51
|
Zhai Y, Yu X, Zhu Z, Wang P, Meng Y, Zhao Q, Li J, Chen J. Nuclear-Cytoplasmic Coevolution Analysis of RuBisCO in Synthesized Cucumis Allopolyploid. Genes (Basel) 2019; 10:genes10110869. [PMID: 31671713 PMCID: PMC6895982 DOI: 10.3390/genes10110869] [Citation(s) in RCA: 10] [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] [Received: 09/26/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 01/03/2023] Open
Abstract
Allopolyploids are often faced with the challenge of maintaining well-coordination between nuclear and cytoplasmic genes inherited from different species. The synthetic allotetraploid Cucumis × hytivus is a useful model to explore cytonuclear coevolution. In this study, the sequences and expression of cytonuclear enzyme complex RuBisCO as well as its content and activity in C. × hytivus were compared to its parents to explore plastid–nuclear coevolution. The plastome-coded rbcL gene sequence was confirmed to be stable maternal inheritance, and parental copy of nuclear rbcS genes were both preserved in C. × hytivus. Thus, the maternal plastid may interact with the biparentally inherited rbcS alleles. The expression of the rbcS gene of C-homoeologs (paternal) was significantly higher than that of H-homoeologs (maternal) in C. × hytivus (HHCC). Protein interaction prediction analysis showed that the rbcL protein has stronger binding affinity to the paternal copy of rbcS protein than that of maternal copy in C. × hytivus, which might explain the transcriptional bias of the rbcS homoeologs. Moreover, both the activity and content of RuBisCO in C. × hytivus showed mid-parent heterosis. In summary, our results indicate a paternal transcriptional bias of the rbcS genes in C. × hytivus, and we found new nuclear–cytoplasmic combination may be one of the reasons for allopolyploids heterosis.
Collapse
Affiliation(s)
- Yufei Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zaobing Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Panqiao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ya Meng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qinzheng Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
52
|
Colle M, Leisner CP, Wai CM, Ou S, Bird KA, Wang J, Wisecaver JH, Yocca AE, Alger EI, Tang H, Xiong Z, Callow P, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Song GQ, Childs KL, Schilmiller A, Vorsa N, Buell CR, VanBuren R, Jiang N, Edger PP. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. Gigascience 2019; 8:5304886. [PMID: 30715294 PMCID: PMC6423372 DOI: 10.1093/gigascience/giz012] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/18/2018] [Accepted: 01/18/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size. FINDINGS Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar "Draper," which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. CONCLUSIONS These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.
Collapse
Affiliation(s)
- Marivi Colle
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA
| | - Courtney P Leisner
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Shujun Ou
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Center for Genomics Enabled Plant Science, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, Purdue University, 610 Purdue Mall, West Lafayette, IN, 47907, USA
| | - Alan E Yocca
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Elizabeth I Alger
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Haibao Tang
- Human Longevity Inc., 4570 Executive Drive, San Diego, CA 92121, USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, 221 Aimin Road, Hohhot, 010070, China
| | - Pete Callow
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Gil Ben-Zvi
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Avital Brodt
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Kobi Baruch
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Thomas Swale
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Lily Shiue
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Guo-Qing Song
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Center for Genomics Enabled Plant Science, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Anthony Schilmiller
- Mass Spectrometry & Metabolomics Core Facility, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA
| | - Nicholi Vorsa
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA.,Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, 125A Lake Oswego Road, Chatsworth, NJ, 08019, USA
| | - C Robin Buell
- MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA.,Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| |
Collapse
|
53
|
Voshall A, Moriyama EN. Next-generation transcriptome assembly and analysis: Impact of ploidy. Methods 2019; 176:14-24. [PMID: 31176772 DOI: 10.1016/j.ymeth.2019.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/30/2019] [Accepted: 06/01/2019] [Indexed: 10/26/2022] Open
Abstract
Whole genome duplications (WGD) occur widely in plants, but the effects of these events impact all branches of life. WGD events have major evolutionary impacts, often leading to major structural changes within the chromosomes and massive changes in gene expression that facilitate rapid speciation and gene diversification. Even for species that currently have diploid genomes, the impact of ancestral duplication events is still present in the genomes, especially in the context of highly similar gene families that are retained from WGD. However, the impact of these ploidies on various bioinformatics workflows has not been studied well. In this review, we overview biological significance of polyploidy in different organisms. We describe the impact of having polyploid transcriptomes on bioinformatics analyses, especially focusing on transcriptome assembly and transcript quantification. We discuss the benefits of using simulated benchmarking data when we examine the performance of various methods. We also present an example strategy to generate simulated allopolyploid transcriptomes and RNAseq datasets and how these benchmark datasets can be used to assess the performance of transcript assembly and quantification methods. Our benchmarking study shows that all transcriptome assembly methods are affected by having polyploid genomes. Quantification accuracy is also impacted by polyploidy depending on the method. These simulated datasets can be adapted for testing, such as, read mapping, variant calling, and differential expression using biologically realistic conditions.
