 2022; 23:547. [PMID: 35915415 PMCID: PMC9341080 DOI: 10.1186/s12864-022-08675-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022] Open
Abstract
Background OSCA (hyperosmolality-gated calcium-permeable channel) is a calcium permeable cation channel protein that plays an important role in regulating plant signal transduction. It is involved in sensing changes in extracellular osmotic potential and an increase in Ca2+ concentration. S. habrochaites is a good genetic material for crop improvement against cold, late blight, planthopper and other diseases. Till date, there is no report on OSCA in S. habrochaites. Thus, in this study, we performed a genome-wide screen to identify OSCA genes in S. habrochaites and characterized their responses to biotic and abiotic stresses. Results A total of 11 ShOSCA genes distributed on 8 chromosomes were identified. Subcellular localization analysis showed that all members of ShOSCA localized on the plasma membrane and contained multiple stress-related cis acting elements. We observed that genome-wide duplication (WGD) occurred in the genetic evolution of ShOSCA5 (Solhab04g250600) and ShOSCA11 (Solhab12g051500). In addition, repeat events play an important role in the expansion of OSCA gene family. OSCA gene family of S. habrochaites used the time lines of expression studies by qRT-PCR, do indicate OSCAs responded to biotic stress (Botrytis cinerea) and abiotic stress (drought, low temperature and abscisic acid (ABA)). Among them, the expression of ShOSCAs changed significantly under four stresses. The resistance of silencing ShOSCA3 plants to the four stresses was reduced. Conclusion This study identified the OSCA gene family of S. habrochaites for the first time and analyzed ShOSCA3 has stronger resistance to low temperature, ABA and Botrytis cinerea stress. This study provides a theoretical basis for clarifying the biological function of OSCA, and lays a foundation for tomato crop improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08675-6.
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Affiliation(s)
- Shuang Miao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Fengshuo Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Han
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zhongtong Yao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Zeqian Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiuling Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Jiayin Liu
- College of Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Yao Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
| | - Aoxue Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China. .,College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
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8
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Johri P, Gout JF, Doak TG, Lynch M. A Population-Genetic Lens into the Process of Gene Loss Following Whole-Genome Duplication. Mol Biol Evol 2022; 39:6594306. [PMID: 35639978 PMCID: PMC9206413 DOI: 10.1093/molbev/msac118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Whole-genome duplications (WGDs) have occurred in many eukaryotic lineages. However, the underlying evolutionary forces and molecular mechanisms responsible for the long-term retention of gene duplicates created by WGDs are not well understood. We employ a population-genomic approach to understand the selective forces acting on paralogs and investigate ongoing duplicate-gene loss in multiple species of Paramecium that share an ancient WGD. We show that mutations that abolish protein function are more likely to be segregating in retained WGD paralogs than in single-copy genes, most likely because of ongoing nonfunctionalization post-WGD. This relaxation of purifying selection occurs in only one WGD paralog, accompanied by the gradual fixation of nonsynonymous mutations and reduction in levels of expression, and occurs over a long period of evolutionary time, “marking” one locus for future loss. Concordantly, the fitness effects of new nonsynonymous mutations and frameshift-causing indels are significantly more deleterious in the highly expressed copy compared with their paralogs with lower expression. Our results provide a novel mechanistic model of gene duplicate loss following WGDs, wherein selection acts on the sum of functional activity of both duplicate genes, allowing the two to wander in expression and functional space, until one duplicate locus eventually degenerates enough in functional efficiency or expression that its contribution to total activity is too insignificant to be retained by purifying selection. Retention of duplicates by such mechanisms predicts long times to duplicate-gene loss, which should not be falsely attributed to retention due to gain/change in function.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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9
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Vance Z, Niezabitowski L, Hurst LD, McLysaght A. Evidence from Drosophila Supports Higher Duplicability of Faster Evolving Genes. Genome Biol Evol 2022; 14:6501445. [PMID: 35018456 PMCID: PMC8765793 DOI: 10.1093/gbe/evac003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/03/2022] Open
Abstract
The faster rate of evolution of duplicated genes relative to singletons has been well documented in multiple lineages. This observation has generally been attributed to a presumed release from constraint following creation of a redundant, duplicate copy. However, it is not obvious that the relationship operates in this direction. An alternative possibility—that the faster rate of evolution predates the duplication event and the observed differences result from a higher propensity to duplicate in fast-evolving genes—has been tested in primates and in insects. However, these studies arrived at different conclusions and clarity is needed on whether these contrasting results relate to differences in methodology or legitimate biological differences between the lineages selected. Here, we test whether duplicable genes are faster evolving independent of duplication in the Drosophila lineage and find that our results support the conclusion that faster evolving genes are more likely to duplicate, in agreement with previous work in primates. Our findings indicate that this characteristic of gene duplication is not restricted to a single lineage and has broad implications for the interpretation of the impact of gene duplication. We identify a subset of “singletons” which defy the general trends and appear to be faster evolving. Further investigation implicates homology detection failure and suggests that these may be duplicable genes with unidentifiable paralogs.
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Affiliation(s)
- Zoe Vance
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | | | - Laurence D Hurst
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
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10
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Chen L, Li B, Chen B, Li C, Zhou Z, Zhou T, Yang W, Xu P. Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio. Mol Ecol Resour 2021; 21:1658-1669. [PMID: 33624395 DOI: 10.1111/1755-0998.13365] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/27/2021] [Accepted: 02/16/2021] [Indexed: 11/27/2022]
Abstract
The diploid Poropuntius huangchuchieni in the cyprinid family, which is widely distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp, which was generated by merging of two diploid genomes during evolution. Therefore, the P. huangchuchieni genome is essential for polyploid evolution studies in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by integrating Oxford Nanopore and Hi-C technologies. The assembled genome size was 1,021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed that P. huangchuchieni diverged from Cyprinus carpio at approximately 12 Mya. Genome comparison between P. huangchuchieni and the B subgenome of C. carpio provided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified between P. huangchuchieni and C. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genetic analyses. The high-quality genomic data set created for P. huangchuchieni provides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Bijun Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Chengyu Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Tao Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Weidi Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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11
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Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z. Pan-Genome of Wild and Cultivated Soybeans. Cell 2020; 182:162-176.e13. [PMID: 32553274 DOI: 10.1016/j.cell.2020.05.023] [Citation(s) in RCA: 392] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022]
Abstract
Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.
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Affiliation(s)
- Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengcheng Li
- Berry Genomics Corporation, Beijing 100015, China
| | - Yanting Shen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hua Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo-An Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Zhi Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao Shi
- Berry Genomics Corporation, Beijing 100015, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yan Li
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Moharana KC, Venancio TM. Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:726-741. [PMID: 32270526 DOI: 10.1111/tpj.14765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/13/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Transcription factors (TFs) are essential for plant growth and development. Several legumes (e.g. soybean) are rich sources of protein and oil and have great economic importance. Here we report a phylogenomic analysis of TF families in legumes and their potential association with important traits (e.g. nitrogen fixation). We used TF DNA-binding domains to systematically screen the genomes of 15 leguminous and five non-leguminous species. Transcription factor orthologous groups (OGs) were used to estimate OG sizes in ancestral nodes using a gene birth-death model, which allowed the identification of lineage-specific expansions. The OG analysis and rate of synonymous substitutions show that major TF expansions are strongly associated with whole-genome duplication (WGD) events in the legume (approximately 58 million years ago) and Glycine (approximately 13 million years ago) lineages, which account for a large fraction of the Phaseolus vulgaris and Glycine max TF repertoires. Of the 3407 G. max TFs, 1808 and 676 have homeologs within single syntenic regions in Phaseolus vulgaris and Vitis vinifera, respectively. We found a trend for TFs expanded in legumes to be preferentially transcribed in roots and nodules, supporting their recruitment early in the evolution of nodulation in the legume clade. Some families also showed count differences between G. max and the wild soybean Glycine soja, including genes located within important quantitative trait loci. Our findings strongly support the roles of two WGDs in shaping the TF repertoires in the legume and Glycine lineages, and these are probably related to important aspects of legume and soybean biology.
