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Zhuang Y, Li X, Hu J, Xu R, Zhang D. Expanding the gene pool for soybean improvement with its wild relatives. ABIOTECH 2022; 3:115-125. [PMID: 36304518 PMCID: PMC9590452 DOI: 10.1007/s42994-022-00072-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022]
Abstract
Genetic diversity is a cornerstone of crop improvement, However, cultivated soybean (Glycine max) has undergone several genetic bottlenecks, including domestication in China, the introduction of landraces to other areas of the world and, latterly, selective breeding, leading to low genetic diversity the poses a major obstacle to soybean improvement. By contrast, there remains a relatively high level of genetic diversity in soybean's wild relatives, especially the perennial soybeans (Glycine subgenus Glycine), which could serve as potential gene pools for improving soybean cultivars. Wild soybeans are phylogenetically diversified and adapted to various habitats, harboring resistance to various biotic and abiotic stresses. Advances in genome and transcriptome sequencing enable alleles associated with desirable traits that were lost during domestication of soybean to be discovered in wild soybean. The collection and conservation of soybean wild relatives and the dissection of their genomic features will accelerate soybean breeding and facilitate sustainable agriculture and food production.
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Affiliation(s)
- Yongbin Zhuang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Xiaoming Li
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Junmei Hu
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 Shandong China
| | - Dajian Zhang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
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Zhuang Y, Wang X, Li X, Hu J, Fan L, Landis JB, Cannon SB, Grimwood J, Schmutz J, Jackson SA, Doyle JJ, Zhang XS, Zhang D, Ma J. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. NATURE PLANTS 2022; 8:233-244. [PMID: 35288665 DOI: 10.1038/s41477-022-01102-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Polyploidy and life-strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and the genetic bases of such transitions remain elusive. We assembled chromosome-level genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. These perennial diploids exhibit greater genome stability and possess fewer centromere repeats than the annuals. Biased subgenomic fractionation occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with pre-existing local subgenomic differentiation. Two genes annotated to modulate vegetative-reproductive phase transition and lateral shoot outgrowth were postulated as candidates underlying the perenniality-annuality transition. Our study provides insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.
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Affiliation(s)
- Yongbin Zhuang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China
| | - Xutong Wang
- Department of Agronomy, and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Xianchong Li
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China
| | - Junmei Hu
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China
| | - Lichuan Fan
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China
| | - Jacob B Landis
- School of Integrative Plant Science Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Steven B Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Jeffrey J Doyle
- School of Integrative Plant Science Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Xian Sheng Zhang
- College of Life Sciences, and State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Dajian Zhang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China.
| | - Jianxin Ma
- Department of Agronomy, and Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
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Molecular Analysis Uncovers the Mechanism of Fertility Restoration in Temperature-Sensitive Polima Cytoplasmic Male-Sterile Brassica napus. Int J Mol Sci 2021; 22:ijms222212450. [PMID: 34830333 PMCID: PMC8617660 DOI: 10.3390/ijms222212450] [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: 09/13/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/17/2022] Open
Abstract
Temperature-sensitive male sterility is a heritable agronomic trait affected by genotype-environment interactions. In rapeseed (Brassica napus), Polima (pol) temperature-sensitive cytoplasmic male sterility (TCMS) is commonly used for two-line breeding, as the fertility of pol TCMS lines can be partially restored at certain temperatures. However, little is known about the underlying molecular mechanism that controls fertility restoration. Therefore, we aimed to investigate the fertility conversion mechanism of the pol TCMS line at two different ambient temperatures (16 °C and 25 °C). Our results showed that the anthers developed and produced vigorous pollen at 16 °C but not at 25 °C. In addition, we identified a novel co-transcript of orf224-atp6 in the mitochondria that might lead to fertility conversion of the pol TCMS line. RNA-seq analysis showed that 1637 genes were significantly differentially expressed in the fertile flowers of 596-L when compared to the sterile flower of 1318 and 596-H. Detailed analysis revealed that differentially expressed genes were involved in temperature response, ROS accumulation, anther development, and mitochondrial function. Single-molecule long-read isoform sequencing combined with RNA sequencing revealed numerous genes produce alternative splicing transcripts at high temperatures. Here, we also found that alternative oxidase, type II NAD(P)H dehydrogenases, and transcription factor Hsfs might play a crucial role in male fertility under the low-temperature condition. RNA sequencing and bulked segregant analysis coupled with whole-genome sequencing identified the candidate genes involved in the post-transcriptional modification of orf224. Overall, our study described a putative mechanism of fertility restoration in a pol TCMS line controlled by ambient temperature that might help utilise TCMS in the two-line breeding of Brassica crops.
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Wang C, Wang T, Yin M, Eller F, Liu L, Brix H, Guo W. Transcriptome Analysis of Tetraploid and Octoploid Common Reed ( Phragmites australis). FRONTIERS IN PLANT SCIENCE 2021; 12:653183. [PMID: 34025698 PMCID: PMC8132968 DOI: 10.3389/fpls.2021.653183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Polyploidization in plants is thought to have occurred as coping mechanism with environmental stresses. Polyploidization-driven adaptation is often achieved through interplay of gene networks involved in differentially expressed genes, which triggers the plant to evolve special phenotypic traits for survival. Phragmites australis is a cosmopolitan species with highly variable phenotypic traits and high adaptation capacity to various habitats. The species' ploidy level varies from 3x to 12x, thus it is an ideal organism to investigate the molecular evolution of polyploidy and gene regulation mediated by different numbers of chromosome copies. In this study, we used high-throughput RNAseq data as a tool, to analyze the gene expression profiles in tetraploid and octoploid P. australis. The estimated divergence time between tetraploid and octoploid P. australis was dated to the border between Pliocene and Pleistocene. This study identified 439 up- and 956 down-regulated transcripts in tetraploids compared to octoploids. Gene ontology and pathway analysis revealed that tetraploids tended to express genes responsible for reproduction and seed germination to complete the reproduction cycle early, and expressed genes related to defense against UV-B light and fungi, whereas octoploids expressed mainly genes related to thermotolerance. Most differentially expressed genes were enriched in chaperones, folding catalysts and protein processing in endoplasmic reticulum pathways. Multiple biased isoform usage of the same gene was detected in differentially expressed genes, and the ones upregulated in octoploids were related to reduced DNA methylation. Our study provides new insights into the role of polyploidization on environmental responses and potential stress tolerance in grass species.
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Affiliation(s)
- Cui Wang
- Institute of Ecology and Biodiversity, Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, School of Life Sciences, Shandong University, Qingdao, China
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tong Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Meiqi Yin
- Institute of Ecology and Biodiversity, Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, School of Life Sciences, Shandong University, Qingdao, China
| | | | - Lele Liu
- Institute of Ecology and Biodiversity, Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, School of Life Sciences, Shandong University, Qingdao, China
| | - Hans Brix
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Weihua Guo
- Institute of Ecology and Biodiversity, Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, School of Life Sciences, Shandong University, Qingdao, China
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Hu G, Grover CE, Arick MA, Liu M, Peterson DG, Wendel JF. Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids. Brief Bioinform 2020; 22:1819-1835. [PMID: 32219306 PMCID: PMC7986634 DOI: 10.1093/bib/bbaa035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/06/2020] [Accepted: 02/24/2020] [Indexed: 12/29/2022] Open
Abstract
Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of duplicated genomes, polyploids offer unique challenges for estimating gene expression levels, which is essential for understanding the massive and various forms of transcriptomic responses accompanying polyploidy. Although previous studies have explored the bioinformatics of polyploid transcriptomic profiling, the causes and consequences of inaccurate quantification of transcripts from duplicated gene copies have not been addressed. Using transcriptomic data from the cotton genus (Gossypium) as an example, we present an analytical workflow to evaluate a variety of bioinformatic method choices at different stages of RNA-seq analysis, from homoeolog expression quantification to downstream analysis used to infer key phenomena of polyploid expression evolution. In general, EAGLE-RC and GSNAP-PolyCat outperform other quantification pipelines tested, and their derived expression dataset best represents the expected homoeolog expression and co-expression divergence. The performance of co-expression network analysis was less affected by homoeolog quantification than by network construction methods, where weighted networks outperformed binary networks. By examining the extent and consequences of homoeolog read ambiguity, we illuminate the potential artifacts that may affect our understanding of duplicate gene expression, including an overestimation of homoeolog co-regulation and the incorrect inference of subgenome asymmetry in network topology. Taken together, our work points to a set of reasonable practices that we hope are broadly applicable to the evolutionary exploration of polyploids.
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Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Mark A Arick
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Meiling Liu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Daniel G Peterson
- 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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Ferreira de Carvalho J, Lucas J, Deniot G, Falentin C, Filangi O, Gilet M, Legeai F, Lode M, Morice J, Trotoux G, Aury JM, Barbe V, Keller J, Snowdon R, He Z, Denoeud F, Wincker P, Bancroft I, Chèvre AM, Rousseau-Gueutin M. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:434-447. [PMID: 30604905 DOI: 10.1111/tpj.14228] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/14/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other donor has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus, on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared with cytosolic protein complexes and with genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and are undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neopolyploids showed no biased subgenome expression or maternal homogenization via gene conversion, despite the presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes that could be tested and generalized in other allopolyploid species.
