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Akiyama R, Goto T, Tameshige T, Sugisaka J, Kuroki K, Sun J, Akita J, Hatakeyama M, Kudoh H, Kenta T, Tonouchi A, Shimahara Y, Sese J, Kutsuna N, Shimizu-Inatsugi R, Shimizu KK. Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation. Nat Commun 2023; 14:5792. [PMID: 37737204 PMCID: PMC10517152 DOI: 10.1038/s41467-023-41260-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/29/2023] [Indexed: 09/23/2023] Open
Abstract
Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software that extracts leaf color by detecting plant individuals automatically. As a case study, we applied PlantServation to examine environmental and genotypic effects on the pigment anthocyanin content estimated from leaf color. We processed >4 million images of small individuals of four Arabidopsis species in the field, where the plant shape, color, and background vary over months. Past radiation, coldness, and precipitation significantly affected the anthocyanin content. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation facilitates the study of plant responses to complex environments termed "in natura".
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Affiliation(s)
- Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Takao Goto
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192, Japan
| | - Jiro Sugisaka
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Ken Kuroki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Jianqiang Sun
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8517, Japan
| | - Junichi Akita
- Department of Electric and Computer Engineering, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Tanaka Kenta
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-kogen, Ueda, 386-2204, Japan
| | - Aya Tonouchi
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yuki Shimahara
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Humanome Lab, Inc., L-HUB 3F, 1-4, Shumomiyabi-cho, Shinjuku, Tokyo, 162-0822, Japan
- AIST-Tokyo Tech RWBC-OIL, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Natsumaro Kutsuna
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan.
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Combes MC, Joët T, Stavrinides AK, Lashermes P. New cup out of old coffee: contribution of parental gene expression legacy to phenotypic novelty in coffee beans of the allopolyploid Coffea arabica L. ANNALS OF BOTANY 2023; 131:157-170. [PMID: 35325016 PMCID: PMC9904342 DOI: 10.1093/aob/mcac041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/21/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Allopolyploidization is a widespread phenomenon known to generate novel phenotypes by merging evolutionarily distinct parental genomes and regulatory networks in a single nucleus. The objective of this study was to investigate the transcriptional regulation associated with phenotypic novelty in coffee beans of the allotetraploid Coffea arabica. METHODS A genome-wide comparative transcriptomic analysis was performed in C. arabica and its two diploid progenitors, C. canephora and C. eugenioides. Gene expression patterns and homeologue expression were studied on seeds at five different maturation stages. The involvement of homeologue expression bias (HEB) in specific traits was addressed both by functional enrichment analyses and by the study of gene expression in the caffeine and chlorogenic acid biosynthesis pathways. KEY RESULTS Expression-level dominance in C. arabica seed was observed for most of the genes differentially expressed between the species. Approximately a third of the genes analysed showed HEB. This proportion increased during seed maturation but the biases remained equally distributed between the sub-genomes. The relative expression levels of homeologues remained relatively constant during maturation and were correlated with those estimated in leaves of C. arabica and interspecific hybrids between C. canephora and C. eugenioides. Functional enrichment analyses performed on genes exhibiting HEB enabled the identification of processes potentially associated with physiological traits. The expression profiles of the genes involved in caffeine biosynthesis mirror the differences observed in the caffeine content of mature seeds of C. arabica and its parental species. CONCLUSIONS Neither of the two sub-genomes is globally preferentially expressed in C. arabica seeds, and homeologues appear to be co-regulated by shared trans-regulatory mechanisms. The observed HEBs are thought to be a legacy of gene expression differences inherited from diploid progenitor species. Pre-existing functional divergences between parental species appear to play an important role in controlling the phenotype of C. arabica seeds.
