1
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Gupta S, Harkess A, Soble A, Van Etten M, Leebens-Mack J, Baucom RS. Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance. New Phytol 2023; 238:1263-1277. [PMID: 36721257 DOI: 10.1111/nph.18782] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.
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Affiliation(s)
- Sonal Gupta
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Alex Harkess
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Anah Soble
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
| | - Megan Van Etten
- Biology Department, Pennsylvania State University, Dunmore, PA, 18512, USA
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
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2
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Xu Q, Jin L, Zheng C, Zhang X, Leebens-Mack J, Sankoff D. From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes. Sci Rep 2023; 13:6095. [PMID: 37055453 PMCID: PMC10102168 DOI: 10.1038/s41598-023-33029-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/06/2023] [Indexed: 04/15/2023] Open
Abstract
To reconstruct the ancestral genome of a set of phylogenetically related descendant species, we use the RACCROCHE pipeline for organizing a large number of generalized gene adjacencies into contigs and then into chromosomes. Separate reconstructions are carried out for each ancestral node of the phylogenetic tree for focal taxa. The ancestral reconstructions are monoploids; they each contain at most one member of each gene family constructed from descendants, ordered along the chromosomes. We design and implement a new computational technique for solving the problem of estimating the ancestral monoploid number of chromosomes x. This involves a "g-mer" analysis to resolve a bias due long contigs, and gap statistics to estimate x. We find that the monoploid number of all the rosid and asterid orders is [Formula: see text]. We show that this is not an artifact of our method by deriving [Formula: see text] for the metazoan ancestor.
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Affiliation(s)
- Qiaoji Xu
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5C9, Canada
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xiaomeng Zhang
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada.
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3
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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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4
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Käfer J, Bewick A, Andres-Robin A, Lapetoule G, Harkess A, Caïus J, Fogliani B, Gâteblé G, Ralph P, dePamphilis CW, Picard F, Scutt C, Marais GAB, Leebens-Mack J. A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants. New Phytol 2022; 233:1636-1642. [PMID: 34342006 DOI: 10.1111/nph.17662] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
The genetic basis and evolution of sex determination in dioecious plants is emerging as an active area of research with exciting advances in genome sequencing and analysis technologies. As the sole species within the sister lineage to all other extant flowering plants, Amborella trichopoda is an important model for understanding the evolution and development of flowers. Plants typically produce only male or female flowers, but sex determination mechanisms are unknown for the species. Sequence data derived from plants of natural origin and an F1 mapping population were used to identify sex-linked genes and the nonrecombining region. Amborella trichopoda has a ZW sex determination system. Analysis of genes in a 4 Mb nonrecombining sex-determination region reveals recent divergence of Z and W gametologs, and few Z- and W-specific genes. The sex chromosomes of A. trichopoda evolved less than 16.5 Myr ago, long after the divergence of the extant angiosperms.
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Affiliation(s)
- Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, F-69622, France
| | - Adam Bewick
- Department of Plant Biology, University of Georgia, Athens, GA, 30602-7271, USA
- Bayer Crop Science, Chesterfield, MO, 63017, USA
| | - Amélie Andres-Robin
- Laboratoire Reproduction et Développement des plantes, UMR 5667, Ecole Normale Supérieure de Lyon, CNRS, Lyon, F-69364, France
| | - Garance Lapetoule
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, F-69622, France
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - José Caïus
- Institute of Plant Sciences, Plateforme transcriptOmique de l'IPS2 (POPS), Université de Paris-Saclay, Gif-sur-Yvette, F-91190, France
| | - Bruno Fogliani
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, Païta, 98890, New Caledonia
- Institute of Exact and Applied Sciences (ISEA), Université de la Nouvelle-Calédonie, BP R4, Nouméa Cedex, 98851, New Caledonia
| | - Gildas Gâteblé
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, Païta, 98890, New Caledonia
| | - Paula Ralph
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, F-69622, France
| | - Charlie Scutt
- Laboratoire Reproduction et Développement des plantes, UMR 5667, Ecole Normale Supérieure de Lyon, CNRS, Lyon, F-69364, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, F-69622, France
- LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, 1349-017, Portugal
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602-7271, USA
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5
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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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6
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Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. Am J Bot 2018; 105:1888-1910. [PMID: 30368769 DOI: 10.1002/ajb2.1178] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [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: 05/14/2018] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | | | - Daniel Spalink
- Department of Ecosystem Science, Texas A&M University, College Station, Texas, 77840, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Chodon Sass
- The University and Jepson Herbarium, University of California-Berkeley, Berkeley, California, 94720, USA
| | - William J D Iles
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Danilo José Lima de Sousa
- Departamento de Ciéncias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, 44036-900, Brazil
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Wendy B Zomlefer
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Maria A Gandolfo
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | | | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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7
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Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC. Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. Am J Bot 2018; 105:463-469. [PMID: 29574686 DOI: 10.1002/ajb2.1040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 08/21/2017] [Accepted: 11/06/2017] [Indexed: 05/10/2023]