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Affiliation(s)
| | - Jérémy Lucas
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Gwenaëlle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Olivier Filangi
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Fabrice Legeai
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Maryse Lode
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
| | - Jean Keller
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Rennes, 35042, France
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - France Denoeud
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
- UMR CNRS 8030, Evry, CP5706, France
- Université d'Evry-Val-d'Essonne, Université Paris-Saclay, Evry, 91000, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
- UMR CNRS 8030, Evry, CP5706, France
- Université d'Evry-Val-d'Essonne, Université Paris-Saclay, Evry, 91000, France
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
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Cenci A, Hueber Y, Zorrilla-Fontanesi Y, van Wesemael J, Kissel E, Gislard M, Sardos J, Swennen R, Roux N, Carpentier SC, Rouard M. Effect of paleopolyploidy and allopolyploidy on gene expression in banana. BMC Genomics 2019; 20:244. [PMID: 30917780 PMCID: PMC6438041 DOI: 10.1186/s12864-019-5618-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
Background Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B genome, respectively). Unresolved hybridizations finally led to banana diversification into several autotriploid (AAA) and allotriploid cultivars (AAB and ABB). Using transcriptomic data, we investigated the impact of the genome structure on gene expression patterns in roots of 12 different triploid genotypes covering AAA, AAB and ABB subgenome constitutions. Results We demonstrate that (i) there are different genome structures, (ii) expression patterns go beyond the predicted genomic groups, and (iii) the proportion of the B genome influences the gene expression. The presence of the B genome is associated with a higher expression of genes involved in flavonoid biosynthesis, fatty acid metabolism, amino sugar and nucleotide sugar metabolism and oxidative phosphorylation. There are cultivar-specific chromosome regions with biased B:A gene expression ratios that demonstrate homoeologous exchanges (HE) between A and B sub-genomes. In two cultivars, aneuploidy was detected. We identified 3674 genes with a different expression level between allotriploid and autotriploid with ~ 57% having recently duplicated copies (paralogous). We propose a Paralog Inclusive Expression (PIE) analysis that appears to be suitable for genomes still in a downsizing and fractionation process following whole genome duplications. Our approach allows highlighting the genes with a maximum likelihood to affect the plant phenotype. Conclusions This study on banana is a good case to investigate the effects of alloploidy in crops. We conclude that allopolyploidy triggered changes in the genome structure of a crop and it clearly influences the gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5618-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France.
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Yasmin Zorrilla-Fontanesi
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Jelle van Wesemael
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Ewaut Kissel
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Marie Gislard
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, F-34396, Montpellier, France
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium.,Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium.,International Institute of Tropical Agriculture. c/o The Nelson Mandela African Institution for Science and Technology (NM-AIST), P.O. Box 447, Arusha, Tanzania
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Sebastien Christian Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium.,Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France.
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Visger CJ, Wong GKS, Zhang Y, Soltis PS, Soltis DE. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. AMERICAN JOURNAL OF BOTANY 2019; 106:280-291. [PMID: 30779448 DOI: 10.1002/ajb2.1239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Studies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Using diploid and autotetraploid Tolmiea, we present an integrated approach for cross-ploidy comparisons that account for differences in transcriptome size and cell density and make multiple comparisons of transcript abundance. METHODS We use RNA spike-in standards in concert with cell size and density to identify and correct for differences in transcriptome size and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass. KEY RESULTS In total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. The per-transcriptome normalization, the method researchers typically use, captured the fewest DEGs (58% of total DEGs) and failed to detect any DEGs not found by the alternative normalizations. When transcript abundance was normalized per biomass and per cell, ~66% and ~82% of the total DEGs were recovered, respectively. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size. CONCLUSIONS While each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.
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Affiliation(s)
- Clayton J Visger
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, 95819, USA
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yong Zhang
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Shenzhen Hua Han Gene Co. Ltd., 7F Jian An Shan Hai Building, No. 8000, Shennan Road, Futian District, Shenzhen, 518040, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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9
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Xia J, Ma YJ, Wang Y, Wang JW. Deciphering transcriptome profiles of tetraploid Artemisia annua plants with high artemisinin content. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:112-126. [PMID: 29982168 DOI: 10.1016/j.plaphy.2018.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
To investigate on the effects of autopolyploidization on growth and artemisinin biosynthesis in Artemisia annua, we performed a comprehensive transcriptomic characterization of diploid and induced autotetraploid A. annua. The polyploidization treatment not only enhanced photosynthetic capacity and endogenous contents of indole-3-acetic acid (IAA), abscisic acid (ABA) and jasmonic acid (JA), oxidative stress, but increased the average level of artemisinin in tetraploids from 42.0 to 63.6%. The obvious phenotypic alterations in tetraploids were observed including shorter stems, larger size of stomata and glandular secretory trichomes (GSTs), larger leaves, more branches and roots. A total of 8763 (8.85%) differentially expressed genes (DEGs) were identified in autotetraploids and mainly involved in carbohydrate metabolic processes, cell wall organization and defense responses. Both the up-regulated expression of DNA methylation unigenes and enhanced level of DNA methylation in autotetraploids indicated a possible role of DNA methylation on transcriptomic remodeling and phenotypic alteration. The up-regulated genes were enriched in response to extracellular protein biosynthesis, photosynthesis and hormone stimulus for cell enlargement and phenotypic alteration. The genomic shock induced by chromosome duplication stimulated the expression of transcripts related to oxidative stress, biosynthesis and signal transduction of ABA and JA, and key enzymes in artemisinin biosynthetic pathway, leading to the increased accumulation of artemisinin. This is the first transcriptomic research that identifies DEGs involved in the polyploidization of A. annua. The results provide novel information for understanding the complexity of polyploidization and for further identification of the factors and genes involve in artemisinin biosynthesis.
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Affiliation(s)
- Jing Xia
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yan Jun Ma
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yue Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Jian Wen Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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Haynsen MS, Vatanparast M, Mahadwar G, Zhu D, Moger-Reischer RZ, Doyle JJ, Crandall KA, Egan AN. De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu. BMC Genomics 2018; 19:439. [PMID: 29871589 PMCID: PMC5989403 DOI: 10.1186/s12864-018-4798-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/15/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Kudzu, Pueraria montana var. lobata, is a woody vine native to Southeast Asia that has been introduced globally for cattle forage and erosion control. The vine is highly invasive in its introduced areas, including the southeastern US. Modern molecular marker resources are limited for the species, despite its importance. Transcriptomes for P. montana var. lobata and a second phaseoloid legume taxon previously ascribed to genus Pueraria, Neustanthus phaseoloides, were generated and mined for microsatellites and single nucleotide polymorphisms. RESULTS Roche 454 sequencing of P. montana var. lobata and N. phaseoloides transcriptomes produced read numbers ranging from ~ 280,000 to ~ 420,000. Trinity assemblies produced an average of 17,491 contigs with mean lengths ranging from 639 bp to 994 bp. Transcriptome completeness, according to BUSCO, ranged between 64 and 77%. After vetting for primer design, there were 1646 expressed simple sequence repeats (eSSRs) identified in P. montana var. lobata and 1459 in N. phaseoloides. From these eSSRs, 17 identical primer pairs, representing inter-generic phaseoloid eSSRs, were created. Additionally, 13 primer pairs specific to P. montana var. lobata were also created. From these 30 primer pairs, a final set of seven primer pairs were used on 68 individuals of P. montana var. lobata for characterization across the US, China, and Japan. The populations exhibited from 20 to 43 alleles across the seven loci. We also conducted pairwise tests for high-confidence SNP discovery from the kudzu transcriptomes we sequenced and two previously sequenced P. montana var. lobata transcriptomes. Pairwise comparisons between P. montana var. lobata ranged from 358 to 24,475 SNPs, while comparisons between P. montana var. lobata and N. phaseoloides ranged from 5185 to 30,143 SNPs. CONCLUSIONS The discovered molecular markers for kudzu provide a starting point for comparative genetic studies within phaseoloid legumes. This study both adds to the current genetic resources and presents the first available genomic resources for the invasive kudzu vine. Additionally, this study is the first to provide molecular evidence to support the hypothesis of Japan as a source of US kudzu and begins to narrow the origin of US kudzu to the central Japanese island of Honshu.