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Affiliation(s)
- Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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13
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Lu HM, Li JD, Zhang YD, Lu XL, Xu C, Huang Y, Gribskov M. The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs. Genome Biol Evol 2020; 12:160-173. [PMID: 32108236 PMCID: PMC7144353 DOI: 10.1093/gbe/evaa038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 01/15/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters play important roles in electron transfer, metabolic and biosynthetic reactions, and the regulation of gene expression. Understanding the biogenesis of Fe-S clusters is therefore relevant to many fields. In the complex process of Fe-S protein formation, the A-type assembly protein (ATAP) family, which consists of several subfamilies, plays an essential role in Fe-S cluster formation and transfer and is highly conserved across the tree of life. However, the taxonomic distribution, motif compositions, and the evolutionary history of the ATAP subfamilies are not well understood. To address these problems, our study investigated the taxonomic distribution of 321 species from a broad cross-section of taxa. Then, we identified common and specific motifs in multiple ATAP subfamilies to explain the functional conservation and nonredundancy of the ATAPs, and a novel, essential motif was found in Eumetazoa IscA1, which has a newly found magnetic function. Finally, we used phylogenetic analytical methods to reconstruct the evolution history of this family. Our results show that two types of ErpA proteins (nonproteobacteria-type ErpA1 and proteobacteria-type ErpA2) exist in bacteria. The ATAP family, consisting of seven subfamilies, can be further classified into two types of ATAPs. Type-I ATAPs include IscA, SufA, HesB, ErpA1, and IscA1, with an ErpA1-like gene as their last common ancestor, whereas type-II ATAPs consist of ErpA2 and IscA2, duplicated from an ErpA2-like gene. During the mitochondrial endosymbiosis, IscA became IscA1 in eukaryotes and ErpA2 became IscA2 in eukaryotes, respectively.
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Affiliation(s)
- Hui-Meng Lu
- School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Jing-Di Li
- School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Yu-Dan Zhang
- School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Xiao-Li Lu
- School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Chang Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, PR China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, PR China
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University
- Department of Computer Science, Purdue University
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14
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Abstract
An attractive and long-standing hypothesis regarding the evolution of genes after duplication posits that the duplication event creates new evolutionary possibilities by releasing a copy of the gene from constraint. Apparent support was found in numerous analyses, particularly, the observation of higher rates of evolution in duplicated as compared with singleton genes. Could it, instead, be that more duplicable genes (owing to mutation, fixation, or retention biases) are intrinsically faster evolving? To uncouple the measurement of rates of evolution from the determination of duplicate or singleton status, we measure the rates of evolution in singleton genes in outgroup primate lineages but classify these genes as to whether they have duplicated or not in a crown group of great apes. We find that rates of evolution are higher in duplicable genes prior to the duplication event. In part this is owing to a negative correlation between coding sequence length and rate of evolution, coupled with a bias toward smaller genes being more duplicable. The effect is masked by difference in expression rate between duplicable genes and singletons. Additionally, in contradiction to the classical assumption, we find no convincing evidence for an increase in dN/dS after duplication, nor for rate asymmetry between duplicates. We conclude that high rates of evolution of duplicated genes are not solely a consequence of the duplication event, but are rather a predictor of duplicability. These results are consistent with a model in which successful gene duplication events in mammals are skewed toward events of minimal phenotypic impact.
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Affiliation(s)
- Áine N O'Toole
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
| | - Aoife McLysaght
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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15
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Wang L, Ma H, Lin J. Angiosperm-Wide and Family-Level Analyses of AP2/ ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication. FRONTIERS IN PLANT SCIENCE 2019; 10:196. [PMID: 30863419 PMCID: PMC6399210 DOI: 10.3389/fpls.2019.00196] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/05/2019] [Indexed: 05/21/2023]
Abstract
Plants are immobile and often face stressful environmental conditions, prompting the evolution of genes regulating environmental responses. Such evolution is achieved largely through gene duplication and subsequent divergence. One of the most important gene families involved in regulating plant environmental responses and development is the AP2/ERF superfamily; however, the evolutionary history of these genes is unclear across angiosperms and in major angiosperm families adapted to various ecological niches. Specifically, the impact on gene copy number of whole-genome duplication events occurring around the time of the origins of several plant families is unknown. Here, we present the first angiosperm-wide comparative study of AP2/ERF genes, identifying 75 Angiosperm OrthoGroups (AOGs), each derived from an ancestral angiosperm gene copy. Among these AOGs, 21 retain duplicates with increased copy number in many angiosperm lineages, while the remaining 54 AOGs tend to maintain low copy number. Further analyses of multiple species in the Brassicaceae family indicated that family-specific duplicates experienced differential selective pressures in coding regions, with some paralogs showing signs of positive selection. Further, cis regulatory elements also exhibit extensive divergence between duplicates in Arabidopsis. Moreover, comparison of expression levels suggested that AP2/ERF genes with frequently retained duplicates are enriched for broad expression patterns, offering increased opportunities for functional diversification via changes in expression patterns, and providing a mechanism for repeated duplicate retention in some AOGs. Our results represent the most comprehensive evolutionary history of the AP2/ERF gene family, and support the hypothesis that AP2/ERF genes with broader expression patterns are more likely to be retained as duplicates than those with narrower expression profiles, which could lead to a higher chance of duplicate gene subfunctionalization. The greater tendency of some AOGs to retain duplicates, allowing expression and functional divergence, may facilitate the evolution of complex signaling networks in response to new environmental conditions.