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Affiliation(s)
| | - Thierry Joët
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
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3
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Phylogenetic Analyses of Some Key Genes Provide Information on Pollinator Attraction in Solanaceae. Genes (Basel) 2022; 13:genes13122278. [PMID: 36553545 PMCID: PMC9778481 DOI: 10.3390/genes13122278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 12/07/2022] Open
Abstract
Floral syndromes are known by the conserved morphological traits in flowers associated with pollinator attraction, such as corolla shape and color, aroma emission and composition, and rewards, especially the nectar volume and sugar concentration. Here, we employed a phylogenetic approach to investigate sequences of genes enrolled in the biosynthetic pathways responsible for some phenotypes that are attractive to pollinators in Solanaceae genomes. We included genes involved in visible color, UV-light response, scent emission, and nectar production to test the hypothesis that these essential genes have evolved by convergence under pollinator selection. Our results refuted this hypothesis as all four studied genes recovered the species' phylogenetic relationships, even though some sites were positively selected. We found differences in protein motifs among genera in Solanaceae that were not necessarily associated with the same floral syndrome. Although it has had a crucial role in plant diversification, the plant-pollinator interaction is complex and still needs further investigation, with genes evolving not only under the influence of pollinators, but by the sum of several evolutionary forces along the speciation process in Solanaceae.
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Berardi AE, Esfeld K, Jäggi L, Mandel T, Cannarozzi GM, Kuhlemeier C. Complex evolution of novel red floral color in Petunia. THE PLANT CELL 2021; 33:2273-2295. [PMID: 33871652 PMCID: PMC8364234 DOI: 10.1093/plcell/koab114] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/12/2021] [Indexed: 05/20/2023]
Abstract
Red flower color has arisen multiple times and is generally associated with hummingbird pollination. The majority of evolutionary transitions to red color proceeded from purple lineages and tend to be genetically simple, almost always involving a few loss-of-function mutations of major phenotypic effect. Here we report on the complex evolution of a novel red floral color in the hummingbird-pollinated Petunia exserta (Solanaceae) from a colorless ancestor. The presence of a red color is remarkable because the genus cannot synthesize red anthocyanins and P. exserta retains a nonfunctional copy of the key MYB transcription factor AN2. We show that moderate upregulation and a shift in tissue specificity of an AN2 paralog, DEEP PURPLE, restores anthocyanin biosynthesis in P. exserta. An essential shift in anthocyanin hydroxylation occurred through rebalancing the expression of three hydroxylating genes. Furthermore, the downregulation of an acyltransferase promotes reddish hues in typically purple pigments by preventing acyl group decoration of anthocyanins. This study presents a rare case of a genetically complex evolutionary transition toward the gain of a novel red color.
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Affiliation(s)
- Andrea E. Berardi
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Korinna Esfeld
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Lea Jäggi
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | | | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
- Author for correspondence:
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Tripp EA, Dexter KG, Stone HB. Reproductive character displacement and potential underlying drivers in a species-rich and florally diverse lineage of tropical angiosperms ( Ruellia; Acanthaceae). Ecol Evol 2021; 11:4719-4730. [PMID: 33976842 PMCID: PMC8093712 DOI: 10.1002/ece3.7371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 12/05/2020] [Accepted: 12/10/2020] [Indexed: 11/08/2022] Open
Abstract
Reproductive character displacement is a pattern whereby sympatric lineages diverge more in reproductive character morphology than allopatric lineages. This pattern has been observed in many plant species, but comparably few have sought to disentangle underlying mechanisms. Here, in a diverse lineage of Neotropical plants (Ruellia; Acanthaceae), we present evidence of reproductive character displacement in a macroevolutionary framework (i.e., among species) and document mechanistic underpinnings. In a series of interspecific hand pollinations in a controlled glasshouse environment, we found that crosses between species that differed more in overall flower size, particularly in style length, were significantly less likely to produce viable seeds. Further, species pairs that failed to set seed were more likely to have sympatric distributions in nature. Competition for pollinators and reinforcement to avoid costly interspecific mating could both result in these patterns and are not mutually exclusive processes. Our results add to growing evidence that reproductive character displacement contributes to exceptional floral diversity of angiosperms.