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Affiliation(s)
- Matthew S. Haynsen
- Department of Biology, George Washington University, Washington, DC USA
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC USA
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Mohammad Vatanparast
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Gouri Mahadwar
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Present address: College of Engineering, Oregon State University, Corvallis, OR USA
| | - Dennis Zhu
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Present address: Department of Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Roy Z. Moger-Reischer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Present address: Department of Biology, Indiana University Bloomington, Bloomington, IN USA
| | - Jeff J. Doyle
- School of Integrated Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY USA
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Ashley N. Egan
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC USA
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
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11
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Albers P, Weytjens B, De Mot R, Marchal K, Springael D. Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics. Microbiologyopen 2018; 7:e00559. [PMID: 29314727 PMCID: PMC5911999 DOI: 10.1002/mbo3.559] [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: 07/08/2017] [Accepted: 10/16/2017] [Indexed: 01/28/2023] Open
Abstract
The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple‐species consortium that synergistically degrades and grows on the phenylurea herbicide linuron. To acquire a better insight into the interactions between the consortium members and the underlying molecular mechanisms, we compared the transcriptomes of the key biodegrading strains WDL7 and WDL1 grown as biofilms in either isolation or consortium conditions by differential RNAseq analysis. Differentially expressed pathways and cellular systems were inferred using the network‐based algorithm PheNetic. Coculturing affected mainly metabolism in WDL1. Significantly enhanced expression of hylA encoding linuron hydrolase was observed. Moreover, differential expression of several pathways involved in carbohydrate, amino acid, nitrogen, and sulfur metabolism was observed indicating that WDL1 gains carbon and energy from linuron indirectly by consuming excretion products from WDL7 and/or WDL6. Moreover, in consortium conditions, WDL1 showed a pronounced stress response and overexpression of cell to cell interaction systems such as quorum sensing, contact‐dependent inhibition, and Type VI secretion. Since the latter two systems can mediate interference competition, it prompts the question if synergistic linuron degradation is the result of true adaptive cooperation or rather a facultative interaction between bacteria that coincidentally occupy complementary metabolic niches.
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Affiliation(s)
- Pieter Albers
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, KU Leuven, Leuven, Belgium
| | - Bram Weytjens
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.,Department of Information Technology, IDLab, IMEC, Ghent University, Gent, Belgium.,Bioinformatics Institute Ghent, Gent, Belgium
| | - René De Mot
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Kathleen Marchal
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.,Department of Information Technology, IDLab, IMEC, Ghent University, Gent, Belgium.,Bioinformatics Institute Ghent, Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, KU Leuven, Leuven, Belgium
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12
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Powell AF, Doyle JJ. Non-Additive Transcriptomic Responses to Inoculation with Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors. Genes (Basel) 2017; 8:E357. [PMID: 29189710 PMCID: PMC5748675 DOI: 10.3390/genes8120357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/29/2022] Open
Abstract
Root nodule symbioses (nodulation) and whole genome duplication (WGD, polyploidy) are both important phenomena in the legume family (Leguminosae). Recently, it has been proposed that polyploidy may have played a critical role in the origin or refinement of nodulation. However, while nodulation and polyploidy have been studied independently, there have been no direct studies of mechanisms affecting the interactions between these phenomena in symbiotic, nodule-forming species. Here, we examined the transcriptome-level responses to inoculation in the young allopolyploid Glycine dolichocarpa (T2) and its diploid progenitor species to identify underlying processes leading to the enhanced nodulation responses previously identified in T2. We assessed the differential expression of genes and, using weighted gene co-expression network analysis (WGCNA), identified modules associated with nodulation and compared their expression between species. These transcriptomic analyses revealed patterns of non-additive expression in T2, with evidence of transcriptional responses to inoculation that were distinct from one or both progenitors. These differential responses elucidate mechanisms underlying the nodulation-related differences observed between T2 and the diploid progenitors. Our results indicate that T2 has reduced stress-related transcription, coupled with enhanced transcription of modules and genes implicated in hormonal signaling, both of which are important for nodulation.
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Affiliation(s)
- Adrian F Powell
- Section of Plant Biology, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
- Boyce Thompson Institute, Ithaca, NY 14853, USA.
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
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13
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Suo Y, Min Y, Dong C, Wang Y, Cheng S, Kang X. MicroRNA expression changes following synthesis of three full-sib Populus triploid populations with different heterozygosities. PLANT MOLECULAR BIOLOGY 2017; 95:215-225. [PMID: 28884266 DOI: 10.1007/s11103-017-0627-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Through high-throughput sequencing, we compared the relative expression levels of miRNA in three full-sib Populus triploid populations with that in their parents and one diploid hybrid population. We found similar numbers of miRNAs differentially expressed between the parents and the four progeny hybrid populations. In addition, unbalanced parental expression level dominance of miRNAs were found in the three allotriploid and interspecific hybrid populations, which may reprogram gene expression networks and contribute to the growth of Populus hybrids. These results indicated that hybridization has a great impact on the miRNA expression variation in the newly synthesized Populus triploid and diploid hybrid populations. However, we also found no significant differences in miRNA expression among one diploid and three triploid hybrid populations, hinting that miRNA abundances do not increase with the genome content. No dosage effect of miRNA expression could lead to dosage-dependent negative effects on target genes and their downstream pathway in polyploids. We speculate that polyploids may gain advantages from the slight decrease in miRNA regulation, suggesting an important molecular mechanism of polyploid advantage. Hybridization with three types of induced 2n gametes transmitted different parental heterozygosities has been proven as an efficient method for Populus triploid production. Several researches have shown that miRNA could be non-additively expressed in allopolyploids. However, it is still unclear whether the non-additively expressed miRNAs result from the effect of hybridization or polyploidization, and whether a dose response to the additional genomic content exists for the expression of miRNA. Toward this end, through high-throughput sequencing, we compared the expression levels of miRNA in three full-sib Populus triploid populations with that in their parents and one interspecific hybrid population. We found similar numbers of miRNAs differentially expressed between the parents and the four progeny hybrid populations. Unbalanced parental expression level dominance of miRNAs were found in the three triploid and diploid hybrid populations, which may reprogram gene expression networks and affect the growth of Populus hybrids. These results indicated that hybridization has a great impact on the miRNA expression variation in the newly synthesized Populus triploid and diploid hybrid populations. However, we also found no significant differences in miRNA expression among the three triploid populations and the diploid hybrid population. No dosage effect of miRNA expression could lead to dosage-dependent negative effects on target genes and their downstream pathway in polyploids. We speculate that polyploids may gain advantages from the decrease in miRNA negative regulation, suggesting an important molecular mechanism of polyploid advantage.
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Affiliation(s)
- Yujing Suo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Tree and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- China Paulownia Research Center, Zhengzhou, 450003, Henan, People's Republic of China
| | - Yu Min
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Tree and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Chunbo Dong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Tree and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Yi Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Tree and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Shiping Cheng
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Tree and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xiangyang Kang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
- Key Laboratory of Genetics and Breeding in Forest Tree and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
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14
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Luo K, Wu F, Zhang D, Dong R, Fan Z, Zhang R, Yan Z, Wang Y, Zhang J. Transcriptomic profiling of Melilotus albus near-isogenic lines contrasting for coumarin content. Sci Rep 2017; 7:4577. [PMID: 28676637 PMCID: PMC5496894 DOI: 10.1038/s41598-017-04111-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/09/2017] [Indexed: 12/30/2022] Open
Abstract
Coumarin and its derivatives are widely used as fragrances in industrial products and have medical value. The goal of the present study was to discover genes and pathways related to coumarin biosynthesis in Melilotus albus using transcriptome analysis. The genes of five M. albus near-isogenic lines (NILs) that had different coumarin content and β-glucosidase activity according to the investigation of pedigree were quantified and then analysed by RNA-Seq. Using transcriptome analysis, differentially expressed genes (DEGs) were identified in two pairwise comparisons that differed in coumarin content as well as in two pairwise comparisons that differed in β-glucosidase activity. Gene expression pattern analysis suggested similar transcriptional trends in the genotypes with the same coumarin levels. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database of DEGs was used to identify functional pathways associated with coumarin biosynthesis. We identified 111 unigenes, with several DEGs among them possibly being related to coumarin synthesis pathways. Unigenes encoding a hexokinase, an abscisic acid receptor, a phenylalanine ammonia-lyase (PAL) and two peroxidases particularly showed correspondence with the coumarin content of different genotypes. These results will contribute to a better understanding of the coumarin biosynthesis in M. albus.
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Affiliation(s)
- Kai Luo
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Daiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Rui Dong
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhichao Fan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Rui Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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15
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Ali SS, Shao J, Lary DJ, Kronmiller BA, Shen D, Strem MD, Amoako-Attah I, Akrofi AY, Begoude BD, ten Hoopen GM, Coulibaly K, Kebe BI, Melnick RL, Guiltinan MJ, Tyler BM, Meinhardt LW, Bailey BA. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms. Genome Biol Evol 2017; 9:2982378. [PMID: 28186564 PMCID: PMC5381587 DOI: 10.1093/gbe/evx021] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/21/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022] Open
Abstract
Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23 Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were specifically induced in planta . Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species’ unique characteristics as pathogens.
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Affiliation(s)
- Shahin S. Ali
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | - Jonathan Shao
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | | | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, China
| | - Mary D. Strem
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | | | - B.A. Didier Begoude
- Regional Laboratory for Biological and Applied Microbiology (IRAD), Yaoundé, Cameroon
| | - G. Martijn ten Hoopen
- Regional Laboratory for Biological and Applied Microbiology (IRAD), Yaoundé, Cameroon
- CIRAD, UPR 106 Bioagresseurs, Montpellier, France
| | | | | | - Rachel L. Melnick
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | - Brett M. Tyler
- Center for Genome Research and Biocomputing, Oregon State University
- Department of Botany and Plant Pathology, Oregon State University
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | - Bryan A. Bailey
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
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16
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Padvitski TA, Galinousky DV, Anisimova NV, Baer GY, Pirko YV, Yemets AI, Khotyleva LV, Blume YB, Kilchevsky AV. Analysis of cellulose synthase gene expression strategies in higher plants using RNA-sequencing data. CYTOL GENET+ 2017. [DOI: 10.3103/s0095452717010121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Boutte J, Ferreira de Carvalho J, Rousseau-Gueutin M, Poulain J, Da Silva C, Wincker P, Ainouche M, Salmon A. Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae). Genome Biol Evol 2016; 8:3030-3044. [PMID: 27614235 PMCID: PMC5633685 DOI: 10.1093/gbe/evw209] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2016] [Indexed: 01/19/2023] Open
Abstract
In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and considering the absence of diploid reference genome and the need of an appropriate analytical strategy, we developed generic bioinformatics tools to (1) detect different haplotypes of each gene within each species and (2) assign a parental origin to haplotypes detected in the hexaploid hybrids and the neo-allopolyploid. The approach described here allows the detection of putative homeologs from sets of short reads. Synonymous substitution rate (KS) comparisons between haplotypes from the hexaploid species revealed the presence of one KS peak (likely resulting from the tetraploid duplication event). The procedure developed in this study can be applied for future differential gene expression or genomics experiments to study the fate of duplicated genes in the invasive allododecaploid S. anglica.