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Affiliation(s)
- Linbo Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Juan Lin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
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16
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Hao Y, Washburn JD, Rosenthal J, Nielsen B, Lyons E, Edger PP, Pires JC, Conant GC. Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived. Genome Biol Evol 2018; 10:999-1011. [PMID: 29617811 PMCID: PMC5887293 DOI: 10.1093/gbe/evy061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2018] [Indexed: 11/21/2022] Open
Abstract
Genes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to assess for how long the influence of polyploidy is felt on these genes’ selective pressures. We analyzed two nested polyploidy events in Brassicaceae: the At-α genome duplication that is the most recent polyploidy in the model plant Arabidopsis thaliana and a more recent hexaploidy shared by the genus Brassica and its relatives. By comparing the strength and direction of the natural selection acting at the population and at the species level, we find evidence for continued intensified purifying selection acting on retained duplicates from both polyploidies even down to the present. The constraint observed in preferentially retained genes is not a result of the polyploidy event: the orthologs of such genes experience even stronger constraint in nonpolyploid outgroup genomes. In both the Arabidopsis and Brassica lineages, we further find evidence for segregating mildly deleterious variants, confirming that the population-level data uncover patterns not visible with between-species comparisons. Using the A. thaliana metabolic network, we also explored whether network position was correlated with the measured selective constraint. At both the population and species level, nodes/genes tended to show similar constraints to their neighbors. Our results paint a picture of the long-lived effects of polyploidy on plant genomes, suggesting that even yesterday’s polyploids still have distinct evolutionary trajectories.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University
| | | | | | - Brandon Nielsen
- Department of Biology and Geosciences, Clarion University of Pennsylvania
| | - Eric Lyons
- School of Plant Sciences, University of Arizona
| | - Patrick P Edger
- Department of Horticulture, Michigan State University.,Ecology, Evolutionary Biology and Behavior Program, Michigan State University
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri- Columbia.,Informatics Institute, University of Missouri- Columbia
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University.,Informatics Institute, University of Missouri- Columbia.,Division of Animal Sciences, University of Missouri- Columbia.,Program in Genetics, North Carolina State University.,Department of Biological Sciences, North Carolina State University
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17
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Alvarez-Ponce D, Feyertag F, Chakraborty S. Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein-Protein Interaction Network. Genome Biol Evol 2018; 9:1742-1756. [PMID: 28854629 PMCID: PMC5570066 DOI: 10.1093/gbe/evx117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2017] [Indexed: 02/06/2023] Open
Abstract
The proteins of any organism evolve at disparate rates. A long list of factors affecting rates of protein evolution have been identified. However, the relative importance of each factor in determining rates of protein evolution remains unresolved. The prevailing view is that evolutionary rates are dominantly determined by gene expression, and that other factors such as network centrality have only a marginal effect, if any. However, this view is largely based on analyses in yeasts, and accurately measuring the importance of the determinants of rates of protein evolution is complicated by the fact that the different factors are often correlated with each other, and by the relatively poor quality of available functional genomics data sets. Here, we use correlation, partial correlation and principal component regression analyses to measure the contributions of several factors to the variability of the rates of evolution of human proteins. For this purpose, we analyzed the entire human protein–protein interaction data set and the human signal transduction network—a network data set of exceptionally high quality, obtained by manual curation, which is expected to be virtually free from false positives. In contrast with the prevailing view, we observe that network centrality (measured as the number of physical and nonphysical interactions, betweenness, and closeness) has a considerable impact on rates of protein evolution. Surprisingly, the impact of centrality on rates of protein evolution seems to be comparable, or even superior according to some analyses, to that of gene expression. Our observations seem to be independent of potentially confounding factors and from the limitations (biases and errors) of interactomic data sets.
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18
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Lokits AD, Indrischek H, Meiler J, Hamm HE, Stadler PF. Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa. BMC Evol Biol 2018; 18:51. [PMID: 29642851 PMCID: PMC5896119 DOI: 10.1186/s12862-018-1147-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/06/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Heterotrimeric G proteins are fundamental signaling proteins composed of three subunits, Gα and a Gβγ dimer. The role of Gα as a molecular switch is critical for transmitting and amplifying intracellular signaling cascades initiated by an activated G protein Coupled Receptor (GPCR). Despite their biochemical and therapeutic importance, the study of G protein evolution has been limited to the scope of a few model organisms. Furthermore, of the five primary Gα subfamilies, the underlying gene structure of only two families has been thoroughly investigated outside of Mammalia evolution. Therefore our understanding of Gα emergence and evolution across phylogeny remains incomplete. RESULTS We have computationally identified the presence and absence of every Gα gene (GNA-) across all major branches of Deuterostomia and evaluated the conservation of the underlying exon-intron structures across these phylogenetic groups. We provide evidence of mutually exclusive exon inclusion through alternative splicing in specific lineages. Variations of splice site conservation and isoforms were found for several paralogs which coincide with conserved, putative motifs of DNA-/RNA-binding proteins. In addition to our curated gene annotations, within Primates, we identified 15 retrotranspositions, many of which have undergone pseudogenization. Most importantly, we find numerous deviations from previous findings regarding the presence and absence of individual GNA- genes, nuanced differences in phyla-specific gene copy numbers, novel paralog duplications and subsequent intron gain and loss events. CONCLUSIONS Our curated annotations allow us to draw more accurate inferences regarding the emergence of all Gα family members across Metazoa and to present a new, updated theory of Gα evolution. Leveraging this, our results are critical for gaining new insights into the co-evolution of the Gα subunit and its many protein binding partners, especially therapeutically relevant G protein - GPCR signaling pathways which radiated in Vertebrata evolution.
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Affiliation(s)
- A. D. Lokits
- 0000 0001 2264 7217grid.152326.1Neuroscience Program, Vanderbilt University, Nashville, TN USA ,0000 0001 2264 7217grid.152326.1Center for Structural Biology, Vanderbilt University, Nashville, TN USA
| | - H. Indrischek
- 0000 0001 2230 9752grid.9647.cBioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany ,0000 0001 2230 9752grid.9647.cComputational EvoDevo Group, Bioinformatics Department, Leipzig University, Leipzig, Germany
| | - J. Meiler
- 0000 0001 2264 7217grid.152326.1Center for Structural Biology, Vanderbilt University, Nashville, TN USA ,0000 0001 2264 7217grid.152326.1Chemistry Department, Vanderbilt University, Nashville, TN USA
| | - H. E. Hamm
- 0000 0004 1936 9916grid.412807.8Pharmacology Department, Vanderbilt University Medical Center, Nashville, TN USA
| | - P. F. Stadler
- 0000 0001 2230 9752grid.9647.cBioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany ,0000 0001 0674 042Xgrid.5254.6Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark ,0000 0001 2286 1424grid.10420.37Institute for Theoretical Chemistry, University of Vienna, Wien, Austria ,0000 0001 2230 9752grid.9647.cIZBI-Interdisciplinary Center for Bioinformatics and LIFE-Leipzig Research Center for Civilization Diseases and Competence Center for Scalable Data Services and Solutions, University Leipzig, Leipzig, Germany ,grid.419532.8Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany ,0000 0001 1941 1940grid.209665.eSanta Fe Institute, Santa Fe, NM USA
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19
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Roux J, Liu J, Robinson-Rechavi M. Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. Mol Biol Evol 2018; 34:2773-2791. [PMID: 28981708 PMCID: PMC5850798 DOI: 10.1093/molbev/msx199] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.
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Affiliation(s)
- Julien Roux
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jialin Liu
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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20
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Hanada K, Tezuka A, Nozawa M, Suzuki Y, Sugano S, Nagano AJ, Ito M, Morinaga SI. Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis. DNA Res 2018; 25:4898128. [PMID: 29481587 PMCID: PMC6014284 DOI: 10.1093/dnares/dsy005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 02/02/2018] [Indexed: 12/02/2022] Open
Abstract
Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae. The duplication frequency of retained genes in the Arabidopsis lineage was ∼10 times higher than the duplication frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss (Physcomitrella patens). The difference of duplication frequencies can be explained by a rapid decay of anciently duplicated genes. To examine the degree of selection pressure on genes duplicated in either the A. halleri-lyrata or the A. halleri lineage, we examined positive and purifying selection in the A. halleri-lyrata and A. halleri lineages throughout the ratios of nonsynonymous to synonymous substitution rates (KA/KS). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. Interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication compared with immediately after gene duplication.
