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Li Z, Zhu Z, Qian K, Tang B, Han B, Zhong Z, Fu T, Zhou P, Stukenbrock EH, Martin FM, Yuan Z. Intraspecific diploidization of a halophyte root fungus drives heterosis. Nat Commun 2024; 15:5872. [PMID: 38997287 PMCID: PMC11245560 DOI: 10.1038/s41467-024-49468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/03/2024] [Indexed: 07/14/2024] Open
Abstract
How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte.
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Affiliation(s)
- Zhongfeng Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Zhiyong Zhu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
- Nanjing Forestry University, Nanjing, 100071, China
| | - Kun Qian
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng, 224002, China
| | - Baocai Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
| | - Zhenhui Zhong
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Tao Fu
- Shenzhen Zhuoyun Haizhi Medical Research Center Co., Ltd, Shenzhen, 518063, China
| | - Peng Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University, 24118, Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Francis M Martin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganisms, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China.
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
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Yoo MJ, Koh J, Boatwright JL, Soltis DE, Soltis PS, Barbazuk WB, Chen S. Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1191-1205. [PMID: 37997015 DOI: 10.1111/tpj.16553] [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: 08/10/2023] [Revised: 10/02/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years).
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, 13699, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, USA
| | - J Lucas Boatwright
- Plant and Environmental Science Department, Clemson University, Clemson, South Carolina, 29634, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, Mississippi, 38677, USA
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Duan T, Sicard A, Glémin S, Lascoux M. Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris. eLife 2024; 12:RP88398. [PMID: 38189348 PMCID: PMC10945474 DOI: 10.7554/elife.88398] [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] [Indexed: 01/09/2024] Open
Abstract
Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Distinguishing the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression-level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen, and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELD were only found in natural allopolyploids. Natural allotetraploids also had more ELD toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of ELD in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of HEB among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.
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Affiliation(s)
- Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural SciencesUppsalaSweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
- UMR CNRS 6553 ECOBIO, Campus BeaulieuRennesFrance
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
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Zhou W, Zhang L, He J, Chen W, Zhao F, Fu C, Li M. Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid. Int J Mol Sci 2023; 24:16238. [PMID: 38003428 PMCID: PMC10671433 DOI: 10.3390/ijms242216238] [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: 10/13/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called 'transcriptome shock'. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis.
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Affiliation(s)
- Weixian Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Wang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Feifan Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
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5
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Combes MC, Joët T, Stavrinides AK, Lashermes P. New cup out of old coffee: contribution of parental gene expression legacy to phenotypic novelty in coffee beans of the allopolyploid Coffea arabica L. ANNALS OF BOTANY 2023; 131:157-170. [PMID: 35325016 PMCID: PMC9904342 DOI: 10.1093/aob/mcac041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/21/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Allopolyploidization is a widespread phenomenon known to generate novel phenotypes by merging evolutionarily distinct parental genomes and regulatory networks in a single nucleus. The objective of this study was to investigate the transcriptional regulation associated with phenotypic novelty in coffee beans of the allotetraploid Coffea arabica. METHODS A genome-wide comparative transcriptomic analysis was performed in C. arabica and its two diploid progenitors, C. canephora and C. eugenioides. Gene expression patterns and homeologue expression were studied on seeds at five different maturation stages. The involvement of homeologue expression bias (HEB) in specific traits was addressed both by functional enrichment analyses and by the study of gene expression in the caffeine and chlorogenic acid biosynthesis pathways. KEY RESULTS Expression-level dominance in C. arabica seed was observed for most of the genes differentially expressed between the species. Approximately a third of the genes analysed showed HEB. This proportion increased during seed maturation but the biases remained equally distributed between the sub-genomes. The relative expression levels of homeologues remained relatively constant during maturation and were correlated with those estimated in leaves of C. arabica and interspecific hybrids between C. canephora and C. eugenioides. Functional enrichment analyses performed on genes exhibiting HEB enabled the identification of processes potentially associated with physiological traits. The expression profiles of the genes involved in caffeine biosynthesis mirror the differences observed in the caffeine content of mature seeds of C. arabica and its parental species. CONCLUSIONS Neither of the two sub-genomes is globally preferentially expressed in C. arabica seeds, and homeologues appear to be co-regulated by shared trans-regulatory mechanisms. The observed HEBs are thought to be a legacy of gene expression differences inherited from diploid progenitor species. Pre-existing functional divergences between parental species appear to play an important role in controlling the phenotype of C. arabica seeds.
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Affiliation(s)
| | - Thierry Joët
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
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Chou JY, Hsu PC, Leu JY. Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. Microbiol Mol Biol Rev 2022; 86:e0009822. [PMID: 36098649 PMCID: PMC9769731 DOI: 10.1128/mmbr.00098-22] [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] [Indexed: 01/01/2023] Open
Abstract
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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7
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Behling AH, Winter DJ, Ganley ARD, Cox MP. Cross-kingdom transcriptomic trends in the evolution of hybrid gene expression. J Evol Biol 2022; 35:1126-1137. [PMID: 35830478 PMCID: PMC9546207 DOI: 10.1111/jeb.14059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
Hybridization is a route to speciation that occurs widely across the eukaryote tree of life. The success of allopolyploids (hybrid species with increased ploidy) and homoploid hybrids (with unchanged ploidy) is well documented. However, their formation and establishment is not straightforward, with a suite of near‐instantaneous and longer term biological repercussions faced by the new species. Central to these challenges is the rewiring of gene regulatory networks following the merger of distinct genomes inherited from both parental species. Research on the evolution of hybrid gene expression has largely involved studies on a single hybrid species or a few gene families. Here, we present the first standardized transcriptome‐wide study exploring the fates of genes following hybridization across three kingdoms: animals, plants and fungi. Within each kingdom, we pair an allopolyploid system with a closely related homoploid hybrid to decouple the influence of increased ploidy from genome merger. Genome merger, not changes in ploidy, has the greatest effect on posthybridization expression patterns across all study systems. Strikingly, we find that differentially expressed genes in parent species preferentially switch to more similar expression in hybrids across all kingdoms, likely as a consequence of regulatory trans‐acting cross‐talk within the hybrid nucleus. We also highlight the prevalence of gene loss or silencing among extremely differentially expressed genes in hybrid species across all kingdoms. These shared patterns suggest that the evolutionary process of hybridization leads to common high‐level expression outcomes, regardless of the particular species or kingdom.
