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Gilman IS, Heyduk K, Maya-Lastra C, Hancock LP, Edwards EJ. Predicting photosynthetic pathway from anatomy using machine learning. New Phytol 2024; 242:1029-1042. [PMID: 38173400 DOI: 10.1111/nph.19488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Plants with Crassulacean acid metabolism (CAM) have long been associated with a specialized anatomy, including succulence and thick photosynthetic tissues. Firm, quantitative boundaries between non-CAM and CAM plants have yet to be established - if they indeed exist. Using novel computer vision software to measure anatomy, we combined new measurements with published data across flowering plants. We then used machine learning and phylogenetic comparative methods to investigate relationships between CAM and anatomy. We found significant differences in photosynthetic tissue anatomy between plants with differing CAM phenotypes. Machine learning-based classification was over 95% accurate in differentiating CAM from non-CAM anatomy, and had over 70% recall of distinct CAM phenotypes. Phylogenetic least squares regression and threshold analyses revealed that CAM evolution was significantly correlated with increased mesophyll cell size, thicker leaves, and decreased intercellular airspace. Our findings suggest that machine learning may be used to aid the discovery of new CAM species and that the evolutionary trajectory from non-CAM to strong, obligate CAM requires continual anatomical specialization.
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Affiliation(s)
- Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, The University of Connecticut, Storrs, CT, 06269, USA
| | - Carlos Maya-Lastra
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Biology, Angelo State University, San Angelo, TX, 76909, USA
| | - Lillian P Hancock
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
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2
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Groot Crego C, Hess J, Yardeni G, de La Harpe M, Priemer C, Beclin F, Saadain S, Cauz-Santos LA, Temsch EM, Weiss-Schneeweiss H, Barfuss MHJ, Till W, Weckwerth W, Heyduk K, Lexer C, Paun O, Leroy T. CAM evolution is associated with gene family expansion in an explosive bromeliad radiation. Plant Cell 2024:koae130. [PMID: 38686825 DOI: 10.1093/plcell/koae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 05/02/2024]
Abstract
The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean acid metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, transposable element (TE) dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species but are not candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.
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Affiliation(s)
- Clara Groot Crego
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Cambrium GmbH, Max-Urich-Str. 3, 13055 Berlin, Germany
| | - Gil Yardeni
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Office for Nature and Environment, Canton of Grisons, Chur, Switzerland
| | - Clara Priemer
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University of Vienna, Vienna, Austria
| | - Francesca Beclin
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Sarah Saadain
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Luiz A Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Karolina Heyduk
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT USA
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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Sage RF, Edwards EJ, Heyduk K, Cushman JC. Crassulacean acid metabolism (CAM) at the crossroads: a special issue to honour 50 years of CAM research by Klaus Winter. Ann Bot 2023; 132:553-561. [PMID: 37856823 PMCID: PMC10799977 DOI: 10.1093/aob/mcad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Affiliation(s)
- Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5R3C6, Canada
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada–Reno, Reno, NV 89557, USA
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Heyduk K, McAssey EV, Field R, Leebens-Mack J. The Agavoideae: an emergent model clade for CAM evolutionary biology. Ann Bot 2023; 132:727-737. [PMID: 37191440 PMCID: PMC10799990 DOI: 10.1093/aob/mcad062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/16/2023] [Accepted: 05/15/2023] [Indexed: 05/17/2023]
Abstract
Crassulacean acid metabolism - or CAM photosynthesis - was described in the early to mid-20th century, and our understanding of this metabolic pathway was later expanded upon through detailed biochemical analyses of carbon balance. Soon after, scientists began to study the ecophysiological implications of CAM, and a large part of this early work was conducted in the genus Agave, in the subfamily Agavoideae of the family Asparagaceae. Today, the Agavoideae continues to be important for the study of CAM photosynthesis, from the ecophysiology of CAM species, to the evolution of the CAM phenotype and to the genomics underlying CAM traits. Here we review past and current work on CAM in the Agavoideae, in particular highlighting the work of Park Nobel in Agave, and focusing on the powerful comparative system the Agavoideae has become for studying the origins of CAM. We also highlight new genomics research and the potential for studying intraspecific variation within species of the Agavoideae, particularly species in the genus Yucca. The Agavoideae has served as an important model clade for CAM research for decades, and undoubtedly will continue to help push our understanding of CAM biology and evolution in the future.