Abstract
PREMISE OF THE STUDY Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family-level phylogeny estimated using the plastid genome. METHODS We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At-α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At-β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, 48864, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Michelle Tang
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jill Coombs
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Setareh Mohammadin
- Biosystematics, Plant Science Group, Wageningen University and Research, Wageningen, Netherlands
| | - M Eric Schranz
- Biosystematics, Plant Science Group, Wageningen University and Research, Wageningen, Netherlands
| | - Zhiyong Xiong
- Potato Engineering & Technology Research Center, Inner Mongolia University, Hohhot, China
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
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8
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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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9
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Johnson KL, Cassin AM, Lonsdale A, Wong GKS, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ. Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes. Plant Physiol 2017; 174:904-921. [PMID: 28446636 PMCID: PMC5462033 DOI: 10.1104/pp.17.00295] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/21/2017] [Indexed: 05/19/2023]
Abstract
The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall-based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins. Using motif and amino acid bias, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 Plants transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and the early radiation of angiosperms. Significantly, data mining reveals the origin of glycosylphosphatidylinositol (GPI)-anchored AGPs in green algae and a 3- to 4-fold increase in GPI-AGPs in liverworts and mosses. The first detection of cross-linking (CL)-EXTs is observed in bryophytes, which suggests that CL-EXTs arose though the juxtaposition of preexisting SPn EXT glycomotifs with refined Y-based motifs. We also detected the loss of CL-EXT in a few lineages, including the grass family (Poaceae), that have a cell wall composition distinct from other monocots and eudicots. A key challenge in HRGP research is tracking individual HRGPs throughout evolution. Using the 1000 Plants output, we were able to find putative orthologs of Arabidopsis pollen-specific GPI-AGPs in basal eudicots.
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Affiliation(s)
- Kim L Johnson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Andrew M Cassin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Andrew Lonsdale
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Gane Ka-Shu Wong
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Douglas E Soltis
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Nicholas W Miles
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Michael Melkonian
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Barbara Melkonian
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Michael K Deyholos
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - James Leebens-Mack
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Carl J Rothfels
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Dennis W Stevenson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Sean W Graham
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Xumin Wang
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Shuangxiu Wu
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - J Chris Pires
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Patrick P Edger
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Eric J Carpenter
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Monika S Doblin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Carolyn J Schultz
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.);
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.);
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.);
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.);
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.);
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.);
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.);
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.);
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.);
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.);
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
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10
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Lin CS, Chen JJW, Chiu CC, Hsiao HCW, Yang CJ, Jin XH, Leebens-Mack J, de Pamphilis CW, Huang YT, Yang LH, Chang WJ, Kui L, Wong GKS, Hu JM, Wang W, Shih MC. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. Plant J 2017; 90:994-1006. [PMID: 28258650 DOI: 10.1111/tpj.13525] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [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: 12/13/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 05/23/2023]
Abstract
The chloroplast NAD(P)H dehydrogenase-like (NDH) complex consists of about 30 subunits from both the nuclear and chloroplast genomes and is ubiquitous across most land plants. In some orchids, such as Phalaenopsis equestris, Dendrobium officinale and Dendrobium catenatum, most of the 11 chloroplast genome-encoded ndh genes (cp-ndh) have been lost. Here we investigated whether functional cp-ndh genes have been completely lost in these orchids or whether they have been transferred and retained in the nuclear genome. Further, we assessed whether both cp-ndh genes and nucleus-encoded NDH-related genes can be lost, resulting in the absence of the NDH complex. Comparative analyses of the genome of Apostasia odorata, an orchid species with a complete complement of cp-ndh genes which represents the sister lineage to all other orchids, and three published orchid genome sequences for P. equestris, D. officinale and D. catenatum, which are all missing cp-ndh genes, indicated that copies of cp-ndh genes are not present in any of these four nuclear genomes. This observation suggests that the NDH complex is not necessary for some plants. Comparative genomic/transcriptomic analyses of currently available plastid genome sequences and nuclear transcriptome data showed that 47 out of 660 photoautotrophic plants and all the heterotrophic plants are missing plastid-encoded cp-ndh genes and exhibit no evidence for maintenance of a functional NDH complex. Our data indicate that the NDH complex can be lost in photoautotrophic plant species. Further, the loss of the NDH complex may increase the probability of transition from a photoautotrophic to a heterotrophic life history.
