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Verta JP, Jacobs A. The evolutionary significance of post-transcriptional gene regulation. Heredity (Edinb) 2024; 132:117-119. [PMID: 38366090 PMCID: PMC10923911 DOI: 10.1038/s41437-024-00674-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| | - Arne Jacobs
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK.
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Ahi EP, Verta JP, Kurko J, Ruokolainen A, Singh P, Debes PV, Erkinaro J, Primmer CR. Gene co-expression patterns in Atlantic salmon adipose tissue provide a molecular link among seasonal changes, energy balance and age at maturity. Mol Ecol 2024:e17313. [PMID: 38429895 DOI: 10.1111/mec.17313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Sexual maturation in many fishes requires a major physiological change that involves a rapid transition between energy storage and usage. In Atlantic salmon, this transition for the initiation of maturation is tightly controlled by seasonality and requires a high-energy status. Lipid metabolism is at the heart of this transition since lipids are the main energy storing molecules. The balance between lipogenesis (lipid accumulation) and lipolysis (lipid use) determines energy status transitions. A genomic region containing a transcription co-factor of the Hippo pathway, vgll3, is the main determinant of maturation timing in Atlantic salmon. Interestingly, vgll3 acts as an inhibitor of adipogenesis in mice and its genotypes are potentially associated with seasonal heterochrony in lipid storage and usage in juvenile Atlantic salmon. Here, we explored changes in expression of more than 300 genes directly involved in the processes of adipogenesis, lipogenesis and lipolysis, as well as the Hippo pathway in the adipose tissue of immature and mature Atlantic salmon with distinct vgll3 genotypes. We found molecular evidence consistent with a scenario in which immature males with different vgll3 genotypes exhibit contrasting seasonal dynamics in their lipid profiles. We also identified components of the Hippo signalling pathway as potential major drivers of vgll3 genotype-specific differences in adipose tissue gene expression. This study demonstrates the importance of adipose gene expression patterns for directly linking environmental changes with energy balance and age at maturity through genetic factors bridging lipid metabolism, seasonality and sexual maturation.
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Affiliation(s)
- Ehsan Pashay Ahi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Johanna Kurko
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Annukka Ruokolainen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pooja Singh
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Center for Ecology, Evolution & Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Paul Vincent Debes
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Aquaculture and Fish Biology, Hólar University, Sauoarkrokur, Iceland
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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Verta JP, Jacobs A. The role of alternative splicing in adaptation and evolution. Trends Ecol Evol 2022; 37:1116. [DOI: 10.1016/j.tree.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
Regulation of gene expression plays a central role in adaptive divergence and evolution. Although the role of gene regulation in microevolutionary processes is gaining wide acceptance, most studies have only investigated the evolution of transcript levels, ignoring the potentially significant role of transcript structures. We argue that variation in alternative splicing plays an important and widely unexplored role in adaptation (e.g., by increasing transcriptome and/or proteome diversity, or buffering potentially deleterious genetic variation). New studies increasingly highlight the potential for independent evolution in alternative splicing and transcript level, providing alternative paths for selection to act upon. We propose that alternative splicing and transcript levels can provide contrasting, nonredundant mechanisms of equal importance for adaptive diversification of gene function and regulation.
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Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, UK.
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Verta JP, Barton HJ, Pritchard V, Primmer CR. Genetic Drift Dominates Genome-Wide Regulatory Evolution Following an Ancient Whole-Genome Duplication in Atlantic Salmon. Genome Biol Evol 2021; 13:evab059. [PMID: 33749748 PMCID: PMC8140206 DOI: 10.1093/gbe/evab059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 11/23/2022] Open
Abstract
Whole-genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Ma. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue-specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained regulatory divergence. Patterns of genetic diversity across natural populations inferred from resequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.
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Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Henry J Barton
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Victoria Pritchard
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
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Andrew SC, Primmer CR, Debes PV, Erkinaro J, Verta JP. The Atlantic salmon whole blood transcriptome and how it relates to major locus maturation genotypes and other tissues. Mar Genomics 2020; 56:100809. [PMID: 33632426 DOI: 10.1016/j.margen.2020.100809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
The Atlantic salmon (Salmo salar) is important to many ecosystems and local economies and has therefore become the focus of a broad range of research questions that have benefited from the availability of high-quality genomic resources. Albeit gene expression studies have been extensive for this species, the transcriptome information for Atlantic salmon whole blood has been lacking. A transcriptome of Atlantic salmon blood would be a valuable resource for future studies, especially those wishing to take non-lethal samples. Here, we report a whole blood transcriptome for Atlantic salmon constructed from twelve 8-month old salmon parr using RNA-seq. We identify transcriptomic proxies for the genotype at the major maturation timing locus vestigial-like 3 (vgll3). Differentially expressed genes between the early and late maturing genotypes showed overrepresented Gene Ontology (GO) terms with the strongest result linked to 13 ribosomal subunit genes. To assess how the whole blood gene expression profile relates to other tissues, we compare the blood transcriptome to the reference transcriptome of fourteen other tissue types using both a common PCA method and a novel method. The novel method compares transcriptomes when gene expression is visualised as a layer using thin-plate spline smoothers. Both methods found similar patterns with the blood transcriptome being quite unique compared to the transcription profiles of other tissues.