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Affiliation(s)
- Karolina Heyduk
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Edward V McAssey
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Richard Field
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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McAssey EV, Downs C, Yorkston M, Morden C, Heyduk K. A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming. Appl Plant Sci 2023; 11:e11527. [PMID: 37342160 PMCID: PMC10278930 DOI: 10.1002/aps3.11527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 06/22/2023]
Abstract
Premise The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library. Methods Plants collected for the Hawaiian Plant DNA Library were simultaneously accessioned as herbarium specimens at the time of collection, from 1994-2019. Paired samples were sequenced using short-read sequencing and assessed for chloroplast assembly and nuclear gene recovery. Results Herbarium specimen-derived DNA was statistically more fragmented than freezer-stored DNA derived from fresh tissue, leading to poorer chloroplast assembly and overall lower coverage. The number of nuclear targets recovered varied mostly by total sequencing reads per library and age of specimen, but not by storage method (herbarium or long-term freezer). Although there was evidence of DNA damage in the samples, there was no evidence that it was related to the length of time in storage, whether frozen or as herbarium specimens. Discussion DNA extracted from herbarium tissues will continue to be invaluable, despite being highly fragmented and degraded. Rare floras would benefit from both traditional herbarium storage methods and extracted DNA freezer banks.
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Affiliation(s)
- Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Cassidy Downs
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Mitsuko Yorkston
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Clifford Morden
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
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6
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Timilsena PR, Wafula EK, Barrett CF, Ayyampalayam S, McNeal JR, Rentsch JD, McKain MR, Heyduk K, Harkess A, Villegente M, Conran JG, Illing N, Fogliani B, Ané C, Pires JC, Davis JI, Zomlefer WB, Stevenson DW, Graham SW, Givnish TJ, Leebens-Mack J, dePamphilis CW. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. Front Plant Sci 2022; 13:876779. [PMID: 36483967 PMCID: PMC9723157 DOI: 10.3389/fpls.2022.876779] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 05/26/2023]
Abstract
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Eric K. Wafula
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Saravanaraj Ayyampalayam
- Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Joel R. McNeal
- Department of Ecology, Evolution, and Organismal Biology, Biology Kennesaw State University, Kennesaw, GA, United States
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Matthieu Villegente
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Bruno Fogliani
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Department of Statistics, University of Wisconsin–Madison, Madison, WI, United States
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jerrold I. Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | | | | | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
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Heyduk K, McAssey EV, Leebens‐Mack J. Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae). New Phytol 2022; 235:2111-2126. [PMID: 35596719 PMCID: PMC9796715 DOI: 10.1111/nph.18267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis has evolved repeatedly across the plant tree of life, however our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM. Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well watered and drought-stressed treatments. We further assessed gene expression and the molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM. Most time-of-day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. By contrast, transcriptional response to drought is highly lineage specific. Yucca and Beschorneria have CAM-like expression of PPC2, a copy of PPC that has never been shown to be recruited for CAM in angiosperms. Together the physiological and transcriptomic comparison of closely related C3 and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function.