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Affiliation(s)
- Kousuke Hanada
- Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
- RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Ayumi Tezuka
- Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Masafumi Nozawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Sumio Sugano
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Atsushi J Nagano
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Center of Ecological Research, Kyoto University, Hirano, Otsu, Shiga 520-2113, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Shin-Ichi Morinaga
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
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21
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Xu Y, Yu Z, Zhang D, Huang J, Wu C, Yang G, Yan K, Zhang S, Zheng C. CYSTM, a Novel Non-Secreted Cysteine-Rich Peptide Family, Involved in Environmental Stresses in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2018; 59:423-438. [PMID: 29272523 DOI: 10.1093/pcp/pcx202] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/12/2017] [Indexed: 05/24/2023]
Abstract
The cysteine-rich transmembrane module (CYSTM) is comprised of a small molecular protein family that is found in a diversity of tail-anchored membrane proteins across eukaryotes. This protein family belongs to novel uncharacteristic non-secreted cysteine-rich peptides (NCRPs) according to their conserved domain and small molecular weight, and genome-wide analysis of this family has not yet been undertaken in plants. In this study, 13 CYSTM genes were identified and located on five chromosomes with diverse densities in Arabidopsis thaliana. The CYSTM proteins could be classified into four subgroups based on domain similarity and phylogenetic topology. Encouragingly, the CYSTM members were expressed in at least one of the tested tissues and dramatically responded to various abiotic stresses, indicating that they played vital roles in diverse developmental processes, especially in stress responses. CYSTM peptides displayed a complex subcellular localization, and most were detected at the plasma membrane and cytoplasm. Of particular interest, CYSTM members could dimerize with themselves or others through the C-terminal domain, and we built a protein-protein interaction map between CYSTM members in Arabidopsis for the first time. In addition, an analysis of CYSTM3 overexpression lines revealed negative regulation for this gene in salt stress responses. We demonstrate that the CYSTM family, as a novel and ubiquitous non-secreted cysteine-rich peptide family, plays a vital role in resistance to abiotic stress. Collectively, our comprehensive analysis of CYSTM members will facilitate future functional studies of the small peptides.
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Affiliation(s)
- Yang Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Zipeng Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Di Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
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22
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Mehlferber EC, Benowitz KM, Roy-Zokan EM, McKinney EC, Cunningham CB, Moore AJ. Duplication and Sub/Neofunctionalization of Malvolio, an Insect Homolog of Nramp, in the Subsocial Beetle Nicrophorus vespilloides. G3 (BETHESDA, MD.) 2017; 7:3393-3403. [PMID: 28830925 PMCID: PMC5633388 DOI: 10.1534/g3.117.300183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/16/2017] [Indexed: 01/04/2023]
Abstract
With growing numbers of sequenced genomes, increasing numbers of duplicate genes are being uncovered. Here we examine Malvolio, a gene in the natural resistance-associated macrophage protein (Nramp) family, that has been duplicated in the subsocial beetle, Nicrophorus vespilloides, which exhibits advanced parental behavior. There is only one copy of Mvl in honey bees and Drosophila, whereas in vertebrates there are two copies that are subfunctionalized. We first compared amino acid sequences for Drosophila, beetles, mice, and humans. We found a high level of conservation between the different species, although there was greater variation in the C-terminal regions. A phylogenetic analysis across multiple insect orders suggested that Mvl has undergone several independent duplications. To examine the potential for different functions where it has been duplicated, we quantified expression levels of Mvl1 and Mvl2 in eight tissues in N. vespilloides We found that while Mvl1 was expressed ubiquitously, albeit at varying levels, expression of Mvl2 was limited to brain and midgut. Because Mvl has been implicated in behavior, we examined expression during different behavioral states that reflected differences in opportunity for social interactions and expression of parental care behaviors. We found differing expression patterns for the two copies, with Mvl1 increasing in expression during resource preparation and feeding offspring, and Mvl2 decreasing in these same states. Given these patterns of expression, along with the protein analysis, we suggest that Mvl in N. vespilloides has experienced sub/neofunctionalization following its duplication, and may be evolving differing and tissue-specific roles in behavior and physiology.
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Affiliation(s)
| | - Kyle M Benowitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | | | - Elizabeth C McKinney
- Department of Entomology, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | | | - Allen J Moore
- Department of Entomology, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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Jin X, Ren J, Nevo E, Yin X, Sun D, Peng J. Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm. FRONTIERS IN PLANT SCIENCE 2017; 8:1156. [PMID: 28713414 PMCID: PMC5492850 DOI: 10.3389/fpls.2017.01156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/15/2017] [Indexed: 05/20/2023]
Abstract
NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses.
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Affiliation(s)
- Xiaoli Jin
- Department of Agronomy and the Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang UniversityHangzhou, China
| | - Jing Ren
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou UniversityDezhou, China
| | - Eviatar Nevo
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Xuegui Yin
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
| | - Dongfa Sun
- Department of Agronomy, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Junhua Peng
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
- Life Science & Technology Center, and the State Key Lab of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., Ltd.Wuhan, China
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Ascencio D, Ochoa S, Delaye L, DeLuna A. Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts. BMC Evol Biol 2017; 17:40. [PMID: 28166720 PMCID: PMC5294719 DOI: 10.1186/s12862-017-0895-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/26/2017] [Indexed: 11/25/2022] Open
Abstract
Background Whole-genome duplication (WGD) events have shaped the genomes of eukaryotic organisms. Relaxed selection after duplication along with inherent functional constraints are thought to determine the fate of the paralogs and, ultimately, the evolution of gene function. Here, we investigated the rate of protein evolution (as measured by dN/dS ratios) before and after the WGD in the hemiascomycete yeasts, and the way in which changes in such rates relate to molecular and biological function. Results For most groups of orthologous genes (81%) we observed a change in the rates of evolution after genome duplication. Genes with atypically-low dN/dS ratio before the WGD were prone to increase their rates of evolution after duplication. Importantly, the paralogs were often different in their rates of evolution after the WGD (50% cases), however, this was more consistent with an asymmetric deceleration in the protein-evolution rates, rather than an asymmetric increase of the initial rates. Functional-category analysis showed that regulatory proteins such as protein kinases and transcription factors were enriched in genes that increase their rates of evolution after the WGD. While changes in the rate of protein-sequence evolution were associated to protein abundance, content of disordered regions, and contribution to fitness, these features were an attribute of specific functional classes. Conclusions Our results indicate that strong purifying selection in ancestral pre-duplication sequences is a strong predictor of increased rates after the duplication in yeasts and that asymmetry in evolution rate is established during the deceleration phase. In addition, changes in the rates at which paralogous sequences evolve before and after WGD are different for specific protein functions; increased rates of protein evolution after duplication occur preferentially in specific protein functions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0895-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana Ascencio
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Soledad Ochoa
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico.
