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Majane AC, Cridland JM, Blair LK, Begun DJ. Evolution and genetics of accessory gland transcriptome divergence between Drosophila melanogaster and D. simulans. Genetics 2024; 227:iyae039. [PMID: 38518250 PMCID: PMC11151936 DOI: 10.1093/genetics/iyae039] [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: 08/27/2023] [Revised: 08/27/2023] [Accepted: 02/15/2024] [Indexed: 03/24/2024] Open
Abstract
Studies of allele-specific expression in interspecific hybrids have provided important insights into gene-regulatory divergence and hybrid incompatibilities. Many such investigations in Drosophila have used transcriptome data from complex mixtures of many tissues or from gonads, however, regulatory divergence may vary widely among species, sexes, and tissues. Thus, we lack sufficiently broad sampling to be confident about the general biological principles of regulatory divergence. Here, we seek to fill some of these gaps in the literature by characterizing regulatory evolution and hybrid misexpression in a somatic male sex organ, the accessory gland, in F1 hybrids between Drosophila melanogaster and D. simulans. The accessory gland produces seminal fluid proteins, which play an important role in male and female fertility and may be subject to adaptive divergence due to male-male or male-female interactions. We find that trans differences are relatively more abundant than cis, in contrast to most of the interspecific hybrid literature, though large effect-size trans differences are rare. Seminal fluid protein genes have significantly elevated levels of expression divergence and tend to be regulated through both cis and trans divergence. We find limited misexpression (over- or underexpression relative to both parents) in this organ compared to most other Drosophila studies. As in previous studies, male-biased genes are overrepresented among misexpressed genes and are much more likely to be underexpressed. ATAC-Seq data show that chromatin accessibility is correlated with expression differences among species and hybrid allele-specific expression. This work identifies unique regulatory evolution and hybrid misexpression properties of the accessory gland and suggests the importance of tissue-specific allele-specific expression studies.
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Affiliation(s)
- Alex C Majane
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Julie M Cridland
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Logan K Blair
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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2
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Shabbir M, Mithani A. Roast: a tool for reference-free optimization of supertranscriptome assemblies. BMC Bioinformatics 2024; 25:2. [PMID: 38166712 PMCID: PMC10763045 DOI: 10.1186/s12859-023-05614-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Transcriptomic studies involving organisms for which reference genomes are not available typically start by generating de novo transcriptome or supertranscriptome assembly from the raw RNA-seq reads. Assembling a supertranscriptome is, however, a challenging task due to significantly varying abundance of mRNA transcripts, alternative splicing, and sequencing errors. As a result, popular de novo supertranscriptome assembly tools generate assemblies containing contigs that are partially-assembled, fragmented, false chimeras or have local mis-assemblies leading to decreased assembly accuracy. Commonly available tools for assembly improvement rely primarily on running BLAST using closely related species making their accuracy and reliability conditioned on the availability of the data for closely related organisms. RESULTS We present ROAST, a tool for optimization of supertranscriptome assemblies that uses paired-end RNA-seq data from Illumina sequencing platform to iteratively identify and fix assembly errors solely using the error signatures generated by RNA-seq alignment tools including soft-clips, unexpected expression coverage, and reads with mates unmapped or mapped on a different contig to identify and fix various supertranscriptome assembly errors without performing BLAST searches against other organisms. Evaluation results using simulated as well as real datasets show that ROAST significantly improves assembly quality by identifying and fixing various assembly errors. CONCLUSION ROAST provides a reference-free approach to optimizing supertranscriptome assemblies highlighting its utility in refining de novo supertranscriptome assemblies of non-model organisms.
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Affiliation(s)
- Madiha Shabbir
- Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore, 54792, Pakistan
| | - Aziz Mithani
- Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore, 54792, Pakistan.
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3
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Bhaskara GB, Haque T, Bonnette JE, Napier JD, Bauer D, Schmutz J, Juenger TE. Evolutionary Analyses of Gene Expression Divergence in Panicum hallii: Exploring Constitutive and Plastic Responses Using Reciprocal Transplants. Mol Biol Evol 2023; 40:msad210. [PMID: 37738160 PMCID: PMC10556983 DOI: 10.1093/molbev/msad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST-QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis-environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.