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Affiliation(s)
- Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
| | - Jim Leebens‐Mack
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
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Heyduk K. Evolution of Crassulacean acid metabolism in response to the environment: past, present, and future. Plant Physiol 2022; 190:19-30. [PMID: 35748752 PMCID: PMC9434201 DOI: 10.1093/plphys/kiac303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) is a mode of photosynthesis that evolved in response to decreasing CO2 levels in the atmosphere some 20 million years ago. An elevated ratio of O2 relative to CO2 caused many plants to face increasing stress from photorespiration, a process exacerbated for plants living under high temperatures or in water-limited environments. Today, our climate is again rapidly changing and plants' ability to cope with and adapt to these novel environments is critical for their success. This review focuses on CAM plant responses to abiotic stressors likely to dominate in our changing climate: increasing CO2 levels, increasing temperatures, and greater variability in drought. Empirical studies that have assessed CAM responses are reviewed, though notably these are concentrated in relatively few CAM lineages. Other aspects of CAM biology, including the effects of abiotic stress on the light reactions and the role of leaf succulence, are also considered in the context of climate change. Finally, more recent studies using genomic techniques are discussed to link physiological changes in CAM plants with the underlying molecular mechanism. Together, the body of work reviewed suggests that CAM plants will continue to thrive in certain environments under elevated CO2. However, how CO2 interacts with other environmental factors, how those interactions affect CAM plants, and whether all CAM plants will be equally affected remain outstanding questions regarding the evolution of CAM on a changing planet.
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Eguiarte LE, Leebens-Mack J, Heyduk K. Editorial: Recent Advances and Future Perspectives for Agavoideae Research: Agave, Yucca and Related Taxa. Front Plant Sci 2021; 12:687596. [PMID: 34040628 PMCID: PMC8141651 DOI: 10.3389/fpls.2021.687596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Luis E. Eguiarte
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Karolina Heyduk
- School of Life Sciences, University of Hawai'i at Mãnoa, Honolulu, HI, United States
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10
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Heyduk K, Ray JN, Leebens-Mack J. Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species, Yucca gloriosa. Ann Bot 2021; 127:437-449. [PMID: 32166326 PMCID: PMC7988526 DOI: 10.1093/aob/mcaa036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 03/05/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Crassulacean acid metabolism (CAM) is often considered to be a complex trait, requiring orchestration of leaf anatomy and physiology for optimal performance. However, the observation of trait correlations is based largely on comparisons between C3 and strong CAM species, resulting in a lack of understanding as to how such traits evolve and the level of intraspecific variability for CAM and associated traits. METHODS To understand intraspecific variation for traits underlying CAM and how these traits might assemble over evolutionary time, we conducted detailed time course physiological screens and measured aspects of leaf anatomy in 24 genotypes of a C3+CAM hybrid species, Yucca gloriosa (Asparagaceae). Comparisons were made to Y. gloriosa's progenitor species, Y. filamentosa (C3) and Y. aloifolia (CAM). KEY RESULTS Based on gas exchange and measurement of leaf acids, Y. gloriosa appears to use both C3 and CAM, and varies across genotypes in the degree to which CAM can be upregulated under drought stress. While correlations between leaf anatomy and physiology exist when testing across all three Yucca species, such correlations break down at the species level in Y. gloriosa. CONCLUSIONS The variation in CAM upregulation in Y. gloriosa is a result of its relatively recent hybrid origin. The lack of trait correlations between anatomy and physiology within Y. gloriosa indicate that the evolution of CAM, at least initially, can proceed through a wide combination of anatomical traits, and more favourable combinations are eventually selected for in strong CAM plants.
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Affiliation(s)
- Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- For correspondence. E-mail
| | - Jeremy N Ray
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, USA
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Heyduk K. The genetic control of succulent leaf development. Curr Opin Plant Biol 2021; 59:101978. [PMID: 33454545 DOI: 10.1016/j.pbi.2020.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/09/2020] [Accepted: 11/14/2020] [Indexed: 05/25/2023]
Abstract
Succulent leaves have long intrigued biologists; much research has been done to define succulence, understand the evolutionary trajectory and implications of leaf succulence, and contextualize the ecological importance of water storage for plants inhabiting dry habitats, particularly those using CAM photosynthesis. Surprisingly little is understood about the molecular regulation of leaf succulence, despite advances in our understanding of the molecular foundation of leaf architecture in model systems. Moreover, leaf succulence is a drought avoidance trait, one that has yet to be fully used for crop improvement. Here, connections between disparate literatures are highlighted: research on the regulation of cell size, the determination of vascular patterning, and water transport between cells have direct implications for our understanding of leaf succulence. Connecting functional genomics of leaf patterning with knowledge of the evolution and ecology of succulent species will guide future research on the determination and maintenance of leaf succulence.