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Affiliation(s)
- Julien Boutte
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Julie Ferreira de Carvalho
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Mathieu Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France UMR Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique, Le Rheu Cedex, France
| | | | | | | | - Malika Ainouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Armel Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
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Powell AF, Doyle JJ. Enhanced rhizobial symbiotic capacity in an allopolyploid species of Glycine (Leguminosae). AMERICAN JOURNAL OF BOTANY 2016; 103:1771-1782. [PMID: 27562208 DOI: 10.3732/ajb.1600060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Previous studies have shown that polyploidy can alter biotic interactions, and it has been suggested that these effects may contribute to the increased ability for colonization of new habitats shown by many allopolyploids. Little is known, however, about the effects of allopolyploidy, which combines hybridity and genome doubling, on symbiotic interactions with rhizobial bacteria. METHODS We examined interactions of the allopolyploid Glycine dolichocarpa (designated T2) with novel rhizobial partners, such as might occur in a context of colonization, and compared these with the responses of its diploid progenitors, G. tomentella (D3) and G. syndetika (D4). We assessed root hair response, nodule formation, nodule mass, nodule number, and plant biomass. KEY RESULTS The allopolyploid (T2) showed a greater root hair deformation response when exposed to rhizobia, compared with either diploid. T2 had a greater probability of forming nodules with NGR234 compared with diploid D4, and greater total nodule mass per nodulated plant compared with diploid D3. T2 also had greater plant biomass responses to nitrogen and when exposed to NGR234. CONCLUSIONS The allopolyploid is characterized by transgressive responses to rhizobia for some variables, while also combining certain parental diploid responses such that its capacity for interactions with rhizobia appears to be greater than for either diploid progenitor. This overall enhanced nodulation capacity and the ability to make greater gains from exposure to both rhizobia and additional nitrogen indicate a greater potential of the allopolyploid to benefit from these factors both generally and in a context of colonization.
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Affiliation(s)
- Adrian F Powell
- Cornell University, Section of Plant Biology, 412 Mann Library, Cornell University, Ithaca, New York 14853 USA
| | - Jeff J Doyle
- Cornell University, Section of Plant Biology, 412 Mann Library, Cornell University, Ithaca, New York 14853 USA
- Cornell University, Section of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, New York 14853 USA
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19
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Segraves KA, Anneberg TJ. Species interactions and plant polyploidy. AMERICAN JOURNAL OF BOTANY 2016; 103:1326-1335. [PMID: 27370313 DOI: 10.3732/ajb.1500529] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/21/2016] [Indexed: 06/06/2023]
Abstract
Polyploidy is a common mode of speciation that can have far-reaching consequences for plant ecology and evolution. Because polyploidy can induce an array of phenotypic changes, there can be cascading effects on interactions with other species. These interactions, in turn, can have reciprocal effects on polyploid plants, potentially impacting their establishment and persistence. Although there is a wealth of information on the genetic and phenotypic effects of polyploidy, the study of species interactions in polyploid plants remains a comparatively young field. Here we reviewed the available evidence for how polyploidy may impact many types of species interactions that range from mutualism to antagonism. Specifically, we focused on three main questions: (1) Does polyploidy directly cause the formation of novel interactions not experienced by diploids, or does it create an opportunity for natural selection to then form novel interactions? (2) Does polyploidy cause consistent, predictable changes in species interactions vs. the evolution of idiosyncratic differences? (3) Does polyploidy lead to greater evolvability in species interactions? From the scarce evidence available, we found that novel interactions are rare but that polyploidy can induce changes in pollinator, herbivore, and pathogen interactions. Although further tests are needed, it is likely that selection following whole-genome duplication is important in all types of species interaction and that there are circumstances in which polyploidy can enhance the evolvability of interactions with other species.
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Affiliation(s)
- Kari A Segraves
- Department of Biology, Syracuse University, Syracuse, New York 13244 USA
| | - Thomas J Anneberg
- Department of Biology, Syracuse University, Syracuse, New York 13244 USA
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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21
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Imadi SR, Kazi AG, Ahanger MA, Gucel S, Ahmad P. Plant transcriptomics and responses to environmental stress: an overview. J Genet 2016; 94:525-37. [PMID: 26440096 DOI: 10.1007/s12041-015-0545-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Different stresses include nutrient deficiency, pathogen attack, exposure to toxic chemicals etc. Transcriptomic studies have been mainly applied to only a few plant species including the model plant, Arabidopsis thaliana. These studies have provided valuable insights into the genetic networks of plant stress responses. Transcriptomics applied to cash crops including barley, rice, sugarcane, wheat and maize have further helped in understanding physiological and molecular responses in terms of genome sequence, gene regulation, gene differentiation, posttranscriptional modifications and gene splicing. On the other hand, comparative transcriptomics has provided more information about plant's response to diverse stresses. Thus, transcriptomics, together with other biotechnological approaches helps in development of stress tolerance in crops against the climate change.
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Affiliation(s)
- Sameen Ruqia Imadi
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, H-12 Campus, Islamabad 25000,
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22
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Brozynska M, Furtado A, Henry RJ. Genomics of crop wild relatives: expanding the gene pool for crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1070-85. [PMID: 26311018 DOI: 10.1111/pbi.12454] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 05/20/2023]
Abstract
Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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23
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Chen C, Li A. Transcriptome Analysis of Differentially Expressed Genes Involved in Proanthocyanidin Accumulation in the Rhizomes of Fagopyrum dibotrys and an Irradiation-Induced Mutant. Front Physiol 2016; 7:100. [PMID: 27047386 PMCID: PMC4796566 DOI: 10.3389/fphys.2016.00100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/02/2016] [Indexed: 12/17/2022] Open
Abstract
The rhizome of Fagopyrum dibotrys is a traditional Chinese medicine that has recently gained attention due to substantial findings regarding its bioactive proanthocyanidin (PA) compounds. However, the molecular mechanism underlying PA accumulation in F. dibotrys remains elusive. We previously obtained an irradiation-induced mutant (RM_R) of F. dibotrys that had a higher PA content compared to that of the wild-type (CK_R). The present study aimed to elucidate the molecular mechanism underlying PA accumulation in F. dibotrys by comparing the rhizome transcriptomes of the irradiation-induced mutant and wild-type using RNA-seq analysis. A total of 53,540 unigenes were obtained, of which 29,901 (55.84%) were annotated based on BLAST searches against public databases, and 501 unique sequences were differentially expressed between the two samples, which consisted of 204 up-regulated and 297 down-regulated unigenes. Further analysis showed that the expression patterns of some unigenes encoding enzymes involved in PAs biosynthesis in F. dibotrys rhizomes differed between RM_R and CK_R. In addition, we identified transcription factor families and several cytochrome P450s that may be involved in PA regulation in F. dibotrys. Finally, 12 unigenes that encode PA biosynthetic enzymes were confirmed by qRT-PCR analysis. This study sheds light on the molecular mechanism underlying radiation-mediated flavonoid accumulation and regulation in F. dibotrys rhizomes. These results will also provide a platform for further functional genomic research on this particular species.
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Affiliation(s)
| | - Ailian Li
- The Cultivation Center, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
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24
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Cornille A, Salcedo A, Kryvokhyzha D, Glémin S, Holm K, Wright SI, Lascoux M. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris). Mol Ecol 2016; 25:616-29. [PMID: 26607306 DOI: 10.1111/mec.13491] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/29/2022]
Abstract
Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.
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Affiliation(s)
- A Cornille
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - A Salcedo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M6R 1M3, Canada
| | - D Kryvokhyzha
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - S Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - K Holm
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - S I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M6R 1M3, Canada
| | - M Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
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Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima. G3-GENES GENOMES GENETICS 2015; 6:29-40. [PMID: 26530424 PMCID: PMC4704722 DOI: 10.1534/g3.115.023242] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.