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Affiliation(s)
- Erin A. Tripp
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderCOUSA
- Museum of Natural HistoryUniversity of ColoradoBoulderCOUSA
| | - Kyle G. Dexter
- School of GeoSciencesUniversity of EdinburghEdinburghUK
- Royal Botanic Garden EdinburghEdinburghUK
| | - Heather B. Stone
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderCOUSA
- Museum of Natural HistoryUniversity of ColoradoBoulderCOUSA
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Sánchez-Cabrera M, Jiménez-López FJ, Narbona E, Arista M, Ortiz PL, Romero-Campero FJ, Ramanauskas K, Igić B, Fuller AA, Whittall JB. Changes at a Critical Branchpoint in the Anthocyanin Biosynthetic Pathway Underlie the Blue to Orange Flower Color Transition in Lysimachia arvensis. FRONTIERS IN PLANT SCIENCE 2021; 12:633979. [PMID: 33692818 PMCID: PMC7937975 DOI: 10.3389/fpls.2021.633979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/01/2021] [Indexed: 05/27/2023]
Abstract
Anthocyanins are the primary pigments contributing to the variety of flower colors among angiosperms and are considered essential for survival and reproduction. Anthocyanins are members of the flavonoids, a broader class of secondary metabolites, of which there are numerous structural genes and regulators thereof. In western European populations of Lysimachia arvensis, there are blue- and orange-petaled individuals. The proportion of blue-flowered plants increases with temperature and daylength yet decreases with precipitation. Here, we performed a transcriptome analysis to characterize the coding sequences of a large group of flavonoid biosynthetic genes, examine their expression and compare our results to flavonoid biochemical analysis for blue and orange petals. Among a set of 140 structural and regulatory genes broadly representing the flavonoid biosynthetic pathway, we found 39 genes with significant differential expression including some that have previously been reported to be involved in similar flower color transitions. In particular, F3'5'H and DFR, two genes at a critical branchpoint in the ABP for determining flower color, showed differential expression. The expression results were complemented by careful examination of the SNPs that differentiate the two color types for these two critical genes. The decreased expression of F3'5'H in orange petals and differential expression of two distinct copies of DFR, which also exhibit amino acid changes in the color-determining substrate specificity region, strongly correlate with the blue to orange transition. Our biochemical analysis was consistent with the transcriptome data indicating that the shift from blue to orange petals is caused by a change from primarily malvidin to largely pelargonidin forms of anthocyanins. Overall, we have identified several flavonoid biosynthetic pathway loci likely involved in the shift in flower color in L. arvensis and even more loci that may represent the complex network of genetic and physiological consequences of this flower color polymorphism.
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Affiliation(s)
- Mercedes Sánchez-Cabrera
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | | | - Eduardo Narbona
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
| | - Montserrat Arista
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Pedro L. Ortiz
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Francisco J. Romero-Campero
- Institute for Plant Biochemistry and Photosynthesis, University of Seville – Centro Superior de Investigación Científica, Seville, Spain
- Department of Computer Science and Artificial Intelligence, University of Seville, Seville, Spain
| | - Karolis Ramanauskas
- Department of Biological Science, University of Illinois at Chicago, Chicago, IL, United States
| | - Boris Igić
- Department of Biological Science, University of Illinois at Chicago, Chicago, IL, United States
| | - Amelia A. Fuller
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Justen B. Whittall
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA, United States
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Gaynor ML, Lim-Hing S, Mason CM. Impact of genome duplication on secondary metabolite composition in non-cultivated species: a systematic meta-analysis. ANNALS OF BOTANY 2020; 126:363-376. [PMID: 32504537 PMCID: PMC7424755 DOI: 10.1093/aob/mcaa107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Whole-genome duplication is known to influence ecological interactions and plant physiology; however, despite abundant case studies, much is still unknown about the typical impact of genome duplication on plant secondary metabolites (PSMs). In this study, we assessed the impact of polyploidy events on PSM characteristics in non-cultivated plants. METHODS We conducted a systematic review and meta-analysis to compare composition and concentration of PSMs among closely related plant species or species complexes differing in ploidy level. KEY RESULTS We assessed 53 studies that focus on PSMs among multiple cytotypes, of which only 14 studies compared concentration quantitatively among cytotypes. We found that whole-genome duplication can have a significant effect on PSM concentration; however, these effects are highly inconsistent. CONCLUSION Overall, there was no consistent effect of whole-genome duplication on PSM concentrations or profiles.