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Affiliation(s)
- Karolina Heyduk
- University of Hawai'i at Mānoa, 1800 East West Rd., Honolulu, HI 96822, USA.
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12
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Heyduk K, Grace OM, McKain MR. Life Without Water. Am J Bot 2021; 108:181-183. [PMID: 33620730 DOI: 10.1002/ajb2.1615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
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13
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Heyduk K, McAssey EV, Grimwood J, Shu S, Schmutz J, McKain MR, Leebens-Mack J. Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae). Front Plant Sci 2021; 11:573767. [PMID: 33519836 PMCID: PMC7843428 DOI: 10.3389/fpls.2020.573767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/17/2020] [Indexed: 05/23/2023]
Abstract
Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy. Yucca gloriosa (Asparagaceae) is a young homoploid hybrid species, resulting from a cross between Yucca aloifolia and Yucca filamentosa. Previous analyses of ∼11 kb of the chloroplast genome and nuclear-encoded microsatellites implicated a single Y. aloifolia genotype as the maternal parent of Y. gloriosa. Using whole genome resequencing, we assembled chloroplast genomes from 41 accessions of all three species to re-assess the hybrid origins of Y. gloriosa. We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin of Y. gloriosa, with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case-Copia LTR transposons-did Y. gloriosa have a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred in Y. gloriosa upon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. The identification and quantification of transposon families paired with expression evidence paves the way for additional work seeking to link epigenetics with the important trait variation seen in this homoploid hybrid system.
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Affiliation(s)
- Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Edward V. McAssey
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Biological Sciences, Quinnipiac University, Hamden, CT, United States
- Department of Biology and Environmental Science, University of New Haven, West Haven, CT, United States
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Shengqiang Shu
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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14
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Heyduk K, Ray JN, Ayyampalayam S, Moledina N, Borland A, Harding SA, Tsai CJ, Leebens-Mack J. Shared expression of crassulacean acid metabolism (CAM) genes pre-dates the origin of CAM in the genus Yucca. J Exp Bot 2019; 70:6597-6609. [PMID: 30870557 PMCID: PMC6883266 DOI: 10.1093/jxb/erz105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/20/2019] [Indexed: 05/05/2023]
Abstract
Crassulacean acid metabolism (CAM) is a carbon-concentrating mechanism that has evolved numerous times across flowering plants and is thought to be an adaptation to water-limited environments. CAM has been investigated from physiological and biochemical perspectives, but little is known about how plants evolve from C3 to CAM at the genetic or metabolic level. Here we take a comparative approach in analyzing time-course data of C3, CAM, and C3+CAM intermediate Yucca (Asparagaceae) species. RNA samples were collected over a 24 h period from both well-watered and drought-stressed plants, and were clustered based on time-dependent expression patterns. Metabolomic data reveal differences in carbohydrate metabolism and antioxidant response between the CAM and C3 species, suggesting that changes to metabolic pathways are important for CAM evolution and function. However, all three species share expression profiles of canonical CAM pathway genes, regardless of photosynthetic pathway. Despite differences in transcript and metabolite profiles between the C3 and CAM species, shared time-structured expression of CAM genes in both CAM and C3Yucca species suggests that ancestral expression patterns required for CAM may have pre-dated its origin in Yucca.