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26
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Cheng S, Yang J, Liao T, Zhu X, Suo Y, Zhang P, Wang J, Kang X. Transcriptomic changes following synthesis of a Populus full-sib diploid and allotriploid population with different heterozygosities driven by three types of 2n female gamete. PLANT MOLECULAR BIOLOGY 2015; 89:493-510. [PMID: 26419948 DOI: 10.1007/s11103-015-0384-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 09/20/2015] [Indexed: 06/05/2023]
Abstract
Diploid gametes are usually applied to produce triploids of Populus [originating from first-division restitution (FDR), second-division restitution (SDR), and postmeiotic restitution (PMR) 2n eggs]. Three types of 2n gametes transmitted different parental heterozygosities in Populus. Failed spindle formation and no chromosomal separation to opposite poles during meiosis I mean that FDR 2n gametes carry nonsister chromatids that are potentially heterozygous. By contrast, SDR 2n gametes result from failed sister chromatid separation in meiosis II, and therefore, they carry sister chromatid that are potentially homozygous. Completely homozygous 2n gametes can arise from the PMR mechanism. The alteration of gene expression resulting from allopolyploidization is a prominent feature in plants. We compared gene expression in the full-sib progeny of three allotriploid Populus populations (triploid-F, triploid-S, and triploid-P) with that in its parent species, and their full-sib diploid F1 hybrid. Genome-wide expression level dominance was biased toward the maternal in the diploid F1 hybrid and three allotriploid populations, whereas our data indicated important, but different, effects of the transmission of different heterozygosity by 2n female gametes in the expression patterns of allopolyploids. Because of the higher level of heterozygosity, the triploids had higher rates of non-additive and transgressive expression patterns in the triploid-F than in triploid-S and triploid-P. Compared with diploid F1, about 30-fold more genes (251) were differently expressed in the triploid-F than in the triploid-S (9) and triploid-P (8), respectively. These findings indicate that hybridization and polyploidization have immediate and distinct effects on the large-scale patterns of gene expression, and different effects on the transmission of heterozygosity by three 2n female gametes.
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Affiliation(s)
- Shiping Cheng
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Pingdingshan University, Pingdingshan, 467000, Henan Province, People's Republic of China
| | - Jun Yang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Ting Liao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xiaohu Zhu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- College of Forestry and Horticulture, Xinjiang Agricultural University, No. 311, East Nongda Road, Urumqi, 830052, People's Republic of China
| | - Yujing Suo
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Jun Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xiangyang Kang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
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27
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Abstract
Allopolyploidy involves hybridization and duplication of divergent parental genomes and provides new avenues for gene expression. The expression levels of duplicated genes in polyploids can show deviation from parental additivity (the arithmetic average of the parental expression levels). Nonadditive expression has been widely observed in diverse polyploids and comprises at least three possible scenarios: (a) The total gene expression level in a polyploid is similar to that of one of its parents (expression-level dominance); (b) total gene expression is lower or higher than in both parents (transgressive expression); and (c) the relative contribution of the parental copies (homeologs) to the total gene expression is unequal (homeolog expression bias). Several factors may result in expression nonadditivity in polyploids, including maternal-paternal influence, gene dosage balance, cis- and/or trans-regulatory networks, and epigenetic regulation. As our understanding of nonadditive gene expression in polyploids remains limited, a new generation of investigators should explore additional phenomena (i.e., alternative splicing) and use other high-throughput "omics" technologies to measure the impact of nonadditive expression on phenotype, proteome, and metabolome.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525; , ,
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28
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Saminathan T, Nimmakayala P, Manohar S, Malkaram S, Almeida A, Cantrell R, Tomason Y, Abburi L, Rahman MA, Vajja VG, Khachane A, Kumar B, Rajasimha HK, Levi A, Wehner T, Reddy UK. Differential gene expression and alternative splicing between diploid and tetraploid watermelon. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1369-85. [PMID: 25520388 PMCID: PMC4438448 DOI: 10.1093/jxb/eru486] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The exploitation of synthetic polyploids for producing seedless fruits is well known in watermelon. Tetraploid progenitors of triploid watermelon plants, compared with their diploid counterparts, exhibit wide phenotypic differences. Although many factors modulate alternative splicing (AS) in plants, the effects of autopolyploidization on AS are still unknown. In this study, we used tissues of leaf, stem, and fruit of diploid and tetraploid sweet watermelon to understand changes in gene expression and the occurrence of AS. RNA-sequencing analysis was performed along with reverse transcription quantitative PCR and rapid amplification of cDNA ends (RACE)-PCR to demonstrate changes in expression and splicing. All vegetative tissues except fruit showed an increased level of AS in the tetraploid watermelon throughout the growth period. The ploidy levels of diploids and the tetraploid were confirmed using a ploidy analyser. We identified 5362 and 1288 genes that were up- and downregulated, respectively, in tetraploid as compared with diploid plants. We further confirmed that 22 genes underwent AS events across tissues, indicating possibilities of generating different protein isoforms with altered functions of important transcription factors and transporters. Arginine biosynthesis, chlorophyllide synthesis, GDP mannose biosynthesis, trehalose biosynthesis, and starch and sucrose degradation pathways were upregulated in autotetraploids. Phloem protein 2, chloroplastic PGR5-like protein, zinc-finger protein, fructokinase-like 2, MYB transcription factor, and nodulin MtN21 showed AS in fruit tissues. These results should help in developing high-quality seedless watermelon and provide additional transcriptomic information related to other cucurbits.
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Affiliation(s)
- Thangasamy Saminathan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Sumanth Manohar
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Sridhar Malkaram
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Aldo Almeida
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Robert Cantrell
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Yan Tomason
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Lavanya Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Mohammad A Rahman
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Venkata G Vajja
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Amit Khachane
- Genome International Corporation, 8000 Excelsior Drive, Suite 202, Madison, WI 53717, USA
| | - Brajendra Kumar
- Genome International Corporation, 8000 Excelsior Drive, Suite 202, Madison, WI 53717, USA
| | - Harsha K Rajasimha
- Genome International Corporation, 8000 Excelsior Drive, Suite 202, Madison, WI 53717, USA
| | - Amnon Levi
- US Vegetable Laboratory, USDA-ARS, 2875 Savannah Highway, Charleston, SC 29414, USA
| | - Todd Wehner
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609, USA
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA
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29
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Buggs RJA, Wendel JF, Doyle JJ, Soltis DE, Soltis PS, Coate JE. The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0354. [PMID: 24958927 DOI: 10.1098/rstb.2013.0354] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Allopolyploidization (hybridization and whole-genome duplication) is a common phenomenon in plant evolution with immediate saltational effects on genome structure and gene expression. New technologies have allowed rapid progress over the past decade in our understanding of the consequences of allopolyploidy. A major question, raised by early pioneer of this field Leslie Gottlieb, concerned the extent to which gene expression differences among duplicate genes present in an allopolyploid are a legacy of expression differences that were already present in the progenitor diploid species. Addressing this question necessitates phylogenetically well-understood natural study systems, appropriate technology, availability of genomic resources and a suitable analytical framework, including a sufficiently detailed and generally accepted terminology. Here, we review these requirements and illustrate their application to a natural study system that Gottlieb worked on and recommended for this purpose: recent allopolyploids of Tragopogon (Asteraceae). We reanalyse recent data from this system within the conceptual framework of parental legacies on duplicate gene expression in allopolyploids. On a broader level, we highlight the intellectual connection between Gottlieb's phrasing of this issue and the more contemporary framework of cis- versus trans-regulation of duplicate gene expression in allopolyploid plants.
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Affiliation(s)
- Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011, USA
| | - Jeffrey J Doyle
- L. H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, OR 97202, USA
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30
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Jiang J, Wang Y, Zhu B, Fang T, Fang Y, Wang Y. Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids. BMC PLANT BIOLOGY 2015; 15:22. [PMID: 25623840 PMCID: PMC4312607 DOI: 10.1186/s12870-015-0417-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/08/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale. RESULTS We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species. CONCLUSION Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.
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Affiliation(s)
- Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Yue Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Bao Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Tingting Fang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Yujie Fang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
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31
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Alvarez M, Schrey AW, Richards CL. Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution? Mol Ecol 2015; 24:710-25. [PMID: 25604587 DOI: 10.1111/mec.13055] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
Abstract
Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
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Affiliation(s)
- Mariano Alvarez
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, USA
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Piccinini F, Tesei A, Paganelli G, Zoli W, Bevilacqua A. Improving reliability of live/dead cell counting through automated image mosaicing. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2014; 117:448-463. [PMID: 25438936 DOI: 10.1016/j.cmpb.2014.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 06/04/2023]
Abstract
Cell counting is one of the basic needs of most biological experiments. Numerous methods and systems have been studied to improve the reliability of counting. However, at present, manual cell counting performed with a hemocytometer still represents the gold standard, despite several problems limiting reproducibility and repeatability of the counts and, at the end, jeopardizing their reliability in general. We present our own approach based on image processing techniques to improve counting reliability. It works in two stages: first building a high-resolution image of the hemocytometer's grid, then counting the live and dead cells by tagging the image with flags of different colours. In particular, we introduce GridMos (http://sourceforge.net/p/gridmos), a fully-automated mosaicing method to obtain a mosaic representing the whole hemocytometer's grid. In addition to offering more significant statistics, the mosaic "freezes" the culture status, thus permitting analysis by more than one operator. Finally, the mosaic achieved can thus be tagged by using an image editor, thus markedly improving counting reliability. The experiments performed confirm the improvements brought about by the proposed counting approach in terms of both reproducibility and repeatability, also suggesting the use of a mosaic of an entire hemocytometer's grid, then labelled trough an image editor, as the best likely candidate for the new gold standard method in cell counting.