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Affiliation(s)
- Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Chi-Chou Chiu
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Han C W Hsiao
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung City, Taiwan
| | - Chen-Jui Yang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Xiao-Hua Jin
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | | | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Ling-Hung Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Wen Wang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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11
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Yoder JB, Leebens-Mack J. The evolutionary ecology of "mutual services" in the 21st century. Am J Bot 2016; 103:1712-1716. [PMID: 27793857 DOI: 10.3732/ajb.1600367] [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: 10/13/2016] [Accepted: 10/13/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Jeremy B Yoder
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602-7271 USA
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12
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Givnish TJ, Spalink D, Ames M, Lyon SP, Hunter SJ, Zuluaga A, Iles WJD, Clements MA, Arroyo MTK, Leebens-Mack J, Endara L, Kriebel R, Neubig KM, Whitten WM, Williams NH, Cameron KM. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proc Biol Sci 2016; 282:rspb.2015.1553. [PMID: 26311671 DOI: 10.1098/rspb.2015.1553] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Orchids are the most diverse family of angiosperms, with over 25 000 species,more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here,we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. Asupermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras),and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp(-1) My(-1)) is 6.8 times that at the Asparagales crown.
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13
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Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GKS, Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A 2014; 111:E4859-68. [PMID: 25355905 PMCID: PMC4234587 DOI: 10.1073/pnas.1323926111] [Citation(s) in RCA: 748] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
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Affiliation(s)
- Norman J Wickett
- Chicago Botanic Garden, Glencoe, IL 60022; Program in Biological Sciences, Northwestern University, Evanston, IL 60208;
| | - Siavash Mirarab
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Nam Nguyen
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Tandy Warnow
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Naim Matasci
- iPlant Collaborative, Tucson, AZ 85721; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Matthew A Gitzendanner
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611
| | - Brad R Ruhfel
- Department of Biology and Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475; Florida Museum of Natural History, Gainesville, FL 32611
| | - Eric Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | - Joshua P Der
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | | | - Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, MA 02138
| | | | - Douglas E Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | - Pamela S Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | | | - Carl J Rothfels
- Department of Biology, Duke University, Durham, NC 27708; Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Lisa Pokorny
- Department of Biology, Duke University, Durham, NC 27708; Department of Biodiversity and Conservation, Real Jardín Botánico-Consejo Superior de Investigaciones Cientificas, 28014 Madrid, Spain
| | | | | | | | - Barbara Surek
- Botanical Institute, Universität zu Köln, Cologne D-50674, Germany
| | - Juan Carlos Villarreal
- Department fur Biologie, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universitat, 80638 Munich, Germany
| | - Béatrice Roure
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7
| | - Hervé Philippe
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7; CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | | | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
| | - Toni M Kutchan
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | | | - Jun Wang
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Yong Zhang
- CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | - Zhijian Tian
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Zhixiang Yan
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiaolei Wu
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiao Sun
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9; BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1
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14
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Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB. Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella. Science 2013; 342:1516-7. [DOI: 10.1126/science.1241130] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Vitte C, Estep MC, Leebens-Mack J, Bennetzen JL. Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Ann Bot 2013; 112:881-9. [PMID: 23887091 PMCID: PMC3747808 DOI: 10.1093/aob/mct155] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [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: 12/21/2012] [Accepted: 05/17/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots. METHODS To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons. KEY RESULTS The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4-5 % (asparagus) or 3-4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize. CONCLUSIONS Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.