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Affiliation(s)
- Samuel C Andrew
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland
| | - Paul V Debes
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland; Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | | | - Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland.
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Verta JP, Jones F. mRNA Extraction from Gill Tissue for RNA-sequencing. Bio Protoc 2020; 10:e3539. [PMID: 33659513 PMCID: PMC7842710 DOI: 10.21769/bioprotoc.3539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 01/15/2020] [Indexed: 11/10/2022] Open
Abstract
Adaptation is thought to proceed in part through spatial and temporal changes in gene expression. Fish species such as the threespine stickleback are powerful vertebrate models to study the genetic architecture of adaptive changes in gene expression since divergent adaptation to different environments is common, they are abundant and easy to study in the wild and lab, and have well-established genetic and genomic resources. Fish gills, due to their respiratory and osmoregulatory roles, show many physiological adaptations to local water chemistry, including differences in gene expression. However, obtaining high-quality RNA using popular column-based extraction methods can be challenging from small tissue samples high in cartilage and bone such as fish gills. Here, we describe a bead-based mRNA extraction and transcriptome RNA-seq protocol that does not use purification columns. The protocol can be readily scaled according to sample size for the purposes of diverse gene expression experiments using animal or plant tissue.
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Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, Germany
| | - Felicity Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, Germany
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Abstract
Regulation of gene expression is thought to play a major role in adaptation, but the relative importance of cis- and trans- regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution.
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Affiliation(s)
- Jukka-Pekka Verta
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
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Verta JP, Landry CR, MacKay J. Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system - insights into compensatory evolution of transcriptional regulation within populations. New Phytol 2016; 211:159-171. [PMID: 26891783 DOI: 10.1111/nph.13888] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
Regulation of gene expression plays a central role in translating genotypic variation into phenotypic variation. Dissection of the genetic basis of expression variation is key to understanding how expression regulation evolves. Such analyses remain challenging in contexts where organisms are outbreeding, highly heterozygous and long-lived such as in the case of conifer trees. We developed an RNA sequencing (RNA-seq)-based approach for both expression-quantitative trait locus (eQTL) mapping and the detection of cis-acting (allele-specific) vs trans-acting (non-allele-specific) eQTLs. This method can be potentially applied to many conifers. We used haploid and diploid meiotic seed tissues of a single self-fertilized white spruce (Picea glauca) individual to dissect eQTLs according to linkage and allele specificity. The genetic architecture of local eQTLs linked to the expressed genes was particularly complex, consisting of cis-acting, trans-acting and, surprisingly, compensatory cis-trans effects. These compensatory effects influence expression in opposite directions and are neutral when combined in homozygotes. Nearly half of local eQTLs were under compensation, indicating that close linkage between compensatory cis-trans factors is common in spruce. Compensated genes were overrepresented in developmental and cell organization functions. Our haploid-diploid eQTL analysis in spruce revealed that compensatory cis-trans eQTLs segregate within populations and evolve in close genetic linkage.
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Affiliation(s)
- Jukka-Pekka Verta
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, Canada G1V 0A6
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
- Département de Biologie, Université Laval, Québec, QC, Canada G1V 0A6
| | - John MacKay
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, Canada G1V 0A6
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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Prunier J, Verta JP, MacKay JJ. Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. New Phytol 2016; 209:44-62. [PMID: 26206592 DOI: 10.1111/nph.13565] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/14/2015] [Indexed: 05/21/2023]
Abstract
Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.
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Affiliation(s)
- Julien Prunier
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Jukka-Pekka Verta
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany
| | - John J MacKay
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
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Verta JP, Landry CR, MacKay JJ. Are long-lived trees poised for evolutionary change? Single locus effects in the evolution of gene expression networks in spruce. Mol Ecol 2013; 22:2369-79. [DOI: 10.1111/mec.12189] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 11/26/2012] [Indexed: 02/04/2023]
Affiliation(s)
- Jukka-Pekka Verta
- Département des Sciences du Bois et de la Forêt & Centre d’Étude de la Forêt; Université Laval; Québec QC Canada G1V 0A6
- Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec QC Canada G1V 0A6
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec QC Canada G1V 0A6
- Département de Biologie & PROTEO; Université Laval; Québec QC Canada G1V 0A6
| | - John J. MacKay
- Département des Sciences du Bois et de la Forêt & Centre d’Étude de la Forêt; Université Laval; Québec QC Canada G1V 0A6
- Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec QC Canada G1V 0A6
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Raherison E, Rigault P, Caron S, Poulin PL, Boyle B, Verta JP, Giguère I, Bomal C, Bohlmann J, MacKay J. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics 2012; 13:434. [PMID: 22931377 PMCID: PMC3534630 DOI: 10.1186/1471-2164-13-434] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/11/2012] [Indexed: 12/22/2022] Open
Abstract
Background Conifers have very large genomes (13 to 30 Gigabases) that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues. Results An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs. Conclusion Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.
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Affiliation(s)
- Elie Raherison
- Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, QC, Canada, G1V 0A6
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Verta JP, Caron S, Giguère I, Boyle B, Landry CR, MacKay J. Haploid transcriptome analysis reveals allelelic gene expression variants, co-expressed gene groups, and linkages between expression and copy number variation. BMC Proc 2011. [PMCID: PMC3239919 DOI: 10.1186/1753-6561-5-s7-o47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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