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Affiliation(s)
- Filippo Piccinini
- Advanced Research Center on Electronic Systems (ARCES) for Information and Communication Technologies "E. De Castro", University of Bologna, Italy.
| | - Anna Tesei
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy.
| | - Giulia Paganelli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy.
| | - Wainer Zoli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy.
| | - Alessandro Bevilacqua
- Advanced Research Center on Electronic Systems (ARCES) for Information and Communication Technologies "E. De Castro", University of Bologna, Italy; Department of Computer Science and Engineering (DISI), University of Bologna, Italy.
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Variation in transcriptome size: are we getting the message? Chromosoma 2014; 124:27-43. [DOI: 10.1007/s00412-014-0496-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/30/2022]
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Kong F, Li H, Sun P, Zhou Y, Mao Y. De novo assembly and characterization of the transcriptome of seagrass Zostera marina using Illumina paired-end sequencing. PLoS One 2014; 9:e112245. [PMID: 25423588 PMCID: PMC4244107 DOI: 10.1371/journal.pone.0112245] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/10/2014] [Indexed: 01/15/2023] Open
Abstract
Background The seagrass Zostera marina is a monocotyledonous angiosperm belonging to a polyphyletic group of plants that can live submerged in marine habitats. Zostera marina L. is one of the most common seagrasses and is considered a cornerstone of marine plant molecular ecology research and comparative studies. However, the mechanisms underlying its adaptation to the marine environment still remain poorly understood due to limited transcriptomic and genomic data. Principal Findings Here we explored the transcriptome of Z. marina leaves under different environmental conditions using Illumina paired-end sequencing. Approximately 55 million sequencing reads were obtained, representing 58,457 transcripts that correspond to 24,216 unigenes. A total of 14,389 (59.41%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. 45.18% and 46.91% of the unigenes had significant similarity with proteins in the Swiss-Prot database and Pfam database, respectively. Among these, 13,897 unigenes were assigned to 57 Gene Ontology (GO) terms and 4,745 unigenes were identified and mapped to 233 pathways via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). We compared the orthologous gene family of the Z. marina transcriptome to Oryza sativa and Pyropia yezoensis and 11,667 orthologous gene families are specific to Z. marina. Furthermore, we identified the photoreceptors sensing red/far-red light and blue light. Also, we identified a large number of genes that are involved in ion transporters and channels including Na+ efflux, K+ uptake, Cl− channels, and H+ pumping. Conclusions Our study contains an extensive sequencing and gene-annotation analysis of Z. marina. This information represents a genetic resource for the discovery of genes related to light sensing and salt tolerance in this species. Our transcriptome can be further utilized in future studies on molecular adaptation to abiotic stress in Z. marina.
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Affiliation(s)
- Fanna Kong
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail:
| | - Hong Li
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peipei Sun
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yang Zhou
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Sherman-Broyles S, Bombarely A, Powell AF, Doyle JL, Egan AN, Coate JE, Doyle JJ. The wild side of a major crop: soybean's perennial cousins from Down Under. AMERICAN JOURNAL OF BOTANY 2014; 101:1651-65. [PMID: 25326613 DOI: 10.3732/ajb.1400121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The accumulation of over 30 years of basic research on the biology, genetic variation, and evolution of the wild perennial relatives of soybean (Glycine max) provides a foundation to improve cultivated soybean. The cultivated soybean and its wild progenitor, G. soja, have a center of origin in eastern Asia and are the only two species in the annual subgenus Soja. Systematic and evolutionary studies of the ca. 30 perennial species of subgenus Glycine, native to Australia, have benefited from the availability of the G. max genomic sequence. The perennial species harbor many traits of interest to soybean breeders, among them resistance to major soybean pathogens such as cyst nematode and leaf rust. New species in the Australian subgenus continue to be described, due to the collection of new material and to insights gleaned through systematic studies of accessions in germplasm collections. Ongoing studies in perennial species focus on genomic regions that contain genes for key traits relevant to soybean breeding. These comparisons also include the homoeologous regions that are the result of polyploidy in the common ancestor of all Glycine species. Subgenus Glycine includes a complex of recently formed allopolyploids that are the focus of studies aimed at elucidating genomic, transcriptomic, physiological, taxonomic, morphological, developmental, and ecological processes related to polyploid evolution. Here we review what has been learned over the past 30 years and outline ongoing work on photosynthesis, nitrogen fixation, and floral biology, much of it drawing on new technologies and resources.
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Affiliation(s)
| | | | - Adrian F Powell
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Jane L Doyle
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Ashley N Egan
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington D.C. 20013-7012 USA
| | - Jeremy E Coate
- Reed College, Department of Biology, 3203 SE Woodstock Blvd., Portland, Oregon 97202 USA
| | - Jeff J Doyle
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
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Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014; 345:950-3. [PMID: 25146293 DOI: 10.1126/science.1253435] [Citation(s) in RCA: 1390] [Impact Index Per Article: 139.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Affiliation(s)
- Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Julien Chiquet
- Laboratoire de Mathématiques et Modélisation d'Evry-UMR 8071 CNRS/Université d'Evry val d'Essonne-USC INRA, Evry, France
| | - Harry Belcram
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Birgit Samans
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Margot Corréa
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jérémy Just
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Chu Shin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Isabelle Le Clainche
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Mathieu Charles
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Dominique Arnaud
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - Salman Alamery
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kamel Jabbari
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Köln, Germany
| | - Meixia Zhao
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Houda Chelaifa
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - David Tack
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Gilles Lassalle
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Imen Mestiri
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Nicolas Schnel
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Marie-Christine Le Paslier
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Victor Renault
- Fondation Jean Dausset-Centre d'Étude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France
| | - Philippe E Bayer
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Agnieszka A Golicz
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sahana Manoli
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Vinh Ha Dinh Thi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Smahane Chalabi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Reece Tollenaere
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yunhai Lu
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aurélie Canaguier
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Chauveau
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Bérard
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gwenaëlle Deniot
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fengming Sun
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA
| | | | - Ian Bancroft
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Dominique Brunel
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Régine Delourme
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Michel Renard
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Jacqueline Batley
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.
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Chen J, Hou K, Qin P, Liu H, Yi B, Yang W, Wu W. RNA-Seq for gene identification and transcript profiling of three Stevia rebaudiana genotypes. BMC Genomics 2014; 15:571. [PMID: 25001368 PMCID: PMC4108789 DOI: 10.1186/1471-2164-15-571] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 06/18/2014] [Indexed: 01/15/2023] Open
Abstract
Background Stevia (Stevia rebaudiana) is an important medicinal plant that yields diterpenoid steviol glycosides (SGs). SGs are currently used in the preparation of medicines, food products and neutraceuticals because of its sweetening property (zero calories and about 300 times sweeter than sugar). Recently, some progress has been made in understanding the biosynthesis of SGs in Stevia, but little is known about the molecular mechanisms underlying this process. Additionally, the genomics of Stevia, a non-model species, remains uncharacterized. The recent advent of RNA-Seq, a next generation sequencing technology, provides an opportunity to expand the identification of Stevia genes through in-depth transcript profiling. Results We present a comprehensive landscape of the transcriptome profiles of three genotypes of Stevia with divergent SG compositions characterized using RNA-seq. 191,590,282 high-quality reads were generated and then assembled into 171,837 transcripts with an average sequence length of 969 base pairs. A total of 80,160 unigenes were annotated, and 14,211 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Gene sequences of all enzymes known to be involved in SG synthesis were examined. A total of 143 UDP-glucosyltransferase (UGT) unigenes were identified, some of which might be involved in SG biosynthesis. The expression patterns of eight of these genes were further confirmed by RT-QPCR. Conclusion RNA-seq analysis identified candidate genes encoding enzymes responsible for the biosynthesis of SGs in Stevia, a non-model plant without a reference genome. The transcriptome data from this study yielded new insights into the process of SG accumulation in Stevia. Our results demonstrate that RNA-Seq can be successfully used for gene identification and transcript profiling in a non-model species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-571) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Wei Wu
- Agronomy College of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China.
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Bombarely A, Coate JE, Doyle JJ. Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ 2014; 2:e391. [PMID: 24883252 PMCID: PMC4034613 DOI: 10.7717/peerj.391] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/01/2014] [Indexed: 12/18/2022] Open
Abstract
Allopolyploidy combines two progenitor genomes in the same nucleus. It is a common speciation process, especially in plants. Deciphering the origins of polyploid species is a complex problem due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid populations, and loss of parental contributions through gene or chromosome loss. Among the perennial species of Glycine, the plant genus that includes the cultivated soybean (G. max), are eight allopolyploid species, three of which are studied here. Previous crossing studies and molecular systematic results from two nuclear gene sequences led to hypotheses of origin for these species from among extant diploid species. We use several phylogenetic and population genomics approaches to clarify the origins of the genomes of three of these allopolyploid species using single nucleotide polymorphism data and a guided transcriptome assembly. The results support the hypothesis that all three polyploid species are fixed hybrids combining the genomes of the two putative parents hypothesized on the basis of previous work. Based on mapping to the soybean reference genome, there appear to be no large regions for which one homoeologous contribution is missing. Phylogenetic analyses of 27 selected transcripts using a coalescent approach also are consistent with multiple origins for these allopolyploid species, and suggest that origins occurred within the last several hundred thousand years.