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Affiliation(s)
- Anna H Behling
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - David J Winter
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
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Interspecific hybridization as a driver of fungal evolution and adaptation. Nat Rev Microbiol 2021; 19:485-500. [PMID: 33767366 DOI: 10.1038/s41579-021-00537-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 02/01/2023]
Abstract
Cross-species gene transfer is often associated with bacteria, which have evolved several mechanisms that facilitate horizontal DNA exchange. However, the increased availability of whole-genome sequences has revealed that fungal species also exchange DNA, leading to intertwined lineages, blurred species boundaries or even novel species. In contrast to prokaryotes, fungal DNA exchange originates from interspecific hybridization, where two genomes are merged into a single, often highly unstable, polyploid genome that evolves rapidly into stabler derivatives. The resulting hybrids can display novel combinations of genetic and phenotypic variation that enhance fitness and allow colonization of new niches. Interspecific hybridization led to the emergence of important pathogens of humans and plants (for example, various Candida and 'powdery mildew' species, respectively) and industrially important yeasts, such as Saccharomyces hybrids that are important in the production of cold-fermented lagers or cold-cellared Belgian ales. In this Review, we discuss the genetic processes and evolutionary implications of fungal interspecific hybridization and highlight some of the best-studied examples. In addition, we explain how hybrids can be used to study molecular mechanisms underlying evolution, adaptation and speciation, and serve as a route towards development of new variants for industrial applications.
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Abstract
Hybridization is an important evolutionary mechanism that can enable organisms to adapt to environmental challenges. It has previously been shown that the fungal allodiploid species Verticillium longisporum, the causal agent of verticillium stem striping in rapeseed, originated from at least three independent hybridization events between two haploid Verticillium species. To reveal the impact of genome duplication as a consequence of hybridization, we studied the genome and transcriptome dynamics upon two independent V. longisporum hybridization events, represented by the hybrid lineages “A1/D1” and “A1/D3.” We show that V. longisporum genomes are characterized by extensive chromosomal rearrangements, including between parental chromosomal sets. V. longisporum hybrids display signs of evolutionary dynamics that are typically associated with the aftermath of allodiploidization, such as haploidization and more relaxed gene evolution. The expression patterns of the two subgenomes within the two hybrid lineages are more similar than those of the shared A1 parent between the two lineages, showing that the expression patterns of the parental genomes homogenized within a lineage. However, as genes that display differential parental expression in planta do not typically display the same pattern in vitro, we conclude that subgenome-specific responses occur in both lineages. Overall, our study uncovers genomic and transcriptomic plasticity during the evolution of the filamentous fungal hybrid V. longisporum and illustrates its adaptive potential.
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Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi. Commun Biol 2021; 4:201. [PMID: 33589695 PMCID: PMC7884421 DOI: 10.1038/s42003-021-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.
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Comparative Transcriptomic Analysis of Gene Expression Inheritance Patterns Associated with Cabbage Head Heterosis. PLANTS 2021; 10:plants10020275. [PMID: 33572601 PMCID: PMC7912167 DOI: 10.3390/plants10020275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 11/16/2022]
Abstract
The molecular mechanism of heterosis or hybrid vigor, where F1 hybrids of genetically diverse parents show superior traits compared to their parents, is not well understood. Here, we studied the molecular regulation of heterosis in four F1 cabbage hybrids that showed heterosis for several horticultural traits, including head size and weight. To examine the molecular mechanisms, we performed a global transcriptome profiling in the hybrids and their parents by RNA sequencing. The proportion of genetic variations detected as single nucleotide polymorphisms and small insertion–deletions as well as the numbers of differentially expressed genes indicated a larger role of the female parent than the male parent in the genetic divergence of the hybrids. More than 86% of hybrid gene expressions were non-additive. More than 81% of the genes showing divergent expressions showed dominant inheritance, and more than 56% of these exhibited maternal expression dominance. Gene expression regulation by cis-regulatory mechanisms appears to mediate most of the gene expression divergence in the hybrids; however, trans-regulatory factors appear to have a higher effect compared to cis-regulatory factors on parental expression divergence. These observations bring new insights into the molecular mechanisms of heterosis during the cabbage head development.
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12
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Gabaldón T. Hybridization and the origin of new yeast lineages. FEMS Yeast Res 2020; 20:5870662. [PMID: 32658267 PMCID: PMC7394516 DOI: 10.1093/femsyr/foaa040] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
Hybrids originate from the mating of two diverged organisms, resulting in novel lineages that have chimeric genomes. Hybrids may exhibit unique phenotypic traits that are not necessarily intermediate between those present in the progenitors. These unique traits may enable them to thrive in new environments. Many hybrid lineages have been discovered among yeasts in the Saccharomycotina, of which many have industrial or clinical relevance, but this might reflect a bias toward investigating species with relevance to humans. Hybridization has also been proposed to be at the root of the whole-genome duplication in the lineage leading to Saccharomyces cerevisiae. Thus, hybridization seems to have played a prominent role in the evolution of Saccharomycotina yeasts, although it is still unclear how common this evolutionary process has been during the evolution of this and other fungal clades. Similarly, the evolutionary aftermath of hybridization, including implications at the genomic, transcriptional, physiological or ecological levels, remains poorly understood. In this review, I survey recent findings from genomic analysis of yeast hybrids of industrial or clinical relevance, and discuss the evolutionary implications of genomic hybridization for the origin of new lineages, including when such hybridization results in a whole-genome duplication.
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Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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13
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Hovhannisyan H, Saus E, Ksiezopolska E, Hinks Roberts AJ, Louis EJ, Gabaldón T. Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization. Front Genet 2020; 11:404. [PMID: 32457798 PMCID: PMC7221068 DOI: 10.3389/fgene.2020.00404] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/30/2020] [Indexed: 12/30/2022] Open
Abstract
The formation of interspecific hybrids results in the coexistence of two diverged genomes within the same nucleus. It has been hypothesized that negative epistatic interactions and regulatory interferences between the two sub-genomes may elicit a so-called genomic shock involving, among other alterations, broad transcriptional changes. To assess the magnitude of this shock in hybrid yeasts, we investigated the transcriptomic differences between a newly formed Saccharomyces cerevisiae × Saccharomyces uvarum diploid hybrid and its diploid parentals, which diverged ∼20 mya. RNA sequencing (RNA-Seq) based allele-specific expression (ASE) analysis indicated that gene expression changes in the hybrid genome are limited, with only ∼1–2% of genes significantly altering their expression with respect to a non-hybrid context. In comparison, a thermal shock altered six times more genes. Furthermore, differences in the expression between orthologous genes in the two parental species tended to be diminished for the corresponding homeologous genes in the hybrid. Finally, and consistent with the RNA-Seq results, we show a limited impact of hybridization on chromatin accessibility patterns, as assessed with assay for transposase-accessible chromatin using sequencing (ATAC-Seq). Overall, our results suggest a limited genomic shock in a newly formed yeast hybrid, which may explain the high frequency of successful hybridization in these organisms.
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Affiliation(s)
- Hrant Hovhannisyan
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Ester Saus
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Ewa Ksiezopolska
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Alex J Hinks Roberts
- Centre for Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Edward J Louis
- Centre for Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Toni Gabaldón
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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14
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The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis. mSphere 2020; 5:5/3/e00282-20. [PMID: 32376704 PMCID: PMC7203458 DOI: 10.1128/msphere.00282-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence. Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight into the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ∼4% of the genes studied. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ∼9.5% of the heterozygous genes in the hybrids. This effect was larger in the hybrid with more extensive loss of heterozygosity, which may indicate a tendency to avoid loss of heterozygosity in these genes. Consistently, the number of shared genes with allele-specific expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. Some of the imbalanced genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids. IMPORTANCE How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence.