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Role of Ectopic Gene Conversion in the Evolution of a Candida krusei Pleiotropic Drug Resistance Transporter Family. Genetics 2017; 205:1619-1639. [PMID: 28159755 PMCID: PMC5378117 DOI: 10.1534/genetics.116.194811] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/31/2017] [Indexed: 11/18/2022] Open
Abstract
Gene duplications enable the evolution of novel gene function, but strong positive selection is required to preserve advantageous mutations in a population. This is because frequent ectopic gene conversions (EGCs) between highly similar, tandem-duplicated, sequences, can rapidly remove fate-determining mutations by replacing them with the neighboring parent gene sequences. Unfortunately, the high sequence similarities between tandem-duplicated genes severely hamper empirical studies of this important evolutionary process, because deciphering their correct sequences is challenging. In this study, we employed the eukaryotic model organism Saccharomyces cerevisiae to clone and functionally characterize all 30 alleles of an important pair of tandem-duplicated multidrug efflux pump genes, ABC1 and ABC11, from seven strains of the diploid pathogenic yeast Candida krusei Discovery and functional characterization of their closest ancestor, C. krusei ABC12, helped elucidate the evolutionary history of the entire gene family. Our data support the proposal that the pleiotropic drug resistance (PDR) transporters Abc1p and Abc11p have evolved by concerted evolution for ∼134 MY. While >90% of their sequences remained identical, very strong purifying selection protected six short DNA patches encoding just 18 core amino acid (aa) differences in particular trans membrane span (TMS) regions causing two distinct efflux pump functions. A proline-kink change at the bottom of Abc11p TMS3 was possibly fate determining. Our data also enabled the first empirical estimates for key parameters of eukaryotic gene evolution, they provided rare examples of intron loss, and PDR transporter phylogeny confirmed that C. krusei belongs to a novel, yet unnamed, third major Saccharomycotina lineage.
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26
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Inkpen SA, Doolittle WF. Molecular Phylogenetics and the Perennial Problem of Homology. J Mol Evol 2016; 83:184-192. [PMID: 27872952 DOI: 10.1007/s00239-016-9766-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 11/12/2016] [Indexed: 01/19/2023]
Abstract
The concept of homology has a long history, during much of which the issue has been how to reconcile similarity and common descent when these are not coextensive. Although thinking molecular phylogeneticists have learned not to say "percent homology," the problems are deeper than that and unresolved.
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Affiliation(s)
- S Andrew Inkpen
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Philosophy, Dalhousie University, Halifax, NS, Canada
| | - W Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.
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27
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Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Sugita T, Iwasaki W. Global deceleration of gene evolution following recent genome hybridizations in fungi. Genome Res 2016; 26:1081-90. [PMID: 27440871 PMCID: PMC4971771 DOI: 10.1101/gr.205948.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/17/2016] [Indexed: 11/27/2022]
Abstract
Polyploidization events such as whole-genome duplication and inter-species hybridization are major evolutionary forces that shape genomes. Although long-term effects of polyploidization have been well-characterized, early molecular evolutionary consequences of polyploidization remain largely unexplored. Here, we report the discovery of two recent and independent genome hybridizations within a single clade of a fungal genus, Trichosporon. Comparative genomic analyses revealed that redundant genes are experiencing decelerations, not accelerations, of evolutionary rates. We identified a relationship between gene conversion and decelerated evolution suggesting that gene conversion may improve the genome stability of young hybrids by restricting gene functional divergences. Furthermore, we detected large-scale gene losses from transcriptional and translational machineries that indicate a global compensatory mechanism against increased gene dosages. Overall, our findings illustrate counteracting mechanisms during an early phase of post-genome hybridization and fill a critical gap in existing theories on genome evolution.
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Affiliation(s)
- Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ri-Ichiroh Manabe
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8568, Japan; Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Chiba 277-8564, Japan
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28
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Yin H, Ma L, Wang G, Li M, Zhang Z. Old genes experience stronger translational selection than young genes. Gene 2016; 590:29-34. [PMID: 27259662 DOI: 10.1016/j.gene.2016.05.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/27/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022]
Abstract
Selection on synonymous codon usage for translation efficiency and/or accuracy has been identified as a widespread mechanism in many living organisms. However, it remains unknown whether translational selection associates closely with gene age and acts differentially on genes with different evolutionary ages. To address this issue, here we investigate the strength of translational selection acting on different aged genes in human. Our results show that old genes present stronger translational selection than young genes, demonstrating that translational selection correlates positively with gene age. We further explore the difference of translational selection in duplicates vs. singletons and in housekeeping vs. tissue-specific genes. We find that translational selection acts comparably in old singletons and old duplicates and stronger translational selection in old genes is contributed primarily by housekeeping genes. For young genes, contrastingly, singletons experience stronger translational selection than duplicates, presumably due to redundant function of duplicated genes during their early evolutionary stage. Taken together, our results indicate that translational selection acting on a gene would not be constant during all stages of evolution, associating closely with gene age.
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Affiliation(s)
- Hongyan Yin
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Ma
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, Beijing 100101, China
| | - Guangyu Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengwei Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, Beijing 100101, China.
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29
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Genge CE, Stevens CM, Davidson WS, Singh G, Peter Tieleman D, Tibbits GF. Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC. Genome Biol Evol 2016; 8:994-1011. [PMID: 26979795 PMCID: PMC4860682 DOI: 10.1093/gbe/evw044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Gene duplication results in extra copies of genes that must coevolve with their interacting partners in multimeric protein complexes. The cardiac troponin (Tn) complex, containing TnC, TnI, and TnT, forms a distinct functional unit critical for the regulation of cardiac muscle contraction. In teleost fish, the function of the Tn complex is modified by the consequences of differential expression of paralogs in response to environmental thermal challenges. In this article, we focus on the interaction between TnI and TnC, coded for by genes that have independent evolutionary origins, but the co-operation of their protein products has necessitated coevolution. In this study, we characterize functional divergence of TnC and TnI paralogs, specifically the interrelated roles of regulatory subfunctionalization and structural subfunctionalization. We determined that differential paralog transcript expression in response to temperature acclimation results in three combinations of TnC and TnI in the zebrafish heart: TnC1a/TnI1.1, TnC1b/TnI1.1, and TnC1a/TnI1.5. Phylogenetic analysis of these highly conserved proteins identified functionally divergent residues in TnI and TnC. The structural and functional effect of these Tn combinations was modeled with molecular dynamics simulation to link divergent sites to changes in interaction strength. Functional divergence in TnI and TnC were not limited to the residues involved with TnC/TnI switch interaction, which emphasizes the complex nature of Tn function. Patterns in domain-specific divergent selection and interaction energies suggest that substitutions in the TnI switch region are crucial to modifying TnI/TnC function to maintain cardiac contraction with temperature changes. This integrative approach introduces Tn as a model of functional divergence that guides the coevolution of interacting proteins.
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Affiliation(s)
- Christine E Genge
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Charles M Stevens
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada Cardiovascular Sciences, Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - William S Davidson
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gurpreet Singh
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Alberta, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Alberta, Canada
| | - Glen F Tibbits
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada Cardiovascular Sciences, Child and Family Research Institute, Vancouver, British Columbia, Canada Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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30
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Li Z, Defoort J, Tasdighian S, Maere S, Van de Peer Y, De Smet R. Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms. THE PLANT CELL 2016; 28:326-44. [PMID: 26744215 PMCID: PMC4790876 DOI: 10.1105/tpc.15.00877] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/04/2016] [Indexed: 05/02/2023]
Abstract
Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes.