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Affiliation(s)
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Jason E Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Diane Bauer
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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4
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Moldovan MA, Gaydukova SA. Unusual Dependence between Gene Expression and Negative Selection in Euplotes. Mol Biol 2022. [DOI: 10.1134/s0026893323010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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Hämälä T, Ning W, Kuittinen H, Aryamanesh N, Savolainen O. Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife 2022; 11:83115. [PMID: 36306157 PMCID: PMC9616567 DOI: 10.7554/elife.83115] [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: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint – the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Weixuan Ning
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Nader Aryamanesh
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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6
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Field JT, Abrams AJ, Cartee JC, McTavish EJ. Rapid alignment updating with Extensiphy. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jasper Toscani Field
- Quantitative and Systems Biology Program School of Natural Sciences University of California Merced CA USA
| | - A. Jeanine Abrams
- Division of STD Prevention National Centers for HIV/AIDS Viral Hepatitis, STD, and TB Prevention Atlanta GA USA
| | - John C. Cartee
- Division of STD Prevention National Centers for HIV/AIDS Viral Hepatitis, STD, and TB Prevention Atlanta GA USA
| | - Emily Jane McTavish
- Life and Environmental Sciences Department School of Natural Sciences University of California Merced CA USA
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7
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Jacobs A, Elmer KR. Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish. Mol Ecol 2021; 30:4955-4969. [PMID: 33502030 PMCID: PMC8653899 DOI: 10.1111/mec.15817] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/06/2021] [Accepted: 01/18/2021] [Indexed: 12/25/2022]
Abstract
Understanding the contribution of different molecular processes to evolution and development is crucial for identifying the mechanisms of adaptation. Here, we used RNA-sequencing data to test the importance of alternative splicing and differential gene expression in a case of parallel adaptive evolution, the replicated postglacial divergence of the salmonid fish Arctic charr (Salvelinus alpinus) into sympatric benthic and pelagic ecotypes across multiple independent lakes. We found that genes differentially spliced between ecotypes were mostly not differentially expressed (<6% overlap) and were involved in different biological processes. Differentially spliced genes were primarily enriched for muscle development and functioning, while differentially expressed genes were involved in metabolism, immunity and growth. Furthermore, alternative splicing and gene expression were mostly controlled by independent cis-regulatory quantitative trait loci (<3.4% overlap). Cis-regulatory regions were associated with the parallel divergence in splicing (16.5% of intron clusters) and expression (6.7%-10.1% of differentially expressed genes), indicating shared regulatory variation across ecotype pairs. Contrary to theoretical expectation, we found that differentially spliced genes tended to be highly central in regulatory networks ("hub genes") and were annotated to significantly more gene ontology terms compared to nondifferentially spliced genes, consistent with a higher level of pleiotropy. Together, our results suggest that the concerted regulation of alternative splicing and differential gene expression through different regulatory regions leads to the divergence of complementary processes important for local adaptation. This provides novel insights into the importance of contrasting but putatively complementary molecular processes in rapid parallel adaptive evolution.
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Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
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8
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Tebben K, Bradwell K, Serre D. Variation in selective constraints along the Plasmodium life cycle. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 92:104908. [PMID: 33975022 PMCID: PMC8205998 DOI: 10.1016/j.meegid.2021.104908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
Plasmodium parasites, the cause of malaria, have a complex life cycle, infecting alternatively vertebrate hosts and female Anopheles mosquitoes and undergoing intra- and extra-cellular development in several organs of these hosts. Most of the ~5000 protein-coding genes present in Plasmodium genomes are only expressed at specific life stages, and different genes might therefore be subject to different selective pressures depending on the biological activity of the parasite and its microenvironment at this point in development. Here, we estimate the selective constraints on the protein-coding sequences of all annotated genes of rodent and primate Plasmodium parasites and, using data from scRNA-seq experiments spanning many developmental stages, analyze their variation with regard to when these genes are expressed in the parasite life cycle. Our study reveals extensive variation in selective constraints throughout the parasites' development and highlights stages that are evolving more rapidly than others. These findings provide novel insights into the biology of these parasites and could provide important information to develop better treatment strategies or vaccines against these medically-important organisms.
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Affiliation(s)
- Kieran Tebben
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Katie Bradwell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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9
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Winkelmüller TM, Entila F, Anver S, Piasecka A, Song B, Dahms E, Sakakibara H, Gan X, Kułak K, Sawikowska A, Krajewski P, Tsiantis M, Garrido-Oter R, Fukushima K, Schulze-Lefert P, Laurent S, Bednarek P, Tsuda K. Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. THE PLANT CELL 2021; 33:1863-1887. [PMID: 33751107 PMCID: PMC8290292 DOI: 10.1093/plcell/koab073] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/24/2021] [Indexed: 05/20/2023]
Abstract
Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5'-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.