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15
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Zhao R, Wang Y, Zou L, Luo Y, Tan H, Yao J, Zhang M, Liu S. Hox genes reveal variations in the genomic DNA of allotetraploid hybrids derived from Carassius auratus red var. (female) × Cyprinus carpio L. (male). BMC Genet 2020; 21:24. [PMID: 32131722 PMCID: PMC7057633 DOI: 10.1186/s12863-020-0823-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/04/2020] [Indexed: 11/10/2022] Open
Abstract
Background Hox transcription factors are master regulators of animal development. Although highly conserved, they can contribute to the formation of novel biological characteristics when modified, such as during the generation of hybrid species, thus potentially serving as species-specific molecular markers. Here, we systematically studied the evolution of genomic sequences of Hox loci in an artificial allotetraploid lineage (4nAT, 4n = 200) derived from a red crucian carp (♀, RCC, 2n = 100) × common carp (♂, CC, 2n = 100) cross and its parents (RCC and CC). Results PCR amplification yielded 23 distinct Hox gene fragments from 160 clones in 4nAT, 22 fragments from 90 clones in RCC, and 19 fragments from 90 clones in CC. Sequence alignment of the HoxA3a and HoxC10a genes indicated both the inheritance and loss of paternal genomic DNA in 4nAT. The HoxA5a gene from 4nAT consisted of two subtypes from RCC and two subtypes from CC, indicating that homologous recombination occurred in the 4nAT hybrid genome. Moreover, 4nAT carried genomic pseudogenization in the HoxA10b and HoxC13a loci. Interestingly, a new type of HoxC9a gene was found in 4nAT as a hybrid sequence of CC and RCC by recombination in the intronic region. Conclusion The results revealed the influence of Hox genes during polyploidization in hybrid fish. The data provided insight into the evolution of vertebrate genomes and might be benefit for artificial breeding programs.
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Affiliation(s)
- Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Zou
- Fisheries Research Institute of Hunan Province, Changsha, 410153, People's Republic of China
| | - Yaxin Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Huifang Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Jiajun Yao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Minghe Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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16
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Bosch J, Czedik-Eysenberg A, Hastreiter M, Khan M, Güldener U, Djamei A. Two Is Better Than One: Studying Ustilago bromivora- Brachypodium Compatibility by Using a Hybrid Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1623-1634. [PMID: 31657673 DOI: 10.1094/mpmi-05-19-0148-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pathogenic fungi can have devastating effects on agriculture and health. One potential challenge in dealing with pathogens is the possibility of a host jump (i.e., when a pathogen infects a new host species). This can lead to the emergence of new diseases or complicate the management of existing threats. We studied host specificity by using a hybrid fungus formed by mating two closely related fungi: Ustilago bromivora, which normally infects Brachypodium spp., and U. hordei, which normally infects barley. Although U. hordei was unable to infect Brachypodium spp., the hybrid could. These hybrids also displayed the same mating-type bias that had been observed in U. bromivora and provide evidence of a dominant spore-killer-like system on the sex chromosome of U. bromivora. By analyzing the genomic composition of 109 hybrid strains, backcrossed with U. hordei over four generations, we identified three regions associated with infection on Brachypodium spp. and 75 potential virulence candidates. The most strongly associated region was located on chromosome 8, where seven genes encoding predicted secreted proteins were identified. The fact that we identified several regions relevant for pathogenicity on Brachypodium spp. but that none were essential suggests that host specificity, in the case of U. bromivora, is a multifactorial trait which can be achieved through different subsets of virulence factors.
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Affiliation(s)
- Jason Bosch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Angelika Czedik-Eysenberg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Maximilian Hastreiter
- TUM School of Life Sciences, Technical University of Munich, Department of Bioinformatics, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Mamoona Khan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Ulrich Güldener
- TUM School of Life Sciences, Technical University of Munich, Department of Bioinformatics, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
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17
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Wu B, Cox MP. Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi. Mol Ecol 2019; 28:5103-5114. [PMID: 31614039 PMCID: PMC7004115 DOI: 10.1111/mec.15275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022]
Abstract
Gene duplicates can act as a source of genetic material from which new functions arise. Most duplicated genes revert to single copy genes and only a small proportion are retained. However, it remains unclear why some duplicate genes persist in the genome for an extended time. We investigate this question by analysing retained gene duplicates in the fungal genus Epichloë, ascomycete fungi that form close endophytic symbioses with their host grasses. Retained duplicates within this genus have two independent origins, but both long pre-date the origin and diversification of the genus Epichloë. We find that loss of retained duplicates within the genus is frequent and often associated with speciation. Retained duplicates have faster evolutionary rates (Ka) and show relaxed selection (Ka/Ks) compared to single copy genes. Both features are time-dependent. Through comparison of conspecific strains, we find greater evolutionary rates in coding regions and sequence divergence in regulatory regions of retained duplicates than single copy genes, with this pattern more pronounced for strains adapted to different grass host species. Consistent with this sequence divergence in regulatory regions, transcriptome analyses show greater expression variation of retained duplicates than single copy genes. This suggest that cis-regulatory changes make important contributions to the expression patterns of retained duplicates. Coupled with supporting observations from the model yeast Saccharomyces cerevisiae, these data suggest that genetic robustness and regulatory plasticity are common drivers behind the retention of duplicated genes in fungi.
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Affiliation(s)
- Baojun Wu
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Murray P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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18
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Behling AH, Shepherd LD, Cox MP. The importance and prevalence of allopolyploidy in Aotearoa New Zealand. J R Soc N Z 2019. [DOI: 10.1080/03036758.2019.1676797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Anna H. Behling
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Murray P. Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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19
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Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Iwasaki W. Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. Commun Biol 2019; 2:263. [PMID: 31341962 PMCID: PMC6642101 DOI: 10.1038/s42003-019-0515-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/25/2019] [Indexed: 11/28/2022] Open
Abstract
Genome hybridization is an important evolutionary event that gives rise to species with novel capabilities. However, the merging of distinct genomes also brings together incompatible regulatory networks that must be resolved during the course of evolution. Understanding of the early stages of post-hybridization evolution is particularly important because changes in these stages have long-term evolutionary consequences. Here, via comparative transcriptomic analyses of two closely related, recently hybridized Trichosporon fungi, T. coremiiforme and T. ovoides, and three extant relatives, we show that early post-hybridization evolutionary processes occur separately at the gene sequence and gene expression levels but together contribute to the stabilization of hybrid genome and transcriptome. Our findings also highlight lineage-specific consequences of genome hybridization, revealing that the transcriptional regulatory dynamics in these hybrids responded completely differently to gene loss events: one involving both subgenomes and another that is strictly subgenome-specific.