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Affiliation(s)
- Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Jeremy N Ray
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | | | - Nida Moledina
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Anne Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, UK
| | - Scott A Harding
- Department of Genetics, University of Georgia, Athens, GA, USA
- Warnell School of Forestry, University of Georgia, Athens, GA, USA
| | - Chung-Jui Tsai
- Department of Genetics, University of Georgia, Athens, GA, USA
- Warnell School of Forestry, University of Georgia, Athens, GA, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, USA
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15
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Gao D, Chu Y, Xia H, Xu C, Heyduk K, Abernathy B, Ozias-Akins P, Leebens-Mack JH, Jackson SA. Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants. Mol Biol Evol 2019; 35:354-364. [PMID: 29069493 PMCID: PMC5850137 DOI: 10.1093/molbev/msx275] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Even though lateral movements of transposons across families and even phyla within multicellular eukaryotic kingdoms have been found, little is known about transposon transfer between the kingdoms Animalia and Plantae. We discovered a novel non-LTR retrotransposon, AdLINE3, in a wild peanut species. Sequence comparisons and phylogenetic analyses indicated that AdLINE3 is a member of the RTE clade, originally identified in a nematode and rarely reported in plants. We identified RTE elements in 82 plants, spanning angiosperms to algae, including recently active elements in some flowering plants. RTE elements in flowering plants were likely derived from a single family we refer to as An-RTE. Interestingly, An-RTEs show significant DNA sequence identity with non-LTR retroelements from 42 animals belonging to four phyla. Moreover, the sequence identity of RTEs between two arthropods and two plants was higher than that of homologous genes. Phylogenetic and evolutionary analyses of RTEs from both animals and plants suggest that the An-RTE family was likely transferred horizontally into angiosperms from an ancient aphid(s) or ancestral arthropod(s). Notably, some An-RTEs were recruited as coding sequences of functional genes participating in metabolic or other biochemical processes in plants. This is the first potential example of horizontal transfer of transposons between animals and flowering plants. Our findings help to understand exchanges of genetic material between the kingdom Animalia and Plantae and suggest arthropods likely impacted on plant genome evolution.
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Affiliation(s)
- Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA
| | - Ye Chu
- Department of Horticulture, University of Georgia, Tifton, GA
| | - Han Xia
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA.,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Chunming Xu
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA
| | - Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA
| | | | | | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA
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16
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Heyduk K, Hwang M, Albert V, Silvera K, Lan T, Farr K, Chang TH, Chan MT, Winter K, Leebens-Mack J. Altered Gene Regulatory Networks Are Associated With the Transition From C 3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae). Front Plant Sci 2019; 9:2000. [PMID: 30745906 PMCID: PMC6360190 DOI: 10.3389/fpls.2018.02000] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/24/2018] [Indexed: 05/21/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis is a modification of the core C3 photosynthetic pathway that improves the ability of plants to assimilate carbon in water-limited environments. CAM plants fix CO2 mostly at night, when transpiration rates are low. All of the CAM pathway genes exist in ancestral C3 species, but the timing and magnitude of expression are greatly altered between C3 and CAM species. Understanding these regulatory changes is key to elucidating the mechanism by which CAM evolved from C3. Here, we use two closely related species in the Orchidaceae, Erycina pusilla (CAM) and Erycina crista-galli (C3), to conduct comparative transcriptomic analyses across multiple time points. Clustering of genes with expression variation across the diel cycle revealed some canonical CAM pathway genes similarly expressed in both species, regardless of photosynthetic pathway. However, gene network construction indicated that 149 gene families had significant differences in network connectivity and were further explored for these functional enrichments. Genes involved in light sensing and ABA signaling were some of the most differently connected genes between the C3 and CAM Erycina species, in agreement with the contrasting diel patterns of stomatal conductance in C3 and CAM plants. Our results suggest changes to transcriptional cascades are important for the transition from C3 to CAM photosynthesis in Erycina.