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Affiliation(s)
- Thomas M Winkelmüller
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Frederickson Entila
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Shajahan Anver
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present address: Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Baoxing Song
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present address: Institute for Genomic Diversity, Cornell University, Ithaca, New York
| | - Eik Dahms
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 230-0045 Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Karolina Kułak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Present address: Department of Computational Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Aneta Sawikowska
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-628 Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Paul Schulze-Lefert
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, 430070 Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, 430070 Wuhan, China
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Author for correspondence:
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10
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Booker TR, Yeaman S, Whitlock MC. Global adaptation complicates the interpretation of genome scans for local adaptation. Evol Lett 2020; 5:4-15. [PMID: 33552532 PMCID: PMC7857299 DOI: 10.1002/evl3.208] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/27/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome‐wide distribution of summary statistics measuring genetic differentiation, such as FST, are often interpreted as evidence for alleles that contribute to local adaptation. However, theoretical studies have shown that in spatially structured populations the spread of beneficial mutations with spatially uniform fitness effects can also induce transient genetic differentiation. In recent years, numerous empirical studies have suggested that such species‐wide, or global, adaptation makes a substantial contribution to molecular evolution. In this perspective, we discuss how commonly such global adaptation may influence the genome‐wide distribution of FST and generate genetic differentiation patterns, which could be mistaken for local adaptation. To illustrate this, we use forward‐in‐time population genetic simulations assuming parameters for the rate and strength of beneficial mutations consistent with estimates from natural populations. We demonstrate that the spread of globally beneficial mutations in parapatric populations may frequently generate FST outliers, which could be misinterpreted as evidence for local adaptation. The spread of beneficial mutations causes selective sweeps at flanking sites, so in some cases, the effects of global versus local adaptation may be distinguished by examining patterns of nucleotide diversity within and between populations in addition to FST. However, when local adaptation has been only recently established, it may be much more difficult to distinguish from global adaptation, due to less accumulation of linkage disequilibrium at flanking sites. Through our discussion, we conclude that a large fraction of FST outliers that are presumed to arise from local adaptation may instead be due to global adaptation.
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Affiliation(s)
- Tom R Booker
- Department of Forest and Conservation Sciences University of British Columbia Vancouver Canada.,Biodiversity Research Centre University of British Columbia Vancouver Canada
| | - Sam Yeaman
- Department of Biological Sciences University of Calgary Calgary Canada
| | - Michael C Whitlock
- Biodiversity Research Centre University of British Columbia Vancouver Canada.,Department of Zoology University of British Columbia Vancouver Canada
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11
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Lian S, Zhou Y, Liu Z, Gong A, Cheng L. The differential expression patterns of paralogs in response to stresses indicate expression and sequence divergences. BMC PLANT BIOLOGY 2020; 20:277. [PMID: 32546126 PMCID: PMC7298774 DOI: 10.1186/s12870-020-02460-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/24/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Theoretically, paralogous genes generated through whole genome duplications should share identical expression levels due to their identical sequences and chromatin environments. However, functional divergences and expression differences have arisen due to selective pressures throughout evolution. A comprehensive investigation of the expression patterns of paralogous gene pairs in response to various stresses and a study of correlations between the expression levels and sequence divergences of the paralogs are needed. RESULTS In this study, we analyzed the expression patterns of paralogous genes under different types of stress and investigated the correlations between the expression levels and sequence divergences of the paralogs. We analyzed the differential expression patterns of the paralogs under four different types of stress (drought, cold, infection, and herbivory) and classified them into three main types according to their expression patterns. We then further analyzed the differential expression patterns under various degrees of stress and constructed corresponding co-expression networks of differentially expressed paralogs and transcription factors. Finally, we investigated the correlations between the expression levels and sequence divergences of the paralogs and identified positive correlations between expression level and sequence divergence. With regard to sequence divergence, we identified correlations between selective pressures and phylogenetic relationships. CONCLUSIONS These results shed light on differential expression patterns of paralogs in response to environmental stresses and are helpful for understanding the relationships between expression levels and sequences divergences.
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Affiliation(s)
- Shuaibin Lian
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Yongjie Zhou
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Zixiao Liu
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Andong Gong
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Lin Cheng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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12
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Popovic I, Riginos C. Comparative genomics reveals divergent thermal selection in warm‐ and cold‐tolerant marine mussels. Mol Ecol 2020; 29:519-535. [DOI: 10.1111/mec.15339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Iva Popovic
- School of Biological Sciences University of Queensland St Lucia Qld Australia
| | - Cynthia Riginos
- School of Biological Sciences University of Queensland St Lucia Qld Australia
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13
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Pyhäjärvi T, Kujala ST, Savolainen O. 275 years of forestry meets genomics in Pinus sylvestris. Evol Appl 2020; 13:11-30. [PMID: 31988655 PMCID: PMC6966708 DOI: 10.1111/eva.12809] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.