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Affiliation(s)
- C Vitte
- CNRS, UMR de Génétique Végétale, Ferme du Moulon, F-91190 Gif sur Yvette, France.
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16
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Johnson MTJ, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, Depamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN, Surek B, Thomsen CJM, Villarreal JC, Wu X, Zhang Y, Deyholos MK, Wong GKS. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 2012. [PMID: 23185583 PMCID: PMC3504007 DOI: 10.1371/journal.pone.0050226] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.
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Affiliation(s)
- Marc T J Johnson
- Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
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Althoff DM, Segraves KA, Smith CI, Leebens-Mack J, Pellmyr O. Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification. Mol Phylogenet Evol 2012; 62:898-906. [DOI: 10.1016/j.ympev.2011.11.024] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 11/07/2011] [Accepted: 11/26/2011] [Indexed: 11/26/2022]
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Steele PR, Hertweck KL, Mayfield D, McKain MR, Leebens-Mack J, Pires JC. Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae. Am J Bot 2012; 99:330-48. [PMID: 22291168 DOI: 10.3732/ajb.1100491] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY Genome survey sequences (GSS) from massively parallel sequencing have potential to provide large, cost-effective data sets for phylogenetic inference, replace single gene or spacer regions as DNA barcodes, and provide a plethora of data for other comparative molecular evolution studies. Here we report on the application of this method to estimating the molecular phylogeny of core Asparagales, investigating plastid gene losses, assembling complete plastid genomes, and determining the type and quality of assembled genomic data attainable from Illumina 80-120-bp reads. METHODS We sequenced total genomic DNA from samples in two lineages of monocotyledonous plants, Poaceae and Asparagales, on the Illumina platform in a multiplex arrangement. We compared reference-based assemblies to de novo contigs, evaluated consistency of assemblies resulting from use of various references sequences, and assessed our methods to obtain sequence assemblies in nonmodel taxa. KEY RESULTS Our method returned reliable, robust organellar and nrDNA sequences in a variety of plant lineages. High quality assemblies are not dependent on genome size, amount of plastid present in the total genomic DNA template, or relatedness of available reference sequences for assembly. Phylogenetic results revealed familial and subfamilial relationships within Asparagales with high bootstrap support, although placement of the monotypic genus Aphyllanthes was placed with moderate confidence. CONCLUSIONS The well-supported molecular phylogeny provides evidence for delineation of subfamilies within core Asparagales. With advances in technology and bioinformatics tools, the use of massively parallel sequencing will continue to become easier and more affordable for phylogenomic and molecular evolutionary biology investigations.
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Affiliation(s)
- P Roxanne Steele
- Department of Biology, 6001 W. Dodge Street, University of Nebraska at Omaha, Omaha, Nebraska 68182-0040, USA
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19
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Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci 2011; 2:34. [PMID: 22645531 PMCID: PMC3355756 DOI: 10.3389/fpls.2011.00034] [Citation(s) in RCA: 255] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Accepted: 07/11/2011] [Indexed: 05/17/2023]
Abstract
The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.