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Affiliation(s)
- Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Michelle Hwang
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Victor Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Katia Silvera
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Kimberly Farr
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Tien-Hao Chang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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17
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Smith SD, Angelovici R, Heyduk K, Maeda HA, Moghe GD, Pires JC, Widhalm JR, Wisecaver JH. The renaissance of comparative biochemistry. Am J Bot 2019; 106:3-13. [PMID: 30629738 DOI: 10.1002/ajb2.1216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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18
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Heyduk K, Ray JN, Ayyampalayam S, Leebens-Mack J. Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism. Am J Bot 2018; 105:587-601. [PMID: 29746718 DOI: 10.1002/ajb2.1017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/19/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The relative ease of high throughput sequencing is facilitating comprehensive phylogenomic and gene expression studies, even for nonmodel groups. To date, however, these two approaches have not been merged; while phylogenomic methods might use transcriptome sequences to resolve relationships, assessment of gene expression patterns in a phylogenetic context is less common. Here we analyzed both carbon assimilation and gene expression patterns of closely related species within the Agavoideae (Asparagaceae) to elucidate changes in gene expression across weak and strong phenotypes for Crassulacean acid metabolism (CAM). METHODS Gene expression patterns were compared across four genera: Agave (CAM), which is paraphyletic with Polianthes (weak CAM) and Manfreda (CAM), and Beschorneria (weak CAM). RNA-sequencing was paired with measures of gas exchange and titratable acidity. Climate niche space was compared across the four lineages to examine abiotic factors and their correlation to CAM. KEY RESULTS Expression of homologous genes showed both shared and variable patterns in weak and strong CAM species. Network analysis highlights that despite shared expression patterns, highly connected genes differ between weak and strong CAM, implicating shifts in regulatory gene function as key for the evolution of CAM. Variation in carbohydrate metabolism between weak and strong CAM supports the importance of sugar turnovers for CAM physiology. CONCLUSIONS Integration of phylogenetics and RNA-sequencing provides a powerful tool to study the evolution of CAM photosynthesis across closely related but photosynthetically variable species. Our findings regarding shared or shifted gene expression and regulation of CAM via carbohydrate metabolism have important implications for efforts to engineer the CAM pathway into C3 food and biofuel crops.
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Affiliation(s)
- Karolina Heyduk
- Miller Plant Sciences, University of Georgia, 120 Carlton Street, 2502, Athens, Georgia, 30602, USA
| | - Jeremy N Ray
- Miller Plant Sciences, University of Georgia, 120 Carlton Street, 2502, Athens, Georgia, 30602, USA
| | | | - James Leebens-Mack
- Miller Plant Sciences, University of Georgia, 120 Carlton Street, 2502, Athens, Georgia, 30602, USA
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19
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Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, Heyduk K, Goodstein DM, Guo HB, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LV, Palla KJ, Albion R, Garcia T, Mayer JA, Don Lim S, Man Wai C, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen JG, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JH, Smith JAC, Cushman JC, Schmutz J, Tuskan GA. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nat Commun 2017; 8:1899. [PMID: 29196618 PMCID: PMC5711932 DOI: 10.1038/s41467-017-01491-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022] Open
Abstract
Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Deborah A Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jungmin Ha
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert C Moseley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Elisabeth Fitzek
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Zhihao Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Juan D Beltrán
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Susanna F Boxall
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Louisa V Dever
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rebecca Albion
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Travis Garcia
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jesse A Mayer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul Peluso
- Pacific Biosciences, Inc., 940 Hamilton Avenue, Menlo Park, CA, 94025, USA
| | - Robert Van Buren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Henrique Cestari De Paoli
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | | | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH. Data supporting the nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Data Brief 2016; 7:532-6. [PMID: 27054154 PMCID: PMC4796708 DOI: 10.1016/j.dib.2016.02.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/14/2016] [Accepted: 02/22/2016] [Indexed: 11/24/2022] Open
Abstract
This data article provides data and supplemental materials referenced in "Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)" (Comer et al., 2016) [1]. Raw sequence reads generated for this study are available through the Sequence Read Archive (SRA Study Accession: SRP061467). An aligned supermatrix of 168 nuclear genes for 35 taxa (34 palms and one outgroup taxon) is provided. Also provided are individual maximum likelihood gene trees used for the coalescent based analyses, output from the maximum parsimony analyses, and two figures.