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Affiliation(s)
| | - Jeremy E Coate
- Department of Biology, Reed College , Portland, OR , USA
| | - Jeff J Doyle
- Department of Plant Biology, Cornell University , Ithaca, NY , USA
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Lashermes P, Combes MC, Hueber Y, Severac D, Dereeper A. Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:674-85. [PMID: 24628823 DOI: 10.1111/tpj.12505] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 05/27/2023]
Abstract
Allopolyploidization is widespread and has played a major role in flowering plant diversification. Genomic changes are common consequences of allopolyploidization, but their mechanisms of occurrence and dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen as a model to investigate genetic changes in allopolyploid using an approach that exploits next-generation sequencing technologies. Genes affected by putative homoeolog loss were inferred by comparing the numbers of single-nucleotide polymorphisms detected using RNA-seq in individual accessions of C. arabica, and between accessions of its two diploid progenitor species for common sequence positions. Their physical locations were investigated and clusters of genes exhibiting homoeolog loss were identified. To validate these results, genome sequencing data were generated from one accession of C. arabica and further analyzed. Genomic rearrangements involving homoeologous exchanges appear to occur in C. arabica and to be a major source of genetic diversity. At least 5% of the C. arabica genes were inferred to have undergone homoeolog loss. The detection of a large number of homoeologous exchange events (HEEs) shared by all accessions of C. arabica strongly reinforces the assumption of a single allopolyploidization event. Furthermore, HEEs were specific to one or a few accessions, suggesting that HEE accumulates gradually. Our results provide evidence for the important role of HEE in allopolyploid genome evolution.
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Affiliation(s)
- Philippe Lashermes
- IRD, UMR RPB (IRD, CIRAD, Université Montpellier II), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
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Goettel W, Xia E, Upchurch R, Wang ML, Chen P, An YQC. Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content. BMC Genomics 2014; 15:299. [PMID: 24755115 PMCID: PMC4023607 DOI: 10.1186/1471-2164-15-299] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 04/07/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. RESULTS In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. CONCLUSIONS As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.
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Affiliation(s)
- Wolfgang Goettel
- USDA-ARS, Midwest Area, Plant Genetics Research Unit at Donald Danforth Plant Science Center, 975 N Warson Rd, St. Louis, MO 63132, USA
| | - Eric Xia
- 508 East Stoughton Street, Champaign, IL 61820, USA
| | - Robert Upchurch
- USDA-ARS, Soybean and Nitrogen Fixation Research, 2417 Gardner Hall, Raleigh, NC 27695, USA
| | - Ming-Li Wang
- USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment St., Griffin, GA 30223, USA
| | - Pengyin Chen
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yong-Qiang Charles An
- USDA-ARS, Midwest Area, Plant Genetics Research Unit at Donald Danforth Plant Science Center, 975 N Warson Rd, St. Louis, MO 63132, USA
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Harbert RS, Brown AHD, Doyle JJ. Climate niche modeling in the perennial Glycine (Leguminosae) allopolyploid complex. AMERICAN JOURNAL OF BOTANY 2014; 101:710-721. [PMID: 24699543 DOI: 10.3732/ajb.1300417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF STUDY Polyploid plants, when compared with diploids, show similar molecular, morphological, physiological, and ecological tendencies across unrelated groups, but the degree to which these form "rules" of polyploid evolution are unclear. The Glycine (Leguminosae) allopolyploid complex affords the opportunity to test whether polyploidy in similar genetic backgrounds produces similar effects on geographical range or climatic space. METHODS We used information on locality presence of four closely related Glycine allopolyploid species and their diploid progenitors to build models of the potentially available Australian ranges based on climate using Maxent3.3.3k. Principal coordinate analysis was used to characterize the multidimensional climate space occupied by each species. KEY RESULTS Each of the four Glycine allopolyploids showed intermediacy in potential geographical space and in ecological space, relative to its diploid progenitors. The four allopolyploids did not have consistently larger ranges than their progenitors, though all four occupied a portion of climate niche space not available to its progenitors. The polyploids also differed in their exploitation of potentially available geographical range. Australian ranges and environmental space did not correlate with greater colonizing ability in these polyploids. CONCLUSIONS The four Glycine allopolyploids do not show many common range- or climate-related features, other than intermediacy. Thus, despite their similar genetic and evolutionary backgrounds, polyploidy has not produced convergent ecological effects.
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Affiliation(s)
- Robert S Harbert
- Cornell University, Department of Plant Biology, 412 Mann Library, Cornell University, Ithaca, New York 14853 USA
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42
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Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT. RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PLoS One 2013; 8:e82634. [PMID: 24324815 PMCID: PMC3855774 DOI: 10.1371/journal.pone.0082634] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
An RNA-Seq experiment was performed using field grown well-watered and naturally rain fed cotton plants to identify differentially expressed transcripts under water-deficit stress. Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns that confirm the accuracy of this technique for future studies in cotton genomics. Additionally, putative sequence based genome localization of differentially expressed transcripts detected A2 genome specific gene expression under water-deficit stress. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.
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Affiliation(s)
- Megan J. Bowman
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Wonkeun Park
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
- Clemson University Pee Dee Research and Education Center, Florence, South Carolina, United States of America
| | - Philip J. Bauer
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Joshua A. Udall
- Brigham Young University, Provo, Utah, United States of America
| | - Justin T. Page
- Brigham Young University, Provo, Utah, United States of America
| | - Joshua Raney
- Brigham Young University, Provo, Utah, United States of America
| | | | - Don. C. Jones
- Cotton Incorporated, Agricultural and Environmental Research, Cary, North Carolina, United States of America
| | - B. Todd Campbell
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
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43
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Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory. Mol Phylogenet Evol 2013; 69:1172-85. [DOI: 10.1016/j.ympev.2013.06.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 06/06/2013] [Accepted: 06/12/2013] [Indexed: 11/22/2022]
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44
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Christensen KA, Brunelli JP, Lambert MJ, DeKoning J, Phillips RB, Thorgaard GH. Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication. BMC Bioinformatics 2013; 14:325. [PMID: 24237905 PMCID: PMC3840595 DOI: 10.1186/1471-2105-14-325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 11/12/2013] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The common ancestor of salmonid fishes, including rainbow trout (Oncorhynchus mykiss), experienced a whole genome duplication between 20 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome. This retention complicates efforts to detect allelic variation in salmonid fishes. Specifically, single nucleotide polymorphism (SNP) detection is problematic because nucleotide variation can be found between the duplicate copies (paralogs) of a gene as well as between alleles. RESULTS We present a method of differentiating between allelic and paralogous (gene copy) sequence variants, allowing identification of SNPs in organisms with multiple copies of a gene or set of genes. The basic strategy is to: 1) identify windows of unique cDNA sequences with homology to each other, 2) compare these unique cDNAs if they are not shared between individuals (i.e. the cDNA is homozygous in one individual and homozygous for another cDNA in the other individual), and 3) give a "SNP score" value between zero and one to each candidate sequence variant based on six criteria. Using this strategy we were able to detect about seven thousand potential SNPs from the transcriptomes of several clonal lines of rainbow trout. When directly compared to a pre-validated set of SNPs in polyploid wheat, we were also able to estimate the false-positive rate of this strategy as 0 to 28% depending on parameters used. CONCLUSIONS This strategy has an advantage over traditional techniques of SNP identification because another dimension of sequencing information is utilized. This method is especially well suited for identifying SNPs in polyploids, both outbred and inbred, but would tend to be conservative for diploid organisms.
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Affiliation(s)
- Kris A Christensen
- School of Molecular Biosciences, Washington State University, Pullman WA 99164-4660, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Joseph P Brunelli
- School of Biological Sciences, Washington State University, Pullman WA 99164-4236, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Matthew J Lambert
- School of Biological Sciences, Washington State University, Vancouver, 14204 NE Salmon Creek Ave, Vancouver WA 98686-9600, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Jenefer DeKoning
- School of Biological Sciences, Washington State University, Vancouver, 14204 NE Salmon Creek Ave, Vancouver WA 98686-9600, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Ruth B Phillips
- School of Biological Sciences, Washington State University, Vancouver, 14204 NE Salmon Creek Ave, Vancouver WA 98686-9600, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Gary H Thorgaard
- School of Biological Sciences, Washington State University, Pullman WA 99164-4236, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
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Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S. Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2699-716. [PMID: 23918062 DOI: 10.1007/s00122-013-2166-x] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 07/12/2013] [Indexed: 05/18/2023]
Abstract
Genotyping by sequencing (GBS) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. Unlike other high-density genotyping technologies which have mainly been applied to general interest "reference" genomes, the low cost of GBS makes it an attractive means of saturating mapping and breeding populations with a high density of SNP markers. One barrier to the widespread use of GBS has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous SNP calls which are not easily diagnosed or corrected. In this study, we use a 384-plex GBS protocol to add 30,984 markers to an indica (IR64) × japonica (Azucena) mapping population consisting of 176 recombinant inbred lines of rice (Oryza sativa) and we release our imputation and error correction pipeline to address initial GBS data sparsity and error, and streamline the process of adding SNPs to RIL populations. Using the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. We mapped QTL for leaf width and aluminum tolerance, and were able to identify additional QTL for both phenotypes when using the full set of 30,984 SNPs that were not identified using a subset of only 1,464 SNPs, including a previously unreported QTL for aluminum tolerance located directly within a recombination hotspot on chromosome 1. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.