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Affiliation(s)
- Zhen Li
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Jonas Defoort
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Setareh Tasdighian
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Riet De Smet
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
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31
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Tine M. Evolutionary significance and diversification of the phosphoglucose isomerase genes in vertebrates. BMC Res Notes 2015; 8:799. [PMID: 26682538 PMCID: PMC4684624 DOI: 10.1186/s13104-015-1683-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/09/2015] [Indexed: 01/20/2024] Open
Abstract
Background Phosphoglucose isomerase (PGI) genes are important multifunctional proteins whose evolution has, until now, not been well elucidated because of the limited number of completely sequenced genomes. Although the multifunctionality of this gene family has been considered as an original and innate characteristic, PGI genes may have acquired novel functions through changes in coding sequences and exon/intron structure, which are known to lead to functional divergence after gene duplication. A whole-genome comparative approach was used to estimate the rates of molecular evolution of this protein family. Results The results confirm the presence of two isoforms in teleost fishes and only one variant in all other vertebrates. Phylogenetic reconstructions grouped the PGI genes into five main groups: lungfishes/coelacanth/cartilaginous fishes, teleost fishes, amphibians, reptiles/birds and mammals, with the teleost group being subdivided into two subclades comprising PGI1 and PGI2. This PGI partitioning into groups is consistent with the synteny and molecular evolution results based on the estimation of the ratios of nonsynonymous to synonymous changes (Ka/Ks) and divergence rates between both PGI paralogs and orthologs. Teleost PGI2 shares more similarity with the variant found in all other vertebrates, suggesting that it has less evolved than PGI1 relative to the PGI of common vertebrate ancestor. Conclusions The diversification of PGI genes into PGI1 and PGI2 is consistent with a teleost-specific duplication before the radiation of this lineage, and after its split from the other infraclasses of ray-finned fishes. The low average Ka/Ks ratios within teleost and mammalian lineages suggest that both PGI1 and PGI2 are functionally constrained by purifying selection and may, therefore, have the same functions. By contrast, the high average Ka/Ks ratios and divergence rates within reptiles and birds indicate that PGI may be involved in different functions. The synteny analyses show that the genomic region harbouring PGI genes has independently undergone genomic rearrangements in mammals versus the reptile/bird lineage in particular, which may have contributed to the actual functional diversification of this gene family. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1683-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mbaye Tine
- Molecular Zoology Laboratory, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa. .,Genome Centre Cologne at MPI for Plant Breeding Research, 22 Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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Dong C, Jiang L, Peng W, Xu J, Mahboob S, Al-Ghanim KA, Sun X, Xu P. Phylogenetic and Evolutionary Analyses of the Frizzled Gene Family in Common Carp (Cyprinus carpio) Provide Insights into Gene Expansion from Whole-Genome Duplications. PLoS One 2015; 10:e0144037. [PMID: 26675214 PMCID: PMC4686014 DOI: 10.1371/journal.pone.0144037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/12/2015] [Indexed: 02/04/2023] Open
Abstract
In humans, the frizzled (FZD) gene family encodes 10 homologous proteins that commonly localize to the plasma membrane. Besides being associated with three main signaling pathways for cell development, most FZDs have different physiological effects and are major determinants in the development process of vertebrates and. Here, we identified and annotated the FZD genes in the whole-genome of common carp (Cyprinus carpio), a teleost fish, and determined their phylogenetic relationships to FZDs in other vertebrates. Our analyses revealed extensive gene duplications in the common carp that have led to the 26 FZD genes that we detected in the common carp genome. All 26 FZD genes were assigned orthology to the 10 FZD genes of on-land vertebrates, with none of genes being specific to the fish lineage. We postulated that the expansion of the FZD gene family in common carp was the result of an additional whole genome duplication event and that the FZD gene family in other teleosts has been lost in their evolution history with the reason that the functions of genes are redundant and conservation. Through the expression profiling of FZD genes in common carp, we speculate that the ancestral gene was likely capable of performing all functions and was expressed broadly, while some descendant duplicate genes only performed partial functions and were specifically expressed at certain stages of development.
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Affiliation(s)
- Chuanju Dong
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Likun Jiang
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenzhu Peng
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jian Xu
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | - Khalid A. Al-Ghanim
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Xiaowen Sun
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
| | - Peng Xu
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
- * E-mail:
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Smith JJ, Keinath MC. The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications. Genome Res 2015; 25:1081-90. [PMID: 26048246 PMCID: PMC4509993 DOI: 10.1101/gr.184135.114] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 06/03/2015] [Indexed: 01/17/2023]
Abstract
It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ∼550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ∼ 99), spanning a total of 5570.25 cM. Comparative mapping data yield strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionarily independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations of vertebrate evolution.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Melissa C Keinath
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
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34
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Kryuchkova-Mostacci N, Robinson-Rechavi M. Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse. PLoS One 2015; 10:e0131673. [PMID: 26121354 PMCID: PMC4488272 DOI: 10.1371/journal.pone.0131673] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/04/2015] [Indexed: 12/23/2022] Open
Abstract
Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.
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Affiliation(s)
- Nadezda Kryuchkova-Mostacci
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Evans BJ, Kwon T. Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs (Xenopus). Cytogenet Genome Res 2015; 145:243-52. [PMID: 26066830 DOI: 10.1159/000431108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost all extant species in this group evolved from a polyploid ancestor. To better understand the nature of selective constraints in a polyploid genome, we examined molecular polymorphism and divergence of duplicates and single-copy genes in 2 tetraploid African clawed frog species, Xenopus laevis and X. victorianus. We found that molecular polymorphism in the coding regions of putative duplicated genes was higher than in singletons, but not significantly so. Our findings also suggest that transcriptome evolution in polyploids is influenced by variation in the genome-wide mutation rate, and do not reject the hypothesis that gene dosage balance is also important.
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Affiliation(s)
- Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ont., Canada
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Zhang J, Ruhlman TA, Sabir J, Blazier JC, Jansen RK. Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae. THE PLANT CELL 2015; 27:563-73. [PMID: 25724640 PMCID: PMC4558654 DOI: 10.1105/tpc.114.134353] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/28/2015] [Accepted: 02/12/2015] [Indexed: 05/08/2023]
Abstract
Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae.
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Affiliation(s)
- Jin Zhang
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Jamal Sabir
- Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - J Chris Blazier
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, Texas 78712 Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Zhao M, Meyers BC, Cai C, Xu W, Ma J. Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean. THE PLANT CELL 2015; 27:546-62. [PMID: 25747880 PMCID: PMC4558674 DOI: 10.1105/tpc.15.00048] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/07/2015] [Accepted: 02/18/2015] [Indexed: 05/04/2023]
Abstract
The evolutionary dynamics of duplicated protein-encoding genes (PEGs) is well documented. However, the evolutionary patterns and consequences of duplicated MIRNAs and the potential influence on the evolution of their PEG targets are poorly understood. Here, we demonstrate the evolution of plant MIRNAs subsequent to a recent whole-genome duplication. Overall, the retention of MIRNA duplicates was correlated to the retention of adjacent PEG duplicates, and the retained MIRNA duplicates exhibited a higher level of interspecific preservation of orthologs than singletons, suggesting that the retention of MIRNA duplicates is related to their functional constraints and local genomic stability. Nevertheless, duplication status, rather than local genic collinearity, was the primary determinant of levels of nucleotide divergence of MIRNAs. In addition, the retention of duplicated MIRNAs appears to be associated with the retention of their corresponding duplicated PEG targets. Furthermore, we characterized the evolutionary novelty of a legume-specific microRNA (miRNA) family, which resulted from rounds of genomic duplication, and consequent dynamic evolution of its NB-LRR targets, an important gene family with primary roles in plant-pathogen interactions. Together, these observations depict evolutionary patterns and novelty of MIRNAs in the context of genomic duplication and evolutionary interplay between MIRNAs and their PEG targets mediated by miRNAs.