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Affiliation(s)
- Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 Japan
- Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathum Wan, Bangkok 10330 Thailand
- Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathum Wan, Bangkok 10330 Thailand
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba-shi, Ibaraki 305-0074 Japan
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 Japan
| | - Ri-ichiroh Manabe
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba-shi, Ibaraki 305-0074 Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8568 Japan
- Atmosphere and Ocean Research Institute, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564 Japan
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20
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Hu G, Wendel JF. Cis-trans controls and regulatory novelty accompanying allopolyploidization. THE NEW PHYTOLOGIST 2019; 221:1691-1700. [PMID: 30290011 DOI: 10.1111/nph.15515] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/30/2018] [Indexed: 05/20/2023]
Abstract
Allopolyploidy is a prevalent process in plants, having important physiological, ecological and evolutionary consequences. Transcriptomic responses to genomic merger and doubling have been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena including homoeolog expression bias, genome dominance, expression-level dominance and revamping of co-expression networks. Notwithstanding the foregoing, there remains a need to develop a conceptual framework that will stimulate a deeper understanding of these diverse phenomena and their mechanistic interrelationships. Here we introduce considerations relevant to this framework with a focus on cis-trans interactions among duplicated genes and alleles in hybrids and allopolyploids. By extending classic allele-specific expression analysis to the allopolyploid level, we distinguish the distinct effects of progenitor regulatory interactions from the novel intergenomic interactions that arise from genome merger and allopolyploidization. This perspective informs experiments designed to reveal the molecular genetic basis of gene regulatory control, and will facilitate the disentangling of genetic from epigenetic and higher-order effects that impact gene expression. Finally, we suggest that the extended cis-trans model may help conceptually unify several presently disparate hallmarks of allopolyploid evolution, including genome-wide expression dominance and biased fractionation, and lead to a new level of understanding of phenotypic novelty accompanying polyploidy.
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Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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21
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Sousa F, Neiva J, Martins N, Jacinto R, Anderson L, Raimondi PT, Serrão EA, Pearson GA. Increased evolutionary rates and conserved transcriptional response following allopolyploidization in brown algae. Evolution 2019; 73:59-72. [PMID: 30421788 DOI: 10.1111/evo.13645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 01/08/2023]
Abstract
Genome mergers between independently evolving lineages, via allopolyploidy, can potentially lead to instantaneous sympatric speciation. However, little is known about the consequences of allopolyploidy and the resultant "genome shock" on genome evolution and expression beyond the plant and fungal branches of the Tree of Life. The aim of this study was to compare substitution rates and gene expression patterns in two allopolyploid brown algae (Phaeophyceae and Heterokonta) and their progenitors in the genus Pelvetiopsis N. L. Gardner in the north-east Pacific, and to date their relationships. We used RNA-seq data, all potential orthologues, and putative single-copy loci for phylogenomic, divergence, and gene expression analyses. The multispecies coalescent placed the origin of allopolyploids in the late Pleistocene (0.35-0.05 Ma). Homoeologues displayed increased nonsynonymous divergence compared with parental orthologues, consistent with relaxed selective constraint following allopolyploidization, including for genes with no evidence of pseudogenization or neofunctionalization. Patterns of homoeologue-orthologue expression conservation and expression level dominance were largely shared with both natural plant and fungal allopolyploids. Our results provide further support for common cross-Kingdom patterns of allopolyploid genome evolution and transcriptional responses, here in the evolutionarily distinct marine heterokont brown algae.
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Affiliation(s)
- Filipe Sousa
- CCMAR-Centro de Ciências do Mar da Universidade do Algarve, Edifício 7, Gambelas, Faro, 8005-139, Portugal
| | - João Neiva
- CCMAR-Centro de Ciências do Mar da Universidade do Algarve, Edifício 7, Gambelas, Faro, 8005-139, Portugal
| | - Neusa Martins
- CCMAR-Centro de Ciências do Mar da Universidade do Algarve, Edifício 7, Gambelas, Faro, 8005-139, Portugal
| | - Rita Jacinto
- CCMAR-Centro de Ciências do Mar da Universidade do Algarve, Edifício 7, Gambelas, Faro, 8005-139, Portugal
| | - Laura Anderson
- Long Marine Laboratory, University of California, Santa Cruz, California, 95064
| | - Peter T Raimondi
- Long Marine Laboratory, University of California, Santa Cruz, California, 95064
| | - Ester A Serrão
- CCMAR-Centro de Ciências do Mar da Universidade do Algarve, Edifício 7, Gambelas, Faro, 8005-139, Portugal
| | - Gareth A Pearson
- CCMAR-Centro de Ciências do Mar da Universidade do Algarve, Edifício 7, Gambelas, Faro, 8005-139, Portugal
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22
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Hubka V, Barrs V, Dudová Z, Sklenář F, Kubátová A, Matsuzawa T, Yaguchi T, Horie Y, Nováková A, Frisvad J, Talbot J, Kolařík M. Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens capable of interspecific hybridization. PERSOONIA 2018; 41:142-174. [PMID: 30728603 PMCID: PMC6344812 DOI: 10.3767/persoonia.2018.41.08] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/14/2018] [Indexed: 12/13/2022]
Abstract
Although Aspergillus fumigatus is the major agent of invasive aspergillosis, an increasing number of infections are caused by its cryptic species, especially A. lentulus and the A. viridinutans species complex (AVSC). Their identification is clinically relevant because of antifungal drug resistance and refractory infections. Species boundaries in the AVSC are unresolved since most species have uniform morphology and produce interspecific hybrids in vitro. Clinical and environmental strains from six continents (n = 110) were characterized by DNA sequencing of four to six loci. Biological compatibilities were tested within and between major phylogenetic clades, and ascospore morphology was characterised. Species delimitation methods based on the multispecies coalescent model (MSC) supported recognition of ten species including one new species. Four species are confirmed opportunistic pathogens; A. udagawae followed by A. felis and A. pseudoviridinutans are known from opportunistic human infections, while A. felis followed by A. udagawae and A. wyomingensis are agents of feline sino-orbital aspergillosis. Recently described human-pathogenic species A. parafelis and A. pseudofelis are synonymized with A. felis and an epitype is designated for A. udagawae. Intraspecific mating assay showed that only a few of the heterothallic species can readily generate sexual morphs in vitro. Interspecific mating assays revealed that five different species combinations were biologically compatible. Hybrid ascospores had atypical surface ornamentation and significantly different dimensions compared to parental species. This suggests that species limits in the AVSC are maintained by both pre- and post-zygotic barriers and these species display a great potential for rapid adaptation and modulation of virulence. This study highlights that a sufficient number of strains representing genetic diversity within a species is essential for meaningful species boundaries delimitation in cryptic species complexes. MSC-based delimitation methods are robust and suitable tools for evaluation of boundaries between these species.