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Affiliation(s)
- Michelle L Gaynor
- Department of Biology, University of Central Florida, Orlando, FL, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Simone Lim-Hing
- Department of Biology, University of Central Florida, Orlando, FL, USA
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Chase M Mason
- Department of Biology, University of Central Florida, Orlando, FL, USA
- For correspondence. E-mail
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Metabolome and Transcriptome Analysis Reveals Putative Genes Involved in Anthocyanin Accumulation and Coloration in White and Pink Tea ( Camellia sinensis) Flower. Molecules 2020; 25:molecules25010190. [PMID: 31906542 PMCID: PMC6983220 DOI: 10.3390/molecules25010190] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/25/2019] [Accepted: 12/31/2019] [Indexed: 12/12/2022] Open
Abstract
A variant of tea tree (Camellia sinensis (L.)) with purple buds and leaves and pink flowers can be used as a unique ornamental plant. However, the mechanism of flower coloration remains unclear. To elucidate the molecular mechanism of coloration, as well as anthocyanin accumulation in white and pink tea flowers, metabolite profiling and transcriptome sequencing was analyzed in various tea flower developmental stages. Results of metabolomics analysis revealed that three specific anthocyanin substances could be identified, i.e., cyanidin O-syringic acid, petunidin 3-O-glucoside, and pelargonidin 3-O-β-d-glucoside, which only accumulated in pink tea flowers, and were not able to be detected in white flowers. RNA-seq and weighted gene co-expression network analysis revealed eight highly expressed structural genes involved in anthocyanin biosynthetic pathway, and particularly, different expression patterns of flavonol synthase and dihydroflavonol-4-reductase genes were observed. We deduced that the disequilibrium of expression levels in flavonol synthases and dihydroflavonol-4-reductases resulted in different levels of anthocyanin accumulation and coloration in white and pink tea flowers. Results of qRT-PCR performed for 9 key genes suggested that the expression profiles of differentially expressed genes were generally consistent with the results of high-throughput sequencing. These findings provide insight into anthocyanin accumulation and coloration mechanisms during tea flower development, which will contribute to the breeding of pink-flowered and anthocyanin-rich tea cultivars.
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Li Z, Vickrey TL, McNally MG, Sato SJ, Clemente TE, Mower JP. Assessing Anthocyanin Biosynthesis in Solanaceae as a Model Pathway for Secondary Metabolism. Genes (Basel) 2019; 10:genes10080559. [PMID: 31349565 PMCID: PMC6723469 DOI: 10.3390/genes10080559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 01/25/2023] Open
Abstract
Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI annotation pipeline generated more and longer FBP annotations on average than genome-specific annotation pipelines. The pattern of diversification of each enzyme among asterids was assessed by phylogenetic analysis, showing that the CHS superfamily encompasses a large paralogous family of ancient and recent duplicates, whereas other FBP enzymes have diversified via recent duplications in particular lineages. Heterologous expression of a pansy F3′5′H gene in tobacco changed flower color from pink to dark purple, demonstrating that anthocyanin production can be predictably modified using reverse genetics. These results suggest that the Solanaceae FBP could be an ideal system to model genotype-to-phenotype interactions for secondary metabolism.
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Affiliation(s)
- Zuo Li
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Trisha L Vickrey
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Moira G McNally
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Biology Department, University of Jamestown, Jamestown, ND 58405, USA
| | - Shirley J Sato
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA
| | - Tom Elmo Clemente
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA.
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA.
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McCarthy EW, Landis JB, Kurti A, Lawhorn AJ, Chase MW, Knapp S, Le Comber SC, Leitch AR, Litt A. Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae). BMC PLANT BIOLOGY 2019; 19:162. [PMID: 31029077 PMCID: PMC6486959 DOI: 10.1186/s12870-019-1771-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/10/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also compare trends in diploid versus allopolyploid evolution to determine if polyploidy modifies floral evolutionary patterns. RESULTS Predicting the ancestral phenotype of a nascent allopolyploid from reconstructions of diploid phenotypes at the time of polyploid formation generates different phenotype predictions than when extant diploid phenotypes are used, the outcome of which can alter conclusions about polyploid evolution; however, most analyses yield the same results. Using ancestral reconstructions of diploid floral phenotypes indicate that young polyploids evolve shorter, wider corolla tubes, but older polyploids and diploids do not show any detectable evolutionary trends. Lability of the traits examined (floral shape, corolla tube length, and corolla tube width) differs across young and older polyploids and diploids. Corolla length is more evolutionarily labile in older polyploids and diploids. Polyploids do not display unique suites of floral characters based on both morphological and color traits, but some suites of characters may be evolving together and seem to have arisen multiple times within Nicotiana, perhaps due to the influence of pollinators. CONCLUSIONS Young polyploids display different trends in floral evolution (shorter, wider corolla tubes, which may result in more generalist pollination) than older polyploids and diploids, suggesting that patterns of divergence are impacted by the early consequences of allopolyploidy, perhaps arising from genomic shock and/or subsequent genome stabilization associated with diploidization. Convergent evolution in floral morphology and color in Nicotiana can be consistent with pollinator preferences, suggesting that pollinators may have shaped floral evolution in Nicotiana.