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Affiliation(s)
- Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47906
| | - Blake C Meyers
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19716
| | - Chunmei Cai
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Wei Xu
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47906 College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
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Tanimoto J, Fujino H, Takahashi H, Murayama T. Human EP2 prostanoid receptors exhibit more constraints to mutations than human DP prostanoid receptors. FEBS Lett 2015; 589:766-72. [DOI: 10.1016/j.febslet.2015.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 01/25/2023]
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Jiao Y, Paterson AH. Polyploidy-associated genome modifications during land plant evolution. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0355. [PMID: 24958928 DOI: 10.1098/rstb.2013.0355] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more 'particulate' understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity.
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Affiliation(s)
- Yuannian Jiao
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30606, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30606, USA
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Pougach K, Voet A, Kondrashov FA, Voordeckers K, Christiaens JF, Baying B, Benes V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen KJ. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nat Commun 2014; 5:4868. [PMID: 25204769 PMCID: PMC4172970 DOI: 10.1038/ncomms5868] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/31/2014] [Indexed: 11/08/2022] Open
Abstract
The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network.
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Affiliation(s)
- Ksenia Pougach
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Arnout Voet
- Structural Bioinformatics, Center for Life Science Technologies (CLST), RIKEN, 230-0045 Yokohama, Japan
| | - Fyodor A. Kondrashov
- Laboratory of Evolutionary Genomics, Centre for genomic regulation (CRG), 08003 Barcelona, Spain
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Joaquin F. Christiaens
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Bianka Baying
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg (EMBL), 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg (EMBL), 69117 Heidelberg, Germany
| | - Ryo Sakai
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, B-3001 Leuven, Belgium
- iMinds Medical Information Technologies Department, KU Leuven, B-3001 Leuven, Belgium
| | - Jan Aerts
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, B-3001 Leuven, Belgium
- iMinds Medical Information Technologies Department, KU Leuven, B-3001 Leuven, Belgium
| | - Bo Zhu
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Patrick Van Dijck
- Molecular Microbiology and Biotechnology Section, KU Leuven, B-3001 Leuven, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
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Pich I Roselló O, Kondrashov FA. Long-term asymmetrical acceleration of protein evolution after gene duplication. Genome Biol Evol 2014; 6:1949-55. [PMID: 25070510 PMCID: PMC4159008 DOI: 10.1093/gbe/evu159] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolution must end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in the mammalian lineage. We find that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications. We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event.
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Affiliation(s)
- Oriol Pich I Roselló
- Facultat de Medicina, Universitat de Barcelona (UB), SpainBioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, SpainUniversitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, SpainUniversitat Pompeu Fabra (UPF), Barcelona, SpainInstitució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L. Patterns of positive selection in seven ant genomes. Mol Biol Evol 2014; 31:1661-85. [PMID: 24782441 PMCID: PMC4069625 DOI: 10.1093/molbev/msu141] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations are associated with patterns of molecular evolution, we searched for signs of positive selection on amino-acid changes in proteins. We identified 24 functional categories of genes which were enriched for positively selected genes in the ant lineage. We also reanalyzed genome-wide data sets in bees and flies with the same methodology to check whether positive selection was specific to ants or also present in other insects. Notably, genes implicated in immunity were enriched for positively selected genes in the three lineages, ruling out the hypothesis that the evolution of hygienic behaviors in social insects caused a major relaxation of selective pressure on immune genes. Our scan also indicated that genes implicated in neurogenesis and olfaction started to undergo increased positive selection before the evolution of sociality in Hymenoptera. Finally, the comparison between these three lineages allowed us to pinpoint molecular evolution patterns that were specific to the ant lineage. In particular, there was ant-specific recurrent positive selection on genes with mitochondrial functions, suggesting that mitochondrial activity was improved during the evolution of this lineage. This might have been an important step toward the evolution of extreme lifespan that is a hallmark of ants.
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Affiliation(s)
- Julien Roux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eyal Privman
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sébastien Moretti
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, SwitzerlandVital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Josephine T Daub
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, SwitzerlandCMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Osborne OG, Batstone TE, Hiscock SJ, Filatov DA. Rapid speciation with gene flow following the formation of Mt. Etna. Genome Biol Evol 2014; 5:1704-15. [PMID: 23973865 PMCID: PMC3787679 DOI: 10.1093/gbe/evt127] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Environmental or geological changes can create new niches that drive ecological species divergence without the immediate cessation of gene flow. However, few such cases have been characterized. On a recently formed volcano, Mt. Etna, Senecio aethnensis and S. chrysanthemifolius inhabit contrasting environments of high and low altitude, respectively. They have very distinct phenotypes, despite hybridizing promiscuously, and thus may represent an important example of ecological speciation “in action,” possibly as a response to the rapid geological changes that Mt. Etna has recently undergone. To elucidate the species’ evolutionary history, and help establish the species as a study system for speciation genomics, we sequenced the transcriptomes of the two Etnean species, and the outgroup, S. vernalis, using Illumina sequencing. Despite the species’ substantial phenotypic divergence, synonymous divergence between the high- and low-altitude species was low (dS = 0.016 ± 0.017 [SD]). A comparison of species divergence models with and without gene flow provided unequivocal support in favor of the former and demonstrated a recent time of species divergence (153,080 ya ± 11,470 [SE]) that coincides with the growth of Mt. Etna to the altitudes that separate the species today. Analysis of dN/dS revealed wide variation in selective constraint between genes, and evidence that highly expressed genes, more “multifunctional” genes, and those with more paralogs were under elevated purifying selection. Taken together, these results are consistent with a model of ecological speciation, potentially as a response to the emergence of a new, high-altitude niche as the volcano grew.
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Affiliation(s)
- Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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44
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Yampolsky LY, Bouzinier MA. Faster evolving Drosophila paralogs lose expression rate and ubiquity and accumulate more non-synonymous SNPs. Biol Direct 2014; 9:2. [PMID: 24438455 PMCID: PMC3906896 DOI: 10.1186/1745-6150-9-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/07/2014] [Indexed: 12/31/2022] Open
Abstract
Background Duplicated genes can indefinately persist in genomes if either both copies retain the original function due to dosage benefit (gene conservation), or one of the copies assumes a novel function (neofunctionalization), or both copies become required to perform the function previously accomplished by a single copy (subfunctionalization), or through a combination of these mechanisms. Different models of duplication retention imply different predictions about substitution rates in the coding portion of paralogs and about asymmetry of these rates. Results We analyse sequence evolution asymmetry in paralogs present in 12 Drosophila genomes using the nearest non-duplicated orthologous outgroup as a reference. Those paralogs present in D. melanogaster are analysed in conjunction with the asymmetry of expression rate and ubiquity and of segregating non-synonymous polymorphisms in the same paralogs. Paralogs accumulate substitutions, on average, faster than their nearest singleton orthologs. The distribution of paralogs’ substitution rate asymmetry is overdispersed relative to that of orthologous clades, containing disproportionally more unusually symmetric and unusually asymmetric clades. We show that paralogs are more asymmetric in: a) clades orthologous to highly constrained singleton genes; b) genes with high expression level; c) genes with ubiquitous expression and d) non-tandem duplications. We further demonstrate that, in each asymmetrically evolving pair of paralogs, the faster evolving member of the pair tends to have lower average expression rate, lower expression uniformity and higher frequency of non-synonymous SNPs than its slower evolving counterpart. Conclusions Our findings are consistent with the hypothesis that many duplications in Drosophila are retained despite stabilising selection being more relaxed in one of the paralogs than in the other, suggesting a widespread unfinished pseudogenization. This phenomenon is likely to make detection of neo- and subfunctionalization signatures difficult, as these models of duplication retention also predict asymmetries in substitution rates and expression profiles. Reviewers This article has been reviewed by Dr. Jia Zeng (nominated by Dr. I. King Jordan), Dr. Fyodor Kondrashov and Dr. Yuri Wolf.