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Affiliation(s)
- V. Hubka
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - V. Barrs
- Sydney School of Veterinary Science, Faculty of Science, and Marie Bashir Institute of Infectious Diseases & Biosecurity, University of Sydney, Camperdown, NSW, Australia
| | - Z. Dudová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - A. Kubátová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
| | - T. Matsuzawa
- University of Nagasaki, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Y. Horie
- Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - A. Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - J.J. Talbot
- Sydney School of Veterinary Science, Faculty of Science, and Marie Bashir Institute of Infectious Diseases & Biosecurity, University of Sydney, Camperdown, NSW, Australia
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
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23
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Göbel U, Arce AL, He F, Rico A, Schmitz G, de Meaux J. Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids. Genome Biol Evol 2018; 10:1403-1415. [PMID: 29788048 PMCID: PMC6007786 DOI: 10.1093/gbe/evy095] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/23/2022] Open
Abstract
The merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. Although our study did not examine TE transposition activity in hybrids, the examination of the transcriptome shows that TE expression is globally robust to hybridization. The term “genomic shock” is perhaps not appropriate to describe transcriptional modification in a viable hybrid merging divergent genomes.
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Affiliation(s)
- Ulrike Göbel
- Botanical Institute, University of Cologne, Germany
| | - Agustin L Arce
- Laboratorio de Biología del ARN, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), 3000 Santa Fe, Argentina
| | - Fei He
- Botanical Institute, University of Cologne, Germany
| | - Alain Rico
- Thermo Fisher Scientific, Villebon-sur-Yvette, France
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Li W, Liu J, Tan H, Luo L, Cui J, Hu J, Wang S, Liu Q, Hu F, Tang C, Ren L, Yang C, Zhao R, Tao M, Zhang C, Qin Q, Liu S. Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish. BMC Genomics 2018; 19:517. [PMID: 29969984 PMCID: PMC6030793 DOI: 10.1186/s12864-018-4883-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/19/2018] [Indexed: 03/05/2023] Open
Abstract
Background Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation following genomic merging or doubling is primarily derived from plants and is sparse for vertebrates. Results We successfully obtained an F1 generation (including allodiploid hybrids and triploid hybrids) from female Megalobrama amblycephala Yih (BSB, 2n = 48) × male Xenocypri davidi Bleeker (YB, 2n = 48). The duplicated-gene expression patterns of the two types of hybrids were explored using RNA-Seq data. In total, 5.44 × 108 (69.32 GB) clean reads and 499,631 assembled unigenes were obtained from the testis transcriptomes. The sequence similarity analysis of 4265 orthologs revealed that the merged genomes were dominantly expressed in different ploidy hybrids. The differentially expressed genes in the two types of hybrids were asymmetric compared with those in both parents. Furthermore, the genome-wide expression level dominance (ELD) was biased toward the maternal BSB genome in both the allodiploid and triploid hybrids. In addition, the dosage-compensation mechanisms that reduced the triploid expression levels to the diploid state were determined in the triploid hybrids. Conclusions Our results indicate that divergent genomes undergo strong interactions and domination in allopolyploid offspring. Genomic merger has a greater effect on the gene-expression patterns than genomic doubling. The various expression mechanisms (including maternal effect and dosage compensation) in different ploidy hybrids suggest that the initial genomic merger and doubling play important roles in polyploidy adaptation and evolution. Electronic supplementary material The online version of this article (10.1186/s12864-018-4883-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Junmei Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Hui Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Lingling Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Jie Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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25
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Fungal species and their boundaries matter – Definitions, mechanisms and practical implications. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii. Appl Environ Microbiol 2018; 84:AEM.02294-17. [PMID: 29269498 PMCID: PMC5812937 DOI: 10.1128/aem.02294-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/12/2017] [Indexed: 12/29/2022] Open
Abstract
Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH and a fermentative metabolism with a high growth rate. Here we used mRNA sequencing (RNA-seq) to analyze Z. parabailii's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than under control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/Aft2, previously described as lactic acid responsive in Saccharomyces cerevisiae. Furthermore, formate dehydrogenase (FDH) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii in comparison to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production. IMPORTANCE Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression under conditions of interest and relating gene expression patterns to protein functions. However, hybrid organisms present a challenge to the standard use of mRNA sequencing (RNA-seq) to study transcriptional responses to stress, because their genomes contain two similar copies of almost every gene. Here we used stringent mapping methods and a high-quality genome sequence to study the transcriptional response to lactic acid stress in Zygosaccharomyces parabailii ATCC 60483, a natural interspecies hybrid yeast that contains two complete subgenomes that are approximately 7% divergent in sequence. Beyond the insights we gained into lactic acid tolerance in this study, the methods we developed will be broadly applicable to other yeast hybrid strains.
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27
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Campbell MA, Tapper BA, Simpson WR, Johnson RD, Mace W, Ram A, Lukito Y, Dupont PY, Johnson LJ, Scott DB, Ganley ARD, Cox MP. Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy. Mycologia 2018; 109:715-729. [PMID: 29370579 DOI: 10.1080/00275514.2017.1406174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Endophytes of the genus Epichloë (Clavicipitaceae, Ascomycota) frequently occur within cool-season grasses and form interactions with their hosts that range from mutualistic to antagonistic. Many Epichloë species have arisen via interspecific hybridization, resulting in species with two or three subgenomes that retain all or nearly all of their original parental genomes, a process termed allopolyploidization. Here, we characterize Epichloë hybrida, sp. nov., a mutualistic species that has increasingly become a model system for investigating allopolyploidy in fungi. The Epichloë species so far identified as the closest known relatives of the two progenitors of E. hybrida are E. festucae var. lolii and E. typhina. We confirm that the nuclear genome of E. hybrida contains two homeologs of most protein-coding genes from E. festucae and E. typhina, with genome-wide gene expression analysis indicating a slight bias in overall gene expression from the E. typhina subgenome. Mitochondrial DNA is detectable only from E. festucae, whereas ribosomal DNA is detectable only from E. typhina. Inheriting ribosomal DNA from just one parent might be expected to preferentially favor interactions with ribosomal proteins from the same parent, but we find that ribosomal protein genes from both parental subgenomes are nearly all expressed equally in E. hybrida. Finally, we provide a comprehensive set of resources for this model system that are intended to facilitate further study of fungal hybridization by other researchers.
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Affiliation(s)
- Matthew A Campbell
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Brian A Tapper
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Wayne R Simpson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Richard D Johnson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Wade Mace
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Arvina Ram
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Yonathan Lukito
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Pierre-Yves Dupont
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Linda J Johnson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - D Barry Scott
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Austen R D Ganley
- c School of Biological Sciences, University of Auckland , Private Bag 92019, Auckland 1142 , New Zealand
| | - Murray P Cox
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
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28
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Sun Y, Wu Y, Yang C, Sun S, Lin X, Liu L, Xu C, Wendel JF, Gong L, Liu B. Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice. Mol Ecol 2017; 26:5451-5466. [PMID: 28802080 DOI: 10.1111/mec.14297] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 06/04/2017] [Accepted: 07/24/2017] [Indexed: 02/03/2023]
Abstract
Allopolyploidization, that is, concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genomewide transcriptome dynamics, a phenomenon referred to as "transcriptomic shock." However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain underinvestigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic and homoeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), in vitro "hybrids" (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5th-selfed generation (S5). We show that hybridization and whole genome duplication (WGD) have opposing effects on allelic and homoeologous expression in the F1 hybrids and tetraploids, respectively. Whereas hybridization exerts strong attenuating effects on allelic expression differences in diploid hybrids, WGD augments the intrinsic parental differences and generates extensive and variable homoeolog content which triggers diversification in expression patterning among the tetraploid plants. Coupled with the vast phenotypic diversity observed among the tetraploid individuals, our results provide experimental evidence in support of the notion that allopolyploidy catalyses rapid phenotypic diversification in higher plants. Our data further suggest that largely stochastic homoeolog content reshuffling rather than alteration in total expression level may be an important feature of evolution in young segmental allopolyploids, which underlies rapid expression diversity at the population level.