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Affiliation(s)
- Jason R. Comer
- University of Georgia, Department of Plant Biology, Athens, GA 30602−7271, USA
| | - Wendy B. Zomlefer
- University of Georgia, Department of Plant Biology, Athens, GA 30602−7271, USA
| | - Craig F. Barrett
- California State University, Los Angeles, Department of Biological Sciences, Los Angeles, CA 90032−8201, USA
| | | | - Karolina Heyduk
- University of Georgia, Department of Plant Biology, Athens, GA 30602−7271, USA
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Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol Phylogenet Evol 2016; 97:32-42. [DOI: 10.1016/j.ympev.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/04/2015] [Accepted: 12/23/2015] [Indexed: 02/02/2023]
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Abstract
While the majority of plants use the typical C3 carbon metabolic pathway, ~6% of angiosperms have adapted to carbon limitation as a result of water stress by employing a modified form of photosynthesis known as Crassulacean acid metabolism (CAM). CAM plants concentrate carbon in the cells by temporally separating atmospheric carbon acquisition from fixation into carbohydrates. CAM has been studied for decades, but the evolutionary progression from C3 to CAM remains obscure. In order to better understand the morphological and physiological characteristics associated with CAM photosynthesis, phenotypic variation was assessed in Yucca aloifolia, a CAM species, Yucca filamentosa, a C3 species, and Yucca gloriosa, a hybrid species derived from these two yuccas exhibiting intermediate C3-CAM characteristics. Gas exchange, titratable leaf acidity, and leaf anatomical traits of all three species were assayed in a common garden under well-watered and drought-stressed conditions. Yucca gloriosa showed intermediate phenotypes for nearly all traits measured, including the ability to acquire carbon at night. Using the variation found among individuals of all three species, correlations between traits were assessed to better understand how leaf anatomy and CAM physiology are related. Yucca gloriosa may be constrained by a number of traits which prevent it from using CAM to as high a degree as Y. aloifolia. The intermediate nature of Y. gloriosa makes it a promising system in which to study the evolution of CAM.
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Affiliation(s)
- Karolina Heyduk
- 2502 Miller Plant Sciences, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Nia Burrell
- 2502 Miller Plant Sciences, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Falak Lalani
- 2502 Miller Plant Sciences, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jim Leebens-Mack
- 2502 Miller Plant Sciences, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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Comer JR, Zomlefer WB, Barrett CF, Davis JI, Stevenson DW, Heyduk K, Leebens-Mack JH. Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing. Am J Bot 2015; 102:888-99. [PMID: 26101415 DOI: 10.3732/ajb.1500057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/28/2015] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous-particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. METHODS Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were used to enrich for chloroplast targets. Ten taxa were enriched using both methods for comparison. Chloroplast sequence data were generated for 31 representatives of the 14 Arecoideae tribes and five outgroup taxa. The phylogeny was reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses. KEY RESULTS Long range PCR and hybrid gene capture both enriched the plastid genome and provided similar sequencing coverage. Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae as the earliest-diverging lineage, implying that the development of flowers in triads defines a synapomorphy for the Arecoideae clade excluding Chamaedoreeae. Three major clades within this group were recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC), Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae + Euterpeae clade was resolved within the core arecoids. The POS clade was sister to a RRC + core arecoids clade, implying a shared ancestral area in South America for these three clades. CONCLUSIONS The plastome phylogeny recovered here provides robust resolution of previously ambiguous studies and new insights into palm evolution.
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Affiliation(s)
- Jason R Comer
- University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA
| | - Wendy B Zomlefer
- University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA
| | - Craig F Barrett
- California State University, Los Angeles, Department of Biological Sciences, Los Angeles, California 90032-8201 USA
| | - Jerrold I Davis
- Cornell University, Department of Plant Biology, Ithaca, New York 14853-4301 USA
| | | | - Karolina Heyduk
- University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA
| | - James H Leebens-Mack
- University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA
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Heyduk K, Trapnell DW, Barrett CF, Leebens-Mack J. Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12551] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Karolina Heyduk
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
| | | | - Craig F. Barrett
- Department of Biological Sciences; California State University; Los Angeles CA 90032 USA
| | - Jim Leebens-Mack
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
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Affiliation(s)
- Travis M Garcia
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
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