Collapse
Affiliation(s)
- Adam Voshall
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Etsuko N Moriyama
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| |
Collapse
|
54
|
Rodionov AV, Amosova AV, Belyakov EA, Zhurbenko PM, Mikhailova YV, Punina EO, Shneyer VS, Loskutov IG, Muravenko OV. Genetic Consequences of Interspecific Hybridization, Its Role in Speciation and Phenotypic Diversity of Plants. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419030141] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
55
|
Hu G, Wendel JF. Cis-trans controls and regulatory novelty accompanying allopolyploidization. THE NEW PHYTOLOGIST 2019; 221:1691-1700. [PMID: 30290011 DOI: 10.1111/nph.15515] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/30/2018] [Indexed: 05/20/2023]
Abstract
Allopolyploidy is a prevalent process in plants, having important physiological, ecological and evolutionary consequences. Transcriptomic responses to genomic merger and doubling have been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena including homoeolog expression bias, genome dominance, expression-level dominance and revamping of co-expression networks. Notwithstanding the foregoing, there remains a need to develop a conceptual framework that will stimulate a deeper understanding of these diverse phenomena and their mechanistic interrelationships. Here we introduce considerations relevant to this framework with a focus on cis-trans interactions among duplicated genes and alleles in hybrids and allopolyploids. By extending classic allele-specific expression analysis to the allopolyploid level, we distinguish the distinct effects of progenitor regulatory interactions from the novel intergenomic interactions that arise from genome merger and allopolyploidization. This perspective informs experiments designed to reveal the molecular genetic basis of gene regulatory control, and will facilitate the disentangling of genetic from epigenetic and higher-order effects that impact gene expression. Finally, we suggest that the extended cis-trans model may help conceptually unify several presently disparate hallmarks of allopolyploid evolution, including genome-wide expression dominance and biased fractionation, and lead to a new level of understanding of phenotypic novelty accompanying polyploidy.
Collapse
Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
56
|
Shekhovtsov SV, Ershov NI, Vasiliev GV, Peltek SE. Transcriptomic analysis confirms differences among nuclear genomes of cryptic earthworm lineages living in sympatry. BMC Evol Biol 2019; 19:50. [PMID: 30813890 PMCID: PMC6391759 DOI: 10.1186/s12862-019-1370-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Many earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date. The status of differences between these lineages on the nuclear level is still unclear. Because of widespread polyploidy in earthworms, most studies were limited to two nuclear loci, the ribosomal and the histone clusters. Here we attempted to elucidate the status of a set of genetic lineages within Eisenia nordenskioldi nordenskioldi, an earthworm species from Northern Asia with high intraspecific diversity. We performed RNA-seq on an IonTorrent platform for five specimens of this species belonging to five genetic lineages, as well as two outgroups from the family Lumbricidae, the congenetic E. andrei, and Lumbricus rubellus. RESULTS We de novo assembled transcriptomes and constructed datasets of genes present in all seven specimens using broad (ProteinOrtho; 809 genes) and narrow (HaMStR; 203 genes) ortholog assignment. The majority of orthologs had identical amino acid sequences in all studied specimens, which we believe was due to strong bias towards the most conserved genes. However, for the rest of genes the differences among the lineages were lower than those between them and the congeneric E. andrei. Both datasets yielded phylogenetic trees with the same topology. E. n. nordenskioldi was found to be monophyletic. The differences on the genetic level had no concordance with geography, implying complex history of dispersal. CONCLUSIONS We found that genetic lineages of E. n. nordenskioldi are genetically distinct on nuclear level and probably diverged long ago. Current data implies that they might even represent distinct species within the E. nordenskioldi species complex.
Collapse
Affiliation(s)
- Sergei V. Shekhovtsov
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
- Institute of Biological Problems of the North FEB RAS, Portovaya St. 18, Magadan, 685000 Russia
| | - Nikita I. Ershov
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
| | - Gennady V. Vasiliev
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
| | - Sergey E. Peltek
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
| |
Collapse
|
57
|
Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ. Origin and evolution of the octoploid strawberry genome. Nat Genet 2019; 51:541-547. [PMID: 30804557 PMCID: PMC6882729 DOI: 10.1038/s41588-019-0356-4] [Citation(s) in RCA: 317] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 01/15/2019] [Indexed: 01/19/2023]
Abstract
Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry. Chromosome-scale assembly for the cultivated octoploid strawberry (Fragaria × ananassa) uncovers the origin and evolutionary processes that shaped this complex allopolyploid, providing a useful resource for genome-wide analyses and molecular breeding.