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Affiliation(s)
- Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | | | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
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14
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Liu K, Hao X, Wang Q, Hou J, Lai X, Dong Z, Shao C. Genome-wide identification and characterization of heat shock protein family 70 provides insight into its divergent functions on immune response and development of Paralichthys olivaceus. PeerJ 2019; 7:e7781. [PMID: 31737440 PMCID: PMC6855204 DOI: 10.7717/peerj.7781] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
Flatfish undergo extreme morphological development and settle to a benthic in the adult stage, and are likely to be more susceptible to environmental stress. Heat shock proteins 70 (hsp70) are involved in embryonic development and stress response in metazoan animals. However, the evolutionary history and functions of hsp70 in flatfish are poorly understood. Here, we identified 15 hsp70 genes in the genome of Japanese flounder (Paralichthys olivaceus), a flatfish endemic to northwestern Pacific Ocean. Gene structure and motifs of the Japanese flounder hsp70 were conserved, and there were few structure variants compared to other fish species. We constructed a maximum likelihood tree to understand the evolutionary relationship of the hsp70 genes among surveyed fish. Selection pressure analysis suggested that four genes, hspa4l, hspa9, hspa13, and hyou1, showed signs of positive selection. We then extracted transcriptome data on the Japanese flounder with Edwardsiella tarda to induce stress, and found that hspa9, hspa12b, hspa4l, hspa13, and hyou1 were highly expressed, likely to protect cells from stress. Interestingly, expression patterns of hsp70 genes were divergent in different developmental stages of the Japanese flounder. We found that at least one hsp70 gene was always highly expressed at various stages of embryonic development of the Japanese flounder, thereby indicating that hsp70 genes were constitutively expressed in the Japanese flounder. Our findings provide basic and useful resources to better understand hsp70 genes in flatfish.
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Affiliation(s)
- Kaiqiang Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China.,Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Xiancai Hao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
| | - Qian Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
| | - Jilun Hou
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Beidaihe, China
| | - Xiaofang Lai
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Changwei Shao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
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15
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Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. G3-GENES GENOMES GENETICS 2019; 9:3409-3421. [PMID: 31427456 PMCID: PMC6778806 DOI: 10.1534/g3.119.400357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
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16
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Chen J, Li L, Milesi P, Jansson G, Berlin M, Karlsson B, Aleksic J, Vendramin GG, Lascoux M. Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce. Evol Appl 2019; 12:1539-1551. [PMID: 31462913 PMCID: PMC6708423 DOI: 10.1111/eva.12801] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 12/23/2022] Open
Abstract
Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.
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Affiliation(s)
- Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Lili Li
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gunnar Jansson
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Mats Berlin
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Bo Karlsson
- Forestry Research Institute of Sweden (Skogforsk)EkeboSweden
| | - Jelena Aleksic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
| | - Giovanni G. Vendramin
- Division of Florence, Institute of Biosciences and BioResourcesNational Research Council (IBBR‐CNR)Sesto FiorentinoItaly
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
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17
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Lu M, Hodgins KA, Degner JC, Yeaman S. Purifying selection does not drive signatures of convergent local adaptation of lodgepole pine and interior spruce. BMC Evol Biol 2019; 19:110. [PMID: 31138118 PMCID: PMC6537219 DOI: 10.1186/s12862-019-1438-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Previous studies identified 47 genes containing variants associated with environmental variables in both species, providing evidence of convergent local adaptation. However, if the intensity of purifying selection varies with the environment, clines in nucleotide diversity could evolve through linked (background) selection that would yield allele frequency-environment signatures resembling local adaptation. If similar geographic patterns in the strength of purifying selection occur in these species, this could result in the convergent signatures of local adaptation, especially if the landscape of recombination is conserved. In the present study, we investigated whether spatially/environmentally varying purifying selection could give rise to the convergent signatures of local adaptation that had previously reported. RESULTS We analyzed 86 lodgepole pine and 50 interior spruce natural populations spanning heterogeneous environments in western Canada where previous analyses had found signatures of convergent local adaptation. We estimated nucleotide diversity and Tajima's D for each gene within each population and calculated the strength of correlations between nucleotide diversity and environmental variables. Overall, these estimates in the genes with previously identified convergent local adaptation signatures had no similar pattern between pine and spruce. Clines in nucleotide diversity along environmental variables were found for interior spruce, but not for lodgepole pine. In spruce, genes with convergent adaption signatures showed a higher strength of correlations than genes without convergent adaption signatures, but there was no such disparity in pine, which suggests the pattern in spruce may have arisen due to a combination of selection and hybridization. CONCLUSIONS The results rule out purifying/background selection as a driver of convergent local adaption signatures in lodgepole pine and interior spruce.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada.
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University - Clayton Campus, Building 17, Wellington Road, Melbourne, 3800, Australia
| | - Jon C Degner
- Department of Forest and Conservation Sciences, Forest Sciences Centre 3041, University of British Columbia, 2424 Main Mall, Vancouver, V6T 1Z4, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada
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18
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Ravindran SP, Herrmann M, Cordellier M. Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations. Ecol Evol 2019; 9:2487-2504. [PMID: 30891195 PMCID: PMC6405927 DOI: 10.1002/ece3.4894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata. Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor.