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Affiliation(s)
- Lev Y Yampolsky
- Department of Biological sciences, East Tennessee State University, Johnson City, TN 37614, USA.
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45
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Behura SK, Singh BK, Severson DW. Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications. Evol Appl 2013; 6:1079-89. [PMID: 24187589 PMCID: PMC3804240 DOI: 10.1111/eva.12088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/14/2013] [Indexed: 12/17/2022] Open
Abstract
Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vectorborne diseases such as malaria, dengue, West Nile, and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the covariance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other nonmosquito insects. By applying a maximum likelihood-based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny-dependent manner, but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame Notre Dame, IN, USA
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46
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Pires IS, Negrão S, Pentony MM, Abreu IA, Oliveira MM, Purugganan MD. Different evolutionary histories of two cation/proton exchanger gene families in plants. BMC PLANT BIOLOGY 2013; 13:97. [PMID: 23822194 PMCID: PMC3726471 DOI: 10.1186/1471-2229-13-97] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 06/27/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Gene duplication events have been proposed to be involved in the adaptation of plants to stress conditions; precisely how is unclear. To address this question, we studied the evolution of two families of antiporters. Cation/proton exchangers are important for normal cell function and in plants, Na+,K+/H+ antiporters have also been implicated in salt tolerance. Two well-known plant cation/proton antiporters are NHX1 and SOS1, which perform Na+ and K+ compartmentalization into the vacuole and Na+ efflux from the cell, respectively. However, our knowledge about the evolution of NHX and SOS1 stress responsive gene families is still limited. RESULTS In this study we performed a comprehensive molecular evolutionary analysis of the NHX and SOS1 families. Using available sequences from a total of 33 plant species, we estimated gene family phylogenies and gene duplication histories, as well as examined heterogeneous selection pressure on amino acid sites. Our results show that, while the NHX family expanded and specialized, the SOS1 family remained a low copy gene family that appears to have undergone neofunctionalization during its evolutionary history. Additionally, we found that both families are under purifying selection although SOS1 is less constrained. CONCLUSIONS We propose that the different evolution histories are related with the proteins' function and localization, and that the NHX and SOS1 families are examples of two different evolutionary paths through which duplication events may result in adaptive evolution of stress tolerance.
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Affiliation(s)
- Inês S Pires
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal and iBET, Apartado 12 2781-901, Oeiras, Portugal
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, US
| | - Sónia Negrão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal and iBET, Apartado 12 2781-901, Oeiras, Portugal
| | - Melissa M Pentony
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, US
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal and iBET, Apartado 12 2781-901, Oeiras, Portugal
| | - Margarida M Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal and iBET, Apartado 12 2781-901, Oeiras, Portugal
| | - Michael D Purugganan
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, US
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Pegueroles C, Laurie S, Albà MM. Accelerated evolution after gene duplication: a time-dependent process affecting just one copy. Mol Biol Evol 2013; 30:1830-42. [PMID: 23625888 DOI: 10.1093/molbev/mst083] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gene duplication is widely regarded as a major mechanism modeling genome evolution and function. However, the mechanisms that drive the evolution of the two, initially redundant, gene copies are still ill defined. Many gene duplicates experience evolutionary rate acceleration, but the relative contribution of positive selection and random drift to the retention and subsequent evolution of gene duplicates, and for how long the molecular clock may be distorted by these processes, remains unclear. Focusing on rodent genes that duplicated before and after the mouse and rat split, we find significantly increased sequence divergence after duplication in only one of the copies, which in nearly all cases corresponds to the novel daughter copy, independent of the mechanism of duplication. We observe that the evolutionary rate of the accelerated copy, measured as the ratio of nonsynonymous to synonymous substitutions, is on average 5-fold higher in the period spanning 4-12 My after the duplication than it was before the duplication. This increase can be explained, at least in part, by the action of positive selection according to the results of the maximum likelihood-based branch-site test. Subsequently, the rate decelerates until purifying selection completely returns to preduplication levels. Reversion to the original rates has already been accomplished 40.5 My after the duplication event, corresponding to a genetic distance of about 0.28 synonymous substitutions per site. Differences in tissue gene expression patterns parallel those of substitution rates, reinforcing the role of neofunctionalization in explaining the evolution of young gene duplicates.
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Affiliation(s)
- Cinta Pegueroles
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Jiang WK, Liu YL, Xia EH, Gao LZ. Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. PLANT PHYSIOLOGY 2013; 161:1844-61. [PMID: 23396833 PMCID: PMC3613460 DOI: 10.1104/pp.112.200147] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs.
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Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci U S A 2013; 110:2898-903. [PMID: 23382190 DOI: 10.1073/pnas.1300127110] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The importance of gene gain through duplication has long been appreciated. In contrast, the importance of gene loss has only recently attracted attention. Indeed, studies in organisms ranging from plants to worms and humans suggest that duplication of some genes might be better tolerated than that of others. Here we have undertaken a large-scale study to investigate the existence of duplication-resistant genes in the sequenced genomes of 20 flowering plants. We demonstrate that there is a large set of genes that is convergently restored to single-copy status following multiple genome-wide and smaller scale duplication events. We rule out the possibility that such a pattern could be explained by random gene loss only and therefore propose that there is selection pressure to preserve such genes as singletons. This is further substantiated by the observation that angiosperm single-copy genes do not comprise a random fraction of the genome, but instead are often involved in essential housekeeping functions that are highly conserved across all eukaryotes. Furthermore, single-copy genes are generally expressed more highly and in more tissues than non-single-copy genes, and they exhibit higher sequence conservation. Finally, we propose different hypotheses to explain their resistance against duplication.
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Sezutsu H, Le Goff G, Feyereisen R. Origins of P450 diversity. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120428. [PMID: 23297351 DOI: 10.1098/rstb.2012.0428] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The P450 enzymes maintain a conserved P450 fold despite a considerable variation in sequence. The P450 family even includes proteins that lack the single conserved cysteine and are therefore no longer haem-thiolate proteins. The mechanisms of successive gene duplications leading to large families in plants and animals are well established. Comparisons of P450 CYP gene clusters in related species illustrate the rapid changes in CYPome sizes. Examples of CYP copy number variation with effects on fitness are emerging, and these provide an opportunity to study the proximal causes of duplication or pseudogenization. Birth and death models can explain the proliferation of CYP genes that is amply illustrated by the sequence of every new genome. Thus, the distribution of P450 diversity within the CYPome of plants and animals, a few families with many genes (P450 blooms) and many families with few genes, follows similar power laws in both groups. A closer look at some families with few genes shows that these, often single member families, are not stable during evolution. The enzymatic prowess of P450 may predispose them to switch back and forth between metabolism of critical structural or signal molecules and metabolism dedicated to environmental response.
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Affiliation(s)
- Hideki Sezutsu
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 3058634, Japan
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