Collapse
Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA. .,Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA.
| | - Thomas J Poorten
- Department of Plant Sciences, University of California-Davis, Davis, California, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.,Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California-Davis, Davis, California, USA
| | - Marivi Colle
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Ronald D Smith
- Department of Biology, College of William and Mary, Williamsburg, VA, USA
| | - Scott J Teresi
- Department of Biology, College of William and Mary, Williamsburg, VA, USA
| | | | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Elizabeth I Alger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA
| | - Alan E Yocca
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Nathan Pumplin
- Department of Plant Sciences, University of California-Davis, Davis, California, USA
| | - Shujun Ou
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA
| | | | | | | | | | | | - Charlotte B Acharya
- Department of Plant Sciences, University of California-Davis, Davis, California, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California-Davis, Davis, California, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.,Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, MI, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, VA, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California-Davis, Davis, California, USA.
| |
Collapse
|
58
|
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.
Collapse
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
| |
Collapse
|
59
|
Folta KM, Barbey CR. The strawberry genome: a complicated past and promising future. HORTICULTURE RESEARCH 2019; 6:97. [PMID: 31645955 PMCID: PMC6804783 DOI: 10.1038/s41438-019-0181-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/15/2019] [Indexed: 05/15/2023]
Affiliation(s)
- Kevin M. Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611 USA
| | | |
Collapse
|
60
|
Clark JW, Donoghue PCJ. Whole-Genome Duplication and Plant Macroevolution. TRENDS IN PLANT SCIENCE 2018; 23:933-945. [PMID: 30122372 DOI: 10.1016/j.tplants.2018.07.006] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/29/2018] [Accepted: 07/12/2018] [Indexed: 05/18/2023]
Abstract
Whole-genome duplication (WGD) is characteristic of almost all fundamental lineages of land plants. Unfortunately, the timings of WGD events are loosely constrained and hypotheses of evolutionary consequence are poorly formulated, making them difficult to test. Using examples from across the plant kingdom, we show that estimates of timing can be improved through the application of molecular clock methodology to multigene datasets. Further, we show that phenotypic change can be quantified in morphospaces and that relative phenotypic disparity can be compared in the light of WGD. Together, these approaches facilitate tests of hypotheses on the role of WGD in plant evolution, underscoring the potential of plants as a model system for investigating the role WGD in macroevolution.
Collapse
Affiliation(s)
- James W Clark
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TH, UK.
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TH, UK.
| |
Collapse
|
61
|
Bird KA, VanBuren R, Puzey JR, Edger PP. The causes and consequences of subgenome dominance in hybrids and recent polyploids. THE NEW PHYTOLOGIST 2018; 220:87-93. [PMID: 29882360 DOI: 10.1111/nph.15256] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/02/2018] [Indexed: 05/22/2023]
Abstract
Contents Summary 87 I. Introduction 87 II. Evolution in action: subgenome dominance within newly formed hybrids and polyploids 88 III. Summary and future directions 90 Acknowledgements 92 References 92 SUMMARY: The merger of divergent genomes, via hybridization or allopolyploidization, frequently results in a 'genomic shock' that induces a series of rapid genetic and epigenetic modifications as a result of conflicts between parental genomes. This conflict among the subgenomes routinely leads one subgenome to become dominant over the other subgenome(s), resulting in subgenome biases in gene content and expression. Recent advances in methods to analyze hybrid and polyploid genomes with comparisons to extant parental progenitors have allowed for major strides in understanding the mechanistic basis for subgenome dominance. In particular, our understanding of the role that homoeologous exchange might play in subgenome dominance and genome evolution is quickly growing. Here we describe recent discoveries uncovering the underlying mechanisms and provide a framework to predict subgenome dominance in hybrids and allopolyploids with far-reaching implications for agricultural, ecological, and evolutionary research.
Collapse
Affiliation(s)
- Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, VA, 23185, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
62
|
Edger PP, McKain MR, Bird KA, VanBuren R. Subgenome assignment in allopolyploids: challenges and future directions. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:76-80. [PMID: 29649616 DOI: 10.1016/j.pbi.2018.03.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/21/2018] [Accepted: 03/26/2018] [Indexed: 05/11/2023]
Abstract
Whole genome duplications (WGDs), also known as polyploid events, have played a crucial role in the evolutionary success of angiosperms across recent and ancient timescales. A recurrent observation from the analysis of allopolyploids is that one of the parental subgenomes is generally more dominant, referred to as 'subgenome dominance', based on higher gene content and expression patterns. Subgenome dominance has far reaching implications to research areas ranging from crop improvement efforts to evolutionary and ecological studies. However, the analysis of subgenome dominance in more ancient polyploids is complicated by a long history of homoeologous exchanges among subgenomes. Here, we will discuss how resulting homoeolog rearrangements and replacements have been ignored in previous studies and urge future studies to integrate phylogenetic approaches to assign homoeologs to parental subgenomes.
Collapse
Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA; Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA.
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA; Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|