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Affiliation(s)
| | - Maike Herrmann
- Department of Veterinary MedicinePaul‐Ehrlich‐InstitutLangenGermany
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19
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Assis R. Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication. Genome Biol Evol 2019; 11:207-219. [PMID: 30398650 PMCID: PMC6331041 DOI: 10.1093/gbe/evy245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2018] [Indexed: 02/02/2023] Open
Abstract
Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here, I address this question on a genome-wide scale by applying a novel branch-based statistic of lineage-specific expression divergence, LED, to RNA-seq data from nine tissues of the wild grass Brachypodium distachyon and its domesticated relatives Oryza sativa japonica (rice) and Sorghum bicolor (sorghum). I find that LED is generally smallest in B. distachyon and largest in O. sativa japonica, which underwent domestication earlier than S. bicolor, supporting the hypothesis that domestication may increase the rate of lineage-specific expression divergence in grasses. Moreover, in all three species, LED is positively correlated with protein-coding sequence divergence and tissue specificity, and negatively correlated with network connectivity. Further analysis reveals that genes with large LED are often primarily expressed in anther, implicating lineage-specific expression divergence in the evolution of male reproductive phenotypes. Gene ontology enrichment analysis also identifies an overrepresentation of terms related to male reproduction in the two domesticated grasses, as well as to those involved in host-pathogen defense in all three species. Last, examinations of genes with the largest LED reveal that their lineage-specific expression divergence may have contributed to antimicrobial functions in B. distachyon, to enhanced adaptation and yield during domestication in O. sativa japonica, and to defense against a widespread and devastating fungal pathogen in S. bicolor. Together, these findings suggest that lineage-specific expression divergence in grasses may increase under domestication and preferentially target rapidly evolving genes involved in male reproduction, host-pathogen defense, and the origin of domesticated phenotypes.
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Affiliation(s)
- Raquel Assis
- Department of Biology, Pennsylvania State University, University Park
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20
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Brown AP, Arias-Rodriguez L, Yee MC, Tobler M, Kelley JL. Concordant Changes in Gene Expression and Nucleotides Underlie Independent Adaptation to Hydrogen-Sulfide-Rich Environments. Genome Biol Evol 2018; 10:2867-2881. [PMID: 30215710 PMCID: PMC6225894 DOI: 10.1093/gbe/evy198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2018] [Indexed: 12/23/2022] Open
Abstract
The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary process. In this study, our objectives were 1) to better understand the qualitative concordance between conclusions drawn from analyses of differential expression and changes in genic sequence and 2) to quantitatively test whether differentially expressed genes were enriched for sites putatively under positive selection within gene regions. To achieve this, we compared populations of fish (Poecilia mexicana) that have independently adapted to hydrogen-sulfide-rich environments in southern Mexico to adjacent populations residing in nonsulfidic waters. Specifically, we used RNA-sequencing data to compare both gene expression and DNA sequence differences between populations. Analyzing these two different data types led to similar conclusions about which biochemical pathways (sulfide detoxification and cellular respiration) were involved in adaptation to sulfidic environments. Additionally, we found a greater overlap between genes putatively under selection and differentially expressed genes than expected by chance. We conclude that considering both differential expression and changes in DNA sequence led to a more comprehensive understanding of how these populations adapted to extreme environmental conditions. Our results imply that changes in both gene expression and DNA sequence-sometimes at the same loci-may be involved in adaptation.
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Affiliation(s)
- Anthony P Brown
- School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, México
| | - Muh-Ching Yee
- Stanford Functional Genomics Facility, CCSR 0120, Stanford, CA 94305
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164
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21
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Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Sci Rep 2018; 8:16147. [PMID: 30385764 PMCID: PMC6212547 DOI: 10.1038/s41598-018-33897-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
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Affiliation(s)
- María José Rivas
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - María Saura
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Tomas Johansson
- Department of Biology, University of Lund, SE-223 62, Lund, Sweden
| | - Carl André
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Emilio Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain.
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22
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Song H, Sun J, Yang G. Comparative analysis of selection mode reveals different evolutionary rate and expression pattern in Arachis duranensis and Arachis ipaënsis duplicated genes. PLANT MOLECULAR BIOLOGY 2018; 98:349-361. [PMID: 30298428 DOI: 10.1007/s11103-018-0784-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
Our results reveal that Ks is a determining factor affecting selective pressure and different evolution and expression patterns are detected between PSGs and NSGs in wild Arachis duplicates. Selective pressure, including purifying (negative) and positive selection, can be detected in organisms. However, studies on comparative evolutionary rates, gene expression patterns and gene features between negatively selected genes (NSGs) and positively selected genes (PSGs) are lagging in paralogs of plants. Arachis duranensis and Arachis ipaënsis are ancestors of the cultivated peanut, an important oil and protein crop. Here, we carried out a series of systematic analyses, comparing NSG and PSG in paralogs, using genome sequences and transcriptome datasets in A. duranensis and A. ipaënsis. We found that synonymous substitution rate (Ks) is a determining factor affecting selective pressure in A. duranensis and A. ipaënsis duplicated genes. Lower expression level, lower gene expression breadth, higher codon bias and shorter polypeptide length were found in PSGs and not in NSGs. The correlation analyses showed that gene expression breadth was positively correlated with polypeptide length and GC content at the first codon site (GC1) in PSGs and NSGs, respectively. There was a negative correlation between expression level and polypeptide length in PSGs. In NSGs, the Ks was positively correlated with expression level, gene expression breadth, GC1, and GC content at the third codon site (GC3), but selective pressure was negatively correlated with expression level, gene expression breadth, polypeptide length, GC1, and GC3 content. The function of most duplicated gene pairs was divergent under drought and nematode stress. Taken together, our results show that different evolution and expression patterns occur between PSGs and NSGs in paralogs of two wild Arachis species.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China.