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Affiliation(s)
- Elizabeth W. McCarthy
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
- Present address: Department of Biological Sciences, SUNY Cortland, Cortland, NY 13045 USA
| | - Jacob B. Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
| | - Amelda Kurti
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
| | - Amber J. Lawhorn
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
| | - Mark W. Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102 Australia
| | | | - Steven C. Le Comber
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS UK
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS UK
| | - Amy Litt
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
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Ng J, Freitas LB, Smith SD. Stepwise evolution of floral pigmentation predicted by biochemical pathway structure. Evolution 2018; 72:2792-2802. [PMID: 30187462 DOI: 10.1111/evo.13589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/11/2018] [Accepted: 08/18/2018] [Indexed: 02/06/2023]
Abstract
Developmental pathways play a major role in influencing the distribution of naturally occurring phenotypes. For example, pathway structure and regulation could make some phenotypes inaccessible or restrict the routes through which phenotypes evolve. In this study, we examine floral anthocyanin pigments across the Solanaceae family and test whether patterns of phenotypic variation are consistent with predicted constraints based on the structure of the flavonoid biosynthetic pathway. We find that anthocyanin evolution occurs in a stepwise manner whereby transitions between the production of red mono hydroxylated pelargonidin pigments and blue trihydroxylated delphinidin pigments first passes through an intermediate step of producing purple dihydroxylated cyanidin pigments. Although the transitions between these three pigment types differ in frequency, we infer that these shifts are often reversible, suggesting that the functionality of the underlying biochemical pathway is generally conserved. Furthermore, our study finds that some pigment combinations are never observed, pointing to additional constraints on naturally occurring phenotypes. Overall, our findings provide insights into how the structure of an angiosperm-wide biochemical pathway has shaped macroevolutionary variation in floral pigmentation.
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Affiliation(s)
- Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 91501, Brazil
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
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Gaynor ML, Ng J, Laport RG. Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids? Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gates DJ, Olson BJSC, Clemente TE, Smith SD. A novel R3 MYB transcriptional repressor associated with the loss of floral pigmentation in Iochroma. THE NEW PHYTOLOGIST 2018; 217:1346-1356. [PMID: 29023752 DOI: 10.1111/nph.14830] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/31/2017] [Indexed: 05/23/2023]
Abstract
Losses of floral pigmentation represent one of the most common evolutionary transitions in flower color, yet the genetic basis for these changes has been elucidated in only a handful of cases. Here we used crossing studies, bulk-segregant RNA sequencing, phylogenetic analyses and functional tests to identify the gene(s) responsible for the transition to white flowers in Iochroma loxense. Crosses between I. loxense and its blue-flowered sister species, I. cyaneum, suggested that a single locus controls the flower color difference and that the white allele causes a nearly complete loss of pigmentation. Examining sequence variation across phenotypic pools from the crosses, we found that alleles at a novel R3 MYB transcription factor were tightly associated with flower color variation. This gene, which we term MYBL1, falls into a class of MYB transcriptional repressors and, accordingly, higher expression of this gene is associated with downregulation of multiple anthocyanin pigment pathway genes. We confirmed the repressive function of MYBL1 through stable transformation of Nicotiana. The mechanism underlying the evolution of white flowers in I. loxense differs from that uncovered in previous studies, pointing to multiple mechanisms for achieving fixed transitions in flower color intensity.
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Affiliation(s)
- Daniel J Gates
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | | | - Tom E Clemente
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80305, USA
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Laport RG, Ng J. Out of one, many: The biodiversity considerations of polyploidy. AMERICAN JOURNAL OF BOTANY 2017; 104:1119-1121. [PMID: 28790089 DOI: 10.3732/ajb.1700190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Robert G Laport
- University of Colorado Boulder, Department of Ecology & Evolutionary Biology, Boulder, Colorado 80309 USA
| | - Julienne Ng
- University of Colorado Boulder, Department of Ecology & Evolutionary Biology, Boulder, Colorado 80309 USA
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