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Affiliation(s)
- Yue Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Shuai Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiuyun Lin
- Jilin Academy of Agriculture, Changchun, China
| | - Lixia Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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29
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Ren L, Tang C, Li W, Cui J, Tan X, Xiong Y, Chen J, Wang J, Xiao J, Zhou Y, Wang J, Tao M, Zhang C, Liu S. Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish. BMC Genomics 2017; 18:38. [PMID: 28056785 PMCID: PMC5216571 DOI: 10.1186/s12864-016-3424-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/14/2016] [Indexed: 12/15/2022] Open
Abstract
Background Polyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates. Results We generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing. In total, 157,878 contigs were assembled and 15,444 genes were annotated. We examined gene expression level changes among the parents and their triploid offspring. The mechanisms of dosage compensation that reduced triploid expression levels to the diploid state were determined in triploid fish. In this situation, novel gene expression and gene silencing were observed. Then, we established a model to determine the extent and direction of expression level dominance (ELD) and homoeolog expression bias (HEB) based on the relative expression level among the parents and their triploid offspring. Conclusions Our results showed that the genome-wide ELD was biased toward maternal genome in triploid. Extensive alterations in homoeolog expression suggested a combination of regulatory and epigenetic interactions through the transcriptome network. Additionally, the expression patterns of growth genes provided insights into the relationship between the characteristics of growth and underlying mechanisms in triploids. Regulation patterns of triploid state suggest that various expression levels from the initial genomic merger have important roles in adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3424-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Xingjun Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Yafeng Xiong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Jie Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Jun Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Yi Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.
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30
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Voisey CR, Christensen MT, Johnson LJ, Forester NT, Gagic M, Bryan GT, Simpson WR, Fleetwood DJ, Card SD, Koolaard JP, Maclean PH, Johnson RD. cAMP Signaling Regulates Synchronised Growth of Symbiotic Epichloë Fungi with the Host Grass Lolium perenne. FRONTIERS IN PLANT SCIENCE 2016; 7:1546. [PMID: 27833620 PMCID: PMC5082231 DOI: 10.3389/fpls.2016.01546] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
The seed-transmitted fungal symbiont, Epichloë festucae, colonizes grasses by infecting host tissues as they form on the shoot apical meristem (SAM) of the seedling. How this fungus accommodates the complexities of plant development to successfully colonize the leaves and inflorescences is unclear. Since adenosine 3', 5'-cyclic monophosphate (cAMP)-dependent signaling is often essential for host colonization by fungal pathogens, we disrupted the cAMP cascade by insertional mutagenesis of the E. festucae adenylate cyclase gene (acyA). Consistent with deletions of this gene in other fungi, acyA mutants had a slow radial growth rate in culture, and hyphae were convoluted and hyper-branched suggesting that fungal apical dominance had been disrupted. Nitro blue tetrazolium (NBT) staining of hyphae showed that cAMP disruption mutants were impaired in their ability to synthesize superoxide, indicating that cAMP signaling regulates accumulation of reactive oxygen species (ROS). Despite significant defects in hyphal growth and ROS production, E. festucae ΔacyA mutants were infectious and capable of forming symbiotic associations with grasses. Plants infected with E. festucae ΔacyA were marginally less robust than the wild-type (WT), however hyphae were hyper-branched, and leaf tissues heavily colonized, indicating that the tight regulation of hyphal growth normally observed in maturing leaves requires functional cAMP signaling.
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Affiliation(s)
- Christine R. Voisey
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Michael T. Christensen
- Formally of Forage Improvement, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Linda J. Johnson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Natasha T. Forester
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Milan Gagic
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Gregory T. Bryan
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Wayne R. Simpson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Damien J. Fleetwood
- Biotelliga Ltd., Institute for Innovation in BiotechnologyAuckland, New Zealand
| | - Stuart D. Card
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - John P. Koolaard
- Bioinformatics and Statistics Team, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Paul H. Maclean
- Bioinformatics and Statistics Team, AgResearch Ltd., Lincoln Research CentreChristchurch, New Zealand
| | - Richard D. Johnson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
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31
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Interspecific hybridization impacts host range and pathogenicity of filamentous microbes. Curr Opin Microbiol 2016; 32:7-13. [DOI: 10.1016/j.mib.2016.04.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/30/2016] [Accepted: 04/08/2016] [Indexed: 11/24/2022]
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32
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Wu Y, Sun Y, Wang X, Lin X, Sun S, Shen K, Wang J, Jiang T, Zhong S, Xu C, Liu B. Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:150-164. [PMID: 25828709 DOI: 10.1111/jipb.12357] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed "transcriptome shock". Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica (2n = 2x = 24, genome AA) and the tetraploid form of O. punctata (2n = 4x = 48, genome, BBCC), and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico "hybrids" (parental mixtures). We found that approximately 16% (2,541) of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the transcriptome response to interspecific hybridization and heterosis.
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Affiliation(s)
- Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yue Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences, Changchun, 130032, China
| | - Shuai Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Kun Shen
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Tingting Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Wang X, Zhang H, Li Y, Zhang Z, Li L, Liu B. Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA-sequencing. THE NEW PHYTOLOGIST 2016; 209:1264-77. [PMID: 26436593 DOI: 10.1111/nph.13678] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/20/2015] [Indexed: 05/20/2023]
Abstract
Allopolyploidization has occurred frequently within the Triticum-Aegilops complex which provides a suitable system to investigate how allopolyploidization shapes the expression patterns of duplicated homeologs. We have conducted transcriptome-profiling of leaves and young inflorescences in wild and domesticated tetraploid wheats, Triticum turgidum ssp. dicoccoides (BBAA) and ssp. durum (BBAA), an extracted tetraploid (BBAA), and a synthetic tetraploid (S(l) S(l) AA) wheat together with its diploid parents, Aegilops longissima (S(l) S(l) ) and Triticum urartu (AA). The two diploid species showed tissue-specific differences in genome-wide ortholog expression, which plays an important role in transcriptome shock-mediated homeolog expression rewiring and hence transcriptome asymmetry in the synthetic tetraploid. Further changes of homeolog expression apparently occurred in natural tetraploid wheats, which led to novel transcriptome asymmetry between the two subgenomes. In particular, our results showed that extremely biased homeolog expression can occur rapidly upon the allotetraploidzation and this trend is further enhanced in the course of domestication and evolution of polyploid wheats. Our results suggest that allopolyploidization is accompanied by distinct phases of homeolog expression changes, with parental legacy playing major roles in the immediate rewiring of homeolog expression upon allopolyploidization, while evolution and domestication under allotetraploidy drive further homeolog-expression changes toward re-established subgenome expression asymmetry.