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China.
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23
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Lotterhos KE, Yeaman S, Degner J, Aitken S, Hodgins KA. Modularity of genes involved in local adaptation to climate despite physical linkage. Genome Biol 2018; 19:157. [PMID: 30290843 PMCID: PMC6173883 DOI: 10.1186/s13059-018-1545-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Linkage among genes experiencing different selection pressures can make natural selection less efficient. Theory predicts that when local adaptation is driven by complex and non-covarying stresses, increased linkage is favored for alleles with similar pleiotropic effects, with increased recombination favored among alleles with contrasting pleiotropic effects. Here, we introduce a framework to test these predictions with a co-association network analysis, which clusters loci based on differing associations. We use this framework to study the genetic architecture of local adaptation to climate in lodgepole pine, Pinus contorta, based on associations with environments. RESULTS We identify many clusters of candidate genes and SNPs associated with distinct environments, including aspects of aridity and freezing, and discover low recombination rates among some candidate genes in different clusters. Only a few genes contain SNPs with effects on more than one distinct aspect of climate. There is limited correspondence between co-association networks and gene regulatory networks. We further show how associations with environmental principal components can lead to misinterpretation. Finally, simulations illustrate both benefits and caveats of co-association networks. CONCLUSIONS Our results support the prediction that different selection pressures favor the evolution of distinct groups of genes, each associating with a different aspect of climate. But our results went against the prediction that loci experiencing different sources of selection would have high recombination among them. These results give new insight into evolutionary debates about the extent of modularity, pleiotropy, and linkage in the evolution of genetic architectures.
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Affiliation(s)
- Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern Marine Science Center, 430 Nahant Rd, Nahant, MA, 01908, USA.
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Jon Degner
- Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC, V6T 1Z4, Canada
| | - Sally Aitken
- Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC, V6T 1Z4, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Melbourne, VIC, 3800, Australia
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24
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Casola C, Koralewski TE. Pinaceae show elevated rates of gene turnover that are robust to incomplete gene annotation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:862-876. [PMID: 29901849 DOI: 10.1111/tpj.13994] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/22/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Gene duplications and gene losses are major determinants of genome evolution and phenotypic diversity. The frequency of gene turnover (gene gains and gene losses combined) is known to vary between organisms. Comparative genomic analyses of gene families can highlight such variation; however, estimates of gene turnover may be biased when using highly fragmented genome assemblies resulting in poor gene annotations. Here, we address potential biases introduced by gene annotation errors in estimates of gene turnover frequencies in a dataset including both well-annotated angiosperm genomes and the incomplete gene sets of four Pinaceae, including two pine species, Norway spruce and Douglas-fir. We show that Pinaceae experienced higher gene turnover rates than angiosperm lineages lacking recent whole-genome duplications. This finding is robust to both known major issues in Pinaceae gene sets: missing gene models and erroneous annotation of pseudogenes. A separate analysis limited to the four Pinaceae gene sets pointed to an accelerated gene turnover rate in pines compared with Norway spruce and Douglas-fir. Our results indicate that gene turnover significantly contributes to genome variation and possibly to speciation in Pinaceae, particularly in pines. Moreover, these findings indicate that reliable estimates of gene turnover frequencies can be discerned in incomplete and potentially inaccurate gene sets. Because gymnosperms are known to exhibit low overall substitution rates compared with angiosperms, our results suggest that the rate of single-base pair mutations is uncoupled from the rate of large DNA duplications and deletions associated with gene turnover in Pinaceae.