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Affiliation(s)
- Jennifer Spindel
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853-1901, USA,
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Combes MC, Dereeper A, Severac D, Bertrand B, Lashermes P. Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures. THE NEW PHYTOLOGIST 2013; 200:251-260. [PMID: 23790161 DOI: 10.1111/nph.12371] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 05/14/2013] [Indexed: 05/02/2023]
Abstract
Polyploidy has occurred throughout the evolutionary history of plants and led to diversification and plant ecological adaptation. Functional plasticity of duplicate genes is believed to play a major role in the environmental adaptation of polyploids. In this context, we characterized genome-wide homoeologous gene expression in Coffea arabica, a recent allopolyploid combining two subgenomes that derive from two closely related diploid species, and investigated its variation in response to changing environment. The transcriptome of leaves of C. arabica cultivated at different growing temperatures suitable for one or the other parental species was examined using RNA-sequencing. The relative contribution of homoeologs to gene expression was estimated for 9959 and 10,628 genes in warm and cold conditions, respectively. Whatever the growing conditions, 65% of the genes showed equivalent levels of homoeologous gene expression. In 92% of the genes, relative homoeologous gene expression varied < 10% between growing temperatures. The subgenome contributions to the transcriptome appeared to be only marginally altered by the different conditions (involving intertwined regulations of homeologs) suggesting that C. arabica's ability to tolerate a broader range of growing temperatures than its diploid parents does not result from differential use of homoeologs.
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Affiliation(s)
- Marie-Christine Combes
- IRD, UMR RPB (IRD, CIRAD, Université Montpellier II), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cédex 5, France
| | - Alexis Dereeper
- IRD, UMR RPB (IRD, CIRAD, Université Montpellier II), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cédex 5, France
| | - Dany Severac
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cédex 5, France
| | - Benoît Bertrand
- CIRAD, UMR RPB (IRD, CIRAD, Université Montpellier II), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cédex 5, France
| | - Philippe Lashermes
- IRD, UMR RPB (IRD, CIRAD, Université Montpellier II), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cédex 5, France
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Hegarty M, Coate J, Sherman-Broyles S, Abbott R, Hiscock S, Doyle J. Lessons from natural and artificial polyploids in higher plants. Cytogenet Genome Res 2013; 140:204-25. [PMID: 23816545 DOI: 10.1159/000353361] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy in higher plants is a major source of genetic novelty upon which selection may act to drive evolution, as evidenced by the widespread success of polyploid species in the wild. However, research into the effects of polyploidy can be confounded by the entanglement of several processes: genome duplication, hybridisation (allopolyploidy is frequent in plants) and subsequent evolution. The discovery of the chemical agent colchicine, which can be used to produce artificial polyploids on demand, has enabled scientists to unravel these threads and understand the complex genomic changes involved in each. We present here an overview of lessons learnt from studies of natural and artificial polyploids, and from comparisons between the 2, covering basic cellular and metabolic consequences through to alterations in epigenetic gene regulation, together with 2 in-depth case studies in Senecio and Glycine. See also the sister article focusing on animals by Arai and Fujimoto in this themed issue.
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Affiliation(s)
- M Hegarty
- IBERS, Aberystwyth University, Aberystwyth, UK. ayh @ aber.ac.uk
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Ruttink T, Sterck L, Rohde A, Bendixen C, Rouzé P, Asp T, Van de Peer Y, Roldan-Ruiz I. Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:605-17. [PMID: 23433242 DOI: 10.1111/pbi.12051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/05/2013] [Accepted: 01/11/2013] [Indexed: 05/09/2023]
Abstract
Despite current advances in next-generation sequencing data analysis procedures, de novo assembly of a reference sequence required for SNP discovery and expression analysis is still a major challenge in genetically uncharacterized, highly heterozygous species. High levels of polymorphism inherent to outbreeding crop species hamper De Bruijn Graph-based de novo assembly algorithms, causing transcript fragmentation and the redundant assembly of allelic contigs. If multiple genotypes are sequenced to study genetic diversity, primary de novo assembly is best performed per genotype to limit the level of polymorphism and avoid transcript fragmentation. Here, we propose an Orthology Guided Assembly procedure that first uses sequence similarity (tBLASTn) to proteins of a model species to select allelic and fragmented contigs from all genotypes and then performs CAP3 clustering on a gene-by-gene basis. Thus, we simultaneously annotate putative orthologues for each protein of the model species, resolve allelic redundancy and fragmentation and create a de novo transcript sequence representing the consensus of all alleles present in the sequenced genotypes. We demonstrate the procedure using RNA-seq data from 14 genotypes of Lolium perenne to generate a reference transcriptome for gene discovery and translational research, to reveal the transcriptome-wide distribution and density of SNPs in an outbreeding crop and to illustrate the effect of polymorphisms on the assembly procedure. The results presented here illustrate that constructing a non-redundant reference sequence is essential for comparative genomics, orthology-based annotation and candidate gene selection but also for read mapping and subsequent polymorphism discovery and/or read count-based gene expression analysis.
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Affiliation(s)
- Tom Ruttink
- Plant Sciences Unit--Growth and Development, Institute for Agricultural and Fisheries Research-ILVO, Melle, Belgium.
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Chang S, Hartman GL, Singh RJ, Lambert KN, Hobbs HA, Domier LL. Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1627-38. [PMID: 23494395 DOI: 10.1007/s00122-013-2079-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/23/2013] [Indexed: 06/01/2023]
Abstract
Like many widely cultivated crops, soybean [Glycine max (L.) Merr.] has a relatively narrow genetic base, while its perennial distant relatives in the subgenus Glycine Willd. are more genetically diverse and display desirable traits not present in cultivated soybean. To identify single-nucleotide polymorphisms (SNPs) between a pair of G. latifolia accessions that were resistant or susceptible to Sclerotinia sclerotiorum (Lib.) de Bary, reduced-representations of DNAs from each accession were sequenced. Approximately 30 % of the 36 million 100-nt reads produced from each of the two G. latifolia accessions aligned primarily to gene-rich euchromatic regions on the distal arms of G. max chromosomes. Because a genome sequence was not available for G. latifolia, the G. max genome sequence was used as a reference to identify 9,303 G. latifolia SNPs that aligned to unique positions in the G. max genome with at least 98 % identity and no insertions and deletions. To validate a subset of the SNPs, nine TaqMan and 384 GoldenGate allele-specific G. latifolia SNP assays were designed and analyzed in F2 G. latifolia populations derived from G. latifolia plant introductions (PI) 559298 and 559300. All nine TaqMan markers and 91 % of the 291 polymorphic GoldenGate markers segregated in a 1:2:1 ratio. Genetic linkage maps were assembled for G. latifolia, nine of which were uninterrupted and nearly collinear with the homoeologous G. max chromosomes. These results made use of a heterologous reference genome sequence to identify more than 9,000 informative high-quality SNPs for G. latifolia, a subset of which was used to generate the first genetic maps for any perennial Glycine species.
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Affiliation(s)
- Sungyul Chang
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
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50
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Coate JE, Powell AF, Owens TG, Doyle JJ. Transgressive physiological and transcriptomic responses to light stress in allopolyploid Glycine dolichocarpa (Leguminosae). Heredity (Edinb) 2013; 110:160-70. [PMID: 23149457 PMCID: PMC3554458 DOI: 10.1038/hdy.2012.77] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/18/2012] [Accepted: 10/01/2012] [Indexed: 12/28/2022] Open
Abstract
Allopolyploidy is often associated with increased photosynthetic capacity as well as enhanced stress tolerance. Excess light is a ubiquitous plant stress associated with photosynthetic light harvesting. We show that under chronic excess light, the capacity for non-photochemical quenching (NPQ(max)), a photoprotective mechanism, was higher in a recently formed natural allotetraploid (Glycine dolichocarpa, designated 'T2') than in its diploid progenitors (G. tomentella, 'D3'; and G. syndetika, 'D4'). This enhancement in NPQ(max) was due to an increase in energy-dependent quenching (qE) relative to D3, combined with an increase in zeaxanthin-dependent quenching (qZ) relative to D4. To explore the genetic basis for this phenotype, we profiled D3, D4 and T2 leaf transcriptomes and found that T2 overexpressed genes of the water-water cycle relative to both diploid progenitors, as well as genes involved in cyclic electron flow around photosystem I (CEF-PSI) and the xanthophyll cycle, relative to D4. Xanthophyll pigments have critical roles in NPQ, and the water-water cycle and CEF-PSI are non-photosynthetic electron transport pathways believed to facilitate NPQ formation. In the absence of CO(2), T2 also exhibited greater quantum yield of photosystem II than either diploid, indicating a greater capacity for non-photosynthetic electron transport. We postulate that, relative to its diploid progenitors, T2 is able to achieve higher NPQ(max) due to an increase in xanthophyll pigments coupled with enhanced electron flow through the water-water cycle and CEF-PSI.
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Affiliation(s)
- J E Coate
- Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA.
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