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Affiliation(s)
- Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yaling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Linfeng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Maneechot N, Yano CF, Bertollo LAC, Getlekha N, Molina WF, Ditcharoen S, Tengjaroenkul B, Supiwong W, Tanomtong A, de Bello Cioffi M. Genomic organization of repetitive DNAs highlights chromosomal evolution in the genus Clarias (Clariidae, Siluriformes). Mol Cytogenet 2016; 9:4. [PMID: 26793275 PMCID: PMC4719708 DOI: 10.1186/s13039-016-0215-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/07/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The genus Clarias (Clariidae, Siluriformes) contains at least 61 species naturally spread over vast regions of Asia, India and Africa. However, Clarias species have also been introduced in many different countries and represent the most widespread catfishes in the world. These fishes are also known as "walking catfishes" due to their ability to move over land. A large degree of chromosomal variation has been previously found in this family, mainly using conventional cytogenetic investigations, with diploid chromosome numbers ranging between 48 and 100. In this study, we analyzed the karyotype structure and distribution of four repetitive DNA sequences (5S and 18S rDNAs and (CA)15 and (GA)15 microsatellites) in three Clarias species (C. batrachus, C. gariepinus, C. macrocephalus), as well as in a probable natural hybrid of the two latter species from different Thailand river basins. RESULTS Clarias gariepinus and C. macrocephalus had 2n = 56 and 2n = 54, respectively, as well as karyotypes composed mainly by metacentric and submetacentric chromosomes. Their karyotypes differed in the number and location of 5S and 18S rDNA sites and in the degree of microsatellite accumulation. An intermediate chromosomal pattern incorporating those of the parental species was found in the probable hybrid, confirming its interspecific origin. Clarias batrachus had 2n = 104 chromosomes and its karyotype was dominated by mainly acrocentric elements, indicating that unusual multiple centric fissions were involved in its karyotype differentiation. The karyotype of this species presented an unexpected dispersion of ribosomal DNAs, possessing 54 and 12 sites of 5S and 18S rDNAs, respectively, as well as a high accumulation and differential distribution of both microsatellite repeats, representing 'hot spots' for chromosomal rearrangement. CONCLUSION Both conventional and molecular cytogenetic markers were useful tools for demonstrating remarkable evolutionary dynamism and highlighting multiple chromosomal rearrangements and hybridization events correlated with the notable karyotypic diversity of these walking catfishes.
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Affiliation(s)
- Nuntiya Maneechot
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Cassia Fernanda Yano
- />Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | | | - Nuntaporn Getlekha
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Wagner Franco Molina
- />Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN Brazil
| | - Sukhonthip Ditcharoen
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Bundit Tengjaroenkul
- />Department of Veterinary Clinical Medicine, Faculty of Veterinary Medicine, Muang, Khon Kaen 40002 Thailand
- />Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen 40002 Thailand
| | - Weerayuth Supiwong
- />Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000 Thailand
| | - Alongklod Tanomtong
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
- />Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen 40002 Thailand
| | - Marcelo de Bello Cioffi
- />Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
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Olarte RA, Worthington CJ, Horn BW, Moore GG, Singh R, Monacell JT, Dorner JW, Stone EA, Xie DY, Carbone I. Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus. Mol Ecol 2015; 24:1889-909. [DOI: 10.1111/mec.13153] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 03/07/2015] [Accepted: 03/11/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Rodrigo A. Olarte
- Center for Integrated Fungal Research; Department of Plant Pathology; North Carolina State University; Raleigh NC 27695 USA
| | - Carolyn J. Worthington
- Center for Integrated Fungal Research; Department of Plant Pathology; North Carolina State University; Raleigh NC 27695 USA
| | - Bruce W. Horn
- National Peanut Research Laboratory; Agricultural Research Service; U.S. Department of Agriculture; Dawson GA 39842 USA
| | - Geromy G. Moore
- Southern Regional Research Center; Agricultural Research Service; U.S. Department of Agriculture; New Orleans LA 70179 USA
| | - Rakhi Singh
- Center for Integrated Fungal Research; Department of Plant Pathology; North Carolina State University; Raleigh NC 27695 USA
| | - James T. Monacell
- Center for Integrated Fungal Research; Department of Plant Pathology; North Carolina State University; Raleigh NC 27695 USA
- Bioinformatics Research Center; North Carolina State University; Raleigh NC 27695 USA
| | - Joe W. Dorner
- National Peanut Research Laboratory; Agricultural Research Service; U.S. Department of Agriculture; Dawson GA 39842 USA
| | - Eric A. Stone
- Bioinformatics Research Center; North Carolina State University; Raleigh NC 27695 USA
- Department of Biological Sciences; North Carolina State University; Raleigh NC 27695 USA
| | - De-Yu Xie
- Department of Plant and Microbial Biology; North Carolina State University; Raleigh NC 27695 USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research; Department of Plant Pathology; North Carolina State University; Raleigh NC 27695 USA
- Bioinformatics Research Center; North Carolina State University; Raleigh NC 27695 USA
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Shoji JY, Charlton ND, Yi M, Young CA, Craven KD. Vegetative hyphal fusion and subsequent nuclear behavior in Epichloë grass endophytes. PLoS One 2015; 10:e0121875. [PMID: 25837972 PMCID: PMC4383479 DOI: 10.1371/journal.pone.0121875] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 02/18/2015] [Indexed: 01/18/2023] Open
Abstract
Epichloë species (including the former genus Neotyphodium) are fungal symbionts of many agronomically important forage grasses, and provide their grass hosts with protection from a wide range of biotic and abiotic stresses. Epichloë species include many interspecific hybrids with allodiploid-like genomes, which may provide the potential for combined traits or recombination to generate new traits. Though circumstantial evidence suggests that such interspecific hybrids might have arisen from nuclear fusion events following vegetative hyphal fusion between different Epichloë strains, this hypothesis has not been addressed empirically. Here, we investigated vegetative hyphal fusion and subsequent nuclear behavior in Epichloë species. A majority of Epichloë strains, especially those having a sexual stage, underwent self vegetative hyphal fusion. Vegetative fusion also occurred between two hyphae from different Epichloë strains. Though Epichloë spp. are uninucleate fungi, hyphal fusion resulted in two nuclei stably sharing the same cytoplasm, which might ultimately lead to nuclear fusion. In addition, protoplast fusion experiments gave rise to uninucleate putative hybrids, which apparently had two markers, one from each parent within the same nucleus. These results are consistent with the notion that interspecific hybrids arise from vegetative hyphal fusion. However, we also discuss additional factors, such as post-hybridization selection, that may be important to explain the recognized prevalence of hybrids in Epichloë species.