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Affiliation(s)
- Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA
| | - Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA
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25
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Herrmann M, Ravindran SP, Schwenk K, Cordellier M. Population transcriptomics in Daphnia
: The role of thermal selection. Mol Ecol 2017; 27:387-402. [DOI: 10.1111/mec.14450] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/22/2017] [Accepted: 11/02/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Maike Herrmann
- Institute for Environmental Sciences; University Koblenz-Landau; Landau in der Pfalz Germany
| | | | - Klaus Schwenk
- Institute for Environmental Sciences; University Koblenz-Landau; Landau in der Pfalz Germany
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26
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Conte GL, Hodgins KA, Yeaman S, Degner JC, Aitken SN, Rieseberg LH, Whitlock MC. Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex. BMC Genomics 2017; 18:970. [PMID: 29246191 PMCID: PMC5731209 DOI: 10.1186/s12864-017-4344-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. Here, we use this approach in the interior spruce (Picea glauca x P. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids exhibit local adaptation to intermediate conditions. We used PROVEAN to bioinformatically predict whether non-synonymous alleles are deleterious, based on conservation of the position and abnormality of the amino acid change. RESULTS As expected, we found that predicted deleterious alleles were at lower average allele frequencies than alleles not predicted to be deleterious. We were unable to detect a phenotypic effect on juvenile growth rate of the many rare alleles predicted to be deleterious. Both the proportion of alleles predicted to be deleterious and the proportion of loci homozygous for predicted deleterious alleles were higher in P. engelmannii (Engelmann spruce) than in P. glauca (white spruce), due to higher diversity and frequencies of rare alleles in Engelmann. Relative to parental species, the proportion of alleles predicted to be deleterious was intermediate in hybrids, and the proportion of loci homozygous for predicted deleterious alleles was lowest. CONCLUSION Given that most deleterious alleles are recessive, this suggests that mutation load is reduced in hybrids due to complementation of deleterious alleles. This effect may enhance the fitness of hybrids.
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Affiliation(s)
- Gina L Conte
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. .,Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
| | - Kathryn A Hodgins
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
| | - Sam Yeaman
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Jon C Degner
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, 4200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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27
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Grivet D, Avia K, Vaattovaara A, Eckert AJ, Neale DB, Savolainen O, González-Martínez SC. High rate of adaptive evolution in two widespread European pines. Mol Ecol 2017; 26:6857-6870. [PMID: 29110402 DOI: 10.1111/mec.14402] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 12/18/2022]
Abstract
Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ωa ), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ωa . Moreover, population contraction-expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.
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Affiliation(s)
- Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain
| | - Komlan Avia
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, Roscoff, France.,UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, Roscoff, France
| | - Aleksia Vaattovaara
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
| | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
| | - Outi Savolainen
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain.,BIOGECO, INRA, Univ. Bordeaux, Cestas, France
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28
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Song H, Gao H, Liu J, Tian P, Nan Z. Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs. Sci Rep 2017; 7:14853. [PMID: 29093502 PMCID: PMC5665869 DOI: 10.1038/s41598-017-13981-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/04/2017] [Indexed: 11/22/2022] Open
Abstract
The relationship between evolutionary rates and gene expression in model plant orthologs is well documented. However, little is known about the relationships between gene expression and evolutionary trends in Arachis orthologs. We identified 7,435 one-to-one orthologs, including 925 single-copy and 6,510 multiple-copy sequences in Arachis duranensis and Arachis ipaënsis. Codon usage was stronger for shorter polypeptides, which were encoded by codons with higher GC contents. Highly expressed coding sequences had higher codon usage bias, GC content, and expression breadth. Additionally, expression breadth was positively correlated with polypeptide length, but there was no correlation between gene expression and polypeptide length. Inferred selective pressure was also negatively correlated with both gene expression and expression breadth in all one-to-one orthologs, while positively but non-significantly correlated with gene expression in sequences with signatures of positive selection. Gene expression levels and expression breadth were significantly higher for single-copy genes than for multiple-copy genes. Similarly, the gene expression and expression breadth in sequences with signatures of purifying selection were higher than those of sequences with positive selective signatures. These results indicated that gene expression differed between single-copy and multiple-copy genes as well as sequences with signatures of positive and purifying selection.
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Affiliation(s)
- Hui Song
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
| | - Hongjuan Gao
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Jing Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Pei Tian
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
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29
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Li Z, De La Torre AR, Sterck L, Cánovas FM, Avila C, Merino I, Cabezas JA, Cervera MT, Ingvarsson PK, Van de Peer Y. Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants. Genome Biol Evol 2017; 9:1130-1147. [PMID: 28460034 PMCID: PMC5414570 DOI: 10.1093/gbe/evx070] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2017] [Indexed: 01/02/2023] Open
Abstract
Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.
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Affiliation(s)
- Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium
| | - Amanda R De La Torre
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Sciences, University of California-Davis, Davis, CA
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, Málaga, Spain
| | - Concepción Avila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, Málaga, Spain
| | - Irene Merino
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | | | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium.,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, South Africa
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30
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De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK. Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants. Mol Biol Evol 2017; 34:1363-1377. [PMID: 28333233 PMCID: PMC5435085 DOI: 10.1093/molbev/msx069] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.