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Affiliation(s)
- Stephen A. Goff
- BIO5 Institute, University of ArizonaTucson, AZ, USA
- *Correspondence: Stephen A. Goff, iPlant Collaborative, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA. e-mail:
| | - Matthew Vaughn
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Sheldon McKay
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Eric Lyons
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Ann E. Stapleton
- Department of Biology, University of North CarolinaWilmington, NC, USA
- Department of Marine Sciences, University of North CarolinaWilmington, NC, USA
| | | | - Naim Matasci
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Liya Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Matthew Hanlon
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | | | - Andy Muir
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | | | - Sonya Lowry
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Stephen Mock
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | | | - Adam Kubach
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Martha Narro
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | | | - David Micklos
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring HarborNY, USA
| | - Uwe Hilgert
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring HarborNY, USA
| | - Michael Gonzales
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Chris Jordan
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | | | - Rion Dooley
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - John Cazes
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Robert McLay
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Lars Koesterke
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | | | - Ruth Grene
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech UniversityBlacksburg, VA, USA
| | | | - Karla Gendler
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Xin Feng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Ontario Center for Cancer ResearchToronto, ON, Canada
| | - Chunlao Tang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Monica Lent
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Seung-Jin Kim
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Kristian Kvilekval
- Center for Bio-image Informatics, University of CaliforniaSanta Barbara, CA, USA
| | - B. S. Manjunath
- Center for Bio-image Informatics, University of CaliforniaSanta Barbara, CA, USA
- Electrical and Computer Engineering, University of CaliforniaSanta Barbara, CA, USA
| | - Val Tannen
- Department of Computer and Information Science, University of PennsylvaniaPhiladelphia, PA, USA
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical StudiesHeidelberg, Germany
| | - Michael Sanderson
- Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - Stephen M. Welch
- Department of Agronomy, Kansas State UniversityManhattan, KS, USA
| | | | - Pamela Soltis
- Florida Museum of Natural History, University of FloridaGainesville, FL, USA
| | - Doug Soltis
- Department of Biology, University of FloridaGainesville, FL, USA
| | - Brian O'Meara
- Department of Ecology and Evolutionary Biology, University of TennesseeKnoxville, TN, USA
| | - Cecile Ane
- Department of Statistics, University of WisconsinMadison, WI, USA
- Department of Botany, University of WisconsinMadison, WI, USA
| | - Tom Brutnell
- Boyce Thompson Institute for Plant Research, Cornell UniversityIthaca, NY, USA
| | | | - Jeffery W. White
- Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research ServiceMaricopa, AZ, USA
| | | | - Michael J. Donoghue
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, CT, USA
| | | | - Todd J. Vision
- Department of Biology, University of North CarolinaChapel Hill, NC, USA
| | | | - David Lowenthal
- Department of Computer Science, University of ArizonaTucson, AZ, USA
| | - Brian J. Enquist
- Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - Brad Boyle
- Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - Ali Akoglu
- Department of Electrical and Computer Engineering, University of ArizonaTucson, AZ, USA
| | - Greg Andrews
- Department of Computer Science, University of ArizonaTucson, AZ, USA
| | - Sudha Ram
- Eller School of Business, University of ArizonaTucson, AZ, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lincoln Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Ontario Center for Cancer ResearchToronto, ON, Canada
| | - Dan Stanzione
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
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Zheng C, Kerr Wall P, Leebens-Mack J, DE Pamphilis C, Albert VA, Sankoff D. Gene loss under neighborhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome. J Bioinform Comput Biol 2009; 7:499-520. [PMID: 19507287 DOI: 10.1142/s0219720009004199] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 11/06/2008] [Accepted: 11/11/2008] [Indexed: 11/18/2022]
Abstract
We develop criteria to detect neighborhood selection effects on gene loss following whole genome duplication, and apply them to the recently sequenced poplar (Populus trichocarpa) genome. We improve on guided genome halving algorithms so that several thousand gene sets, each containing two paralogs in the descendant T of the doubling event and their single ortholog from an undoubled reference genome R, can be analyzed to reconstruct the ancestor A of T at the time of doubling. At the same time, large numbers of defective gene sets, either missing one paralog from T or missing their ortholog in R, may be incorporated into the analysis in a consistent way. We apply this genomic rearrangement distance-based approach to the poplar and grapevine (Vitis vinifera) genomes, as T and R respectively. We conclude that, after chromosome doubling, the "choice" of which paralogous gene pairs will lose copies is random, but that the retention of strings of single-copy genes on one chromosome versus the other is decidedly non-random.