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Affiliation(s)
- Jun-ya Shoji
- The Samuel Roberts Noble Foundation, Plant Biology Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
| | - Nikki D. Charlton
- The Samuel Roberts Noble Foundation, Forage Improvement Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
| | - Mihwa Yi
- The Samuel Roberts Noble Foundation, Forage Improvement Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
| | - Carolyn A. Young
- The Samuel Roberts Noble Foundation, Forage Improvement Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
| | - Kelly D. Craven
- The Samuel Roberts Noble Foundation, Plant Biology Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
- * E-mail:
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Combes MC, Hueber Y, Dereeper A, Rialle S, Herrera JC, Lashermes P. Regulatory divergence between parental alleles determines gene expression patterns in hybrids. Genome Biol Evol 2015; 7:1110-21. [PMID: 25819221 PMCID: PMC4419803 DOI: 10.1093/gbe/evv057] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Both hybridization and allopolyploidization generate novel phenotypes by conciliating divergent genomes and regulatory networks in the same cellular context. To understand the rewiring of gene expression in hybrids, the total expression of 21,025 genes and the allele-specific expression of over 11,000 genes were quantified in interspecific hybrids and their parental species, Coffea canephora and Coffea eugenioides using RNA-seq technology. Between parental species, cis- and trans-regulatory divergences affected around 32% and 35% of analyzed genes, respectively, with nearly 17% of them showing both. The relative importance of trans-regulatory divergences between both species could be related to their low genetic divergence and perennial habit. In hybrids, among divergently expressed genes between parental species and hybrids, 77% was expressed like one parent (expression level dominance), including 65% like C. eugenioides. Gene expression was shown to result from the expression of both alleles affected by intertwined parental trans-regulatory factors. A strong impact of C. eugenioides trans-regulatory factors on the upregulation of C. canephora alleles was revealed. The gene expression patterns appeared determined by complex combinations of cis- and trans-regulatory divergences. In particular, the observed biased expression level dominance seemed to be derived from the asymmetric effects of trans-regulatory parental factors on regulation of alleles. More generally, this study illustrates the effects of divergent trans-regulatory parental factors on the gene expression pattern in hybrids. The characteristics of the transcriptional response to hybridization appear to be determined by the compatibility of gene regulatory networks and therefore depend on genetic divergences between the parental species and their evolutionary history.
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Affiliation(s)
| | | | | | - Stéphanie Rialle
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier Cédex 5, France
| | - Juan-Carlos Herrera
- Centro Nacional de Investigaciones de Cafe, CENICAFE - FNC, Manizales, Colombia
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Fan G, Wang L, Deng M, Niu S, Zhao Z, Xu E, Cao X, Zhang X. Transcriptome analysis of the variations between autotetraploid Paulownia tomentosa and its diploid using high-throughput sequencing. Mol Genet Genomics 2015; 290:1627-38. [PMID: 25773315 DOI: 10.1007/s00438-015-1023-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/01/2015] [Indexed: 11/30/2022]
Abstract
Timber properties of autotetraploid Paulownia tomentosa are heritable with whole genome duplication, but the molecular mechanisms for the predominant characteristics remain unclear. To illuminate the genetic basis, high-throughput sequencing technology was used to identify the related unigenes. 2677 unigenes were found to be significantly differentially expressed in autotetraploid P. tomentosa. In total, 30 photosynthesis-related, 21 transcription factor-related, and 22 lignin-related differentially expressed unigenes were detected, and the roles of the peroxidase in lignin biosynthesis, MYB DNA-binding proteins, and WRKY proteins associated with the regulation of relevant hormones are extensively discussed. The results provide transcriptome data that may bring a new perspective to explain the polyploidy mechanism in the long growth cycle of plants and offer some help to the future Paulownia breeding.
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Affiliation(s)
- Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan, China,
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Rapid genomic DNA changes in allotetraploid fish hybrids. Heredity (Edinb) 2015; 114:601-9. [PMID: 25669608 PMCID: PMC4434252 DOI: 10.1038/hdy.2015.3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/17/2014] [Accepted: 12/19/2014] [Indexed: 12/22/2022] Open
Abstract
Rapid genomic change has been demonstrated in several allopolyploid plant systems; however, few studies focused on animals. We addressed this issue using an allotetraploid lineage (4nAT) of freshwater fish originally derived from the interspecific hybridization of red crucian carp (Carassius auratus red var., ♀, 2n=100) × common carp (Cyprinus carpio L., ♂, 2n=100). We constructed a bacterial artificial chromosome (BAC) library from allotetraploid hybrids in the 20th generation (F20) and sequenced 14 BAC clones representing a total of 592.126 kb, identified 11 functional genes and estimated the guanine-cytosine content (37.10%) and the proportion of repetitive elements (17.46%). The analysis of intron evolution using nine orthologous genes across a number of selected fish species detected a gain of 39 introns and a loss of 30 introns in the 4nAT lineage. A comparative study based on seven functional genes among 4nAT, diploid F1 hybrids (2nF1) (first generation of hybrids) and their original parents revealed that both hybrid types (2nF1 and 4nAT) not only inherited genomic DNA from their parents, but also demonstrated rapid genomic DNA changes (homoeologous recombination, parental DNA fragments loss and formation of novel genes). However, 4nAT presented more genomic variations compared with their parents than 2nF1. Interestingly, novel gene fragments were found for the iqca1 gene in both hybrid types. This study provided a preliminary genomic characterization of allotetraploid F20 hybrids and revealed evolutionary and functional genomic significance of allopolyploid animals.
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Duchemin W, Dupont PY, Campbell MA, Ganley ARD, Cox MP. HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species. BMC Bioinformatics 2015; 16:8. [PMID: 25592117 PMCID: PMC4300824 DOI: 10.1186/s12859-014-0433-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/16/2014] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Forming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution of many biological systems. However, little is known about how expression of parental gene copies (homeologs) responds following genome merger. High throughput RNA sequencing now makes this analysis technically feasible, but tools to determine homeolog expression are still in their infancy. RESULTS Here we present HyLiTE - a single-step analysis to obtain tables of homeolog expression in a hybrid or allopolyploid and its parent species directly from raw mRNA sequence files. By implementing on-the-fly detection of diagnostic parental polymorphisms, HyLiTE can perform SNP calling and read classification simultaneously, thus allowing HyLiTE to be run as parallelized code. HyLiTE accommodates any number of parent species, multiple data sources (including genomic DNA reads to improve SNP detection), and implements a statistical framework optimized for genes with low to moderate expression. CONCLUSIONS HyLiTE is a flexible and easy-to-use program designed for bench biologists to explore patterns of gene expression following genome merger. HyLiTE offers practical advantages over manual methods and existing programs, has been designed to accommodate a wide range of genome merger systems, can identify SNPs that arose following genome merger, and offers accurate performance on non-model organisms.
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Affiliation(s)
- Wandrille Duchemin
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. .,Present address: Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Lyon I, Villeurbanne, F-69622, France.
| | - Pierre-Yves Dupont
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| | - Matthew A Campbell
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| | - Austen R D Ganley
- Institute of Mathematical and Natural Sciences, Massey University, Auckland, New Zealand.
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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