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Affiliation(s)
- Amanda R De La Torre
- Department of Plant Sciences, University of California-Davis, Davis, CA.,Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Zhen Li
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, South Africa
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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31
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Liu Y, El-Kassaby YA. Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories. FRONTIERS IN PLANT SCIENCE 2017; 8:1719. [PMID: 29046688 PMCID: PMC5632664 DOI: 10.3389/fpls.2017.01719] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18-24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration. We applied diverse profiling methods to examine sRNA and miRNA features, including size distribution, sequence conservation and reproduction-specific regulation, as well as to predict their putative targets. The top 27 most abundant miRNAs were highly overlapped between the two species (e.g., miR166,-319 and-396), but in P. glauca, they were less abundant and significantly less correlated with seed-set phases. The most abundant sRNAs in libraries were deeply conserved miRNAs in the plant kingdom for Arabidopsis but long sRNAs (24-nt) for P. glauca. We also found significant difference in normalized expression between populations for population-specific sRNAs but not for lineage-specific ones. Moreover, lineage-specific sRNAs were enriched in the 21-nt size class. This pattern is consistent in both species and alludes to a specific type of sRNAs (e.g., miRNA, tasiRNA) being selected for. In addition, we deemed 24 and 9 sRNAs in P. glauca and Arabidopsis, respectively, as sRNA candidates targeting known adaptive genes. Temperature had significant influence on selected gene and miRNA expression at seed development in both species. This study increases our integrated understanding of sRNA evolution and its potential link to genomic architecture (e.g., sRNA derivation from genome and sRNA-mediated genomic events) and organismal complexity (e.g., association between different sRNA expression and their functionality).
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32
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Pespeni MH, Ladner JT, Moczek AP. Signals of selection in conditionally expressed genes in the diversification of three horned beetle species. J Evol Biol 2017; 30:1644-1657. [PMID: 28379613 DOI: 10.1111/jeb.13079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/05/2017] [Indexed: 01/20/2023]
Abstract
Species radiations may be facilitated by phenotypic differences already present within populations, such as those arising through sex-specific development or developmental processes biased towards particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among- and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism and degree of nutritional sensitivity. Our approach combined de novo transcript assembly, assessment of amino acid substitutions (dN/dS) across orthologous gene pairs and integration of gene function and conditional gene expression data. We identified 17 genes across the three species pairs related to axis patterning, development and metabolism with dN/dS > 1 and detected elevated dN/dS in genes related to metabolism and biosynthesis in the most closely related species pair, which is characterized by a loss of nutritional polyphenism and a reversal of sexual dimorphism. Further, we found that genes that are conditionally expressed (i.e. as a function of sex, nutrition or body region) within one of our focal species also showed significantly stronger signals of positive or relaxed purifying selection between species divergent along the same morphological axis (i.e. polarity of sexual dimorphism, degree of nutritional sensitivity or location of horns). Our findings thus reveal a positive relationship between intraspecific differentiation due to condition-specific development and genetic divergences among species.
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Affiliation(s)
- M H Pespeni
- Department of Biology, Indiana University, Bloomington, IN, USA.,Department of Biology, University of Vermont, Burlington, VT, USA
| | - J T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - A P Moczek
- Department of Biology, Indiana University, Bloomington, IN, USA
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33
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Josephs EB, Wright SI, Stinchcombe JR, Schoen DJ. The Relationship between Selection, Network Connectivity, and Regulatory Variation within a Population of Capsella grandiflora. Genome Biol Evol 2017; 9:1099-1109. [PMID: 28402527 PMCID: PMC5408089 DOI: 10.1093/gbe/evx068] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2017] [Indexed: 12/12/2022] Open
Abstract
Interactions between genes can have important consequences for how selection shapes sequence variation at these genes. Specifically, genes that have pleiotropic effects by affecting the expression level of many other genes may be under stronger selective constraint. We used coexpression networks to measure connectivity between genes and investigated the relationship between gene connectivity and selection in a natural population of the plant Capsella grandiflora. We observed that network connectivity was negatively correlated with genetic divergence due to stronger negative selection on highly-connected genes even when controlling for variation in gene expression level. However, the presence of local regulatory variation for a gene's expression level was also associated with reduced negative selection and lower gene connectivity. While it is difficult to disentangle the causal relationships between these factors, our results show that both connectivity and local regulatory variation are important factors for explaining variation in selection between genes.
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Affiliation(s)
- Emily B. Josephs
- Department of Evolution and Ecology, University of California, Davis
| | - Stephen I. Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Daniel J. Schoen
- Department of Biology, McGill University, Stewart Biology Building, Montreal, Quebec, Canada
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34
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Yeaman S, Hodgins KA, Lotterhos KE, Suren H, Nadeau S, Degner JC, Nurkowski KA, Smets P, Wang T, Gray LK, Liepe KJ, Hamann A, Holliday JA, Whitlock MC, Rieseberg LH, Aitken SN. Convergent local adaptation to climate in distantly related conifers. Science 2016; 353:1431-1433. [DOI: 10.1126/science.aaf7812] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023]
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