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Affiliation(s)
- Chunfang Zheng
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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21
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Smith CI, Pellmyr O, Althoff DM, Balcázar-Lara M, Leebens-Mack J, Segraves KA. Pattern and timing of diversification in Yucca (Agavaceae): specialized pollination does not escalate rates of diversification. Proc Biol Sci 2008; 275:249-58. [PMID: 18048283 DOI: 10.1098/rspb.2007.1405] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The yucca-yucca moth interaction is one of the most well-known and remarkable obligate pollination mutualisms, and is an important study system for understanding coevolution. Previous research suggests that specialist pollinators can promote rapid diversification in plants, and theoretical work has predicted that obligate pollination mutualism promotes cospeciation between plants and their pollinators, resulting in contemporaneous, parallel diversification. However, a lack of information about the age of Yucca has impeded efforts to test these hypotheses. We used analyses of 4322 AFLP markers and cpDNA sequence data representing six non-protein-coding regions (trnT-trnL, trnL, trnL intron, trnL-trnF, rps16 and clpP intron 2) from all 34 species to recover a consensus organismal phylogeny, and used penalized likelihood to estimate divergence times and speciation rates in Yucca. The results indicate that the pollination mutualism did not accelerate diversification, as Yucca diversity (34 species) is not significantly greater than that of its non-moth-pollinated sister group, Agave sensu latissimus (240 species). The new phylogenetic estimates also corroborate the suggestion that the plant-moth pollination mutualism has at least two origins within the Agavaceae. Finally, age estimates show significant discord between the age of Yucca (ca 6-10Myr) and the current best estimates for the age of their pollinators (32-40Myr).
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23
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Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A 2007; 104:19369-74. [PMID: 18048330 PMCID: PMC2148296 DOI: 10.1073/pnas.0709121104] [Citation(s) in RCA: 713] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Indexed: 11/18/2022] Open
Abstract
Angiosperms are the largest and most successful clade of land plants with >250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and several of the major clades remain either incompletely resolved or weakly supported. We performed phylogenetic analyses of 81 plastid genes in 64 sequenced genomes, including 13 new genomes, to estimate relationships among the major angiosperm clades, and the resulting trees are used to examine the evolution of gene and intron content. Phylogenetic trees from multiple methods, including model-based approaches, provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales. The plastid genome trees also provide strong support for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Resolution of relationships among the major clades of angiosperms provides the necessary framework for addressing numerous evolutionary questions regarding the rapid diversification of angiosperms. Gene and intron content are highly conserved among the early diverging angiosperms and basal eudicots, but 62 independent gene and intron losses are limited to the more derived monocot and eudicot clades. Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements.
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Affiliation(s)
- Robert K Jansen
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
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24
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Pellmyr O, Segraves KA, Althoff DM, Balcázar-Lara M, Leebens-Mack J. The phylogeny of yuccas. Mol Phylogenet Evol 2007; 43:493-501. [PMID: 17289405 DOI: 10.1016/j.ympev.2006.12.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 12/02/2006] [Accepted: 12/18/2006] [Indexed: 11/29/2022]
Abstract
The genus Yucca is widely recognized for its pollination mutualism with yucca moths. Analysis of diversification in this interaction has been hampered by the lack of a robust phylogeny for the genus. Here we attempt the first extensive nuclear DNA based assessment of the phylogenetic relationships of Yucca. We used AFLP markers to recover the phylogeny of 87 samples representing 38 Yucca taxa. An analysis based on 4322 markers strongly supported a topology consistent with morphological classification at the section level (capsular-fruited Chaenocarpa, fleshy-fruited Sarcocarpa, and spongy-fruited Clistocarpa). Within Sarcocarpa, all but two of the traditional species were monophyletic. Within Chaenocarpa, the morphologically distinct series Rupicolae was strongly supported. In the remaining Chaenocarpa, a western group (Colorado Plateau southward) and an eastern group (Great Plains, central Texas east to Florida) were recovered. Within these groups, where taxonomic circumscriptions are narrow and historically contested, there was at most limited monophyly of traditional taxa, suggesting rapid recent diversification, introgression, or non-monophyletically circumscribed taxa.
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Affiliation(s)
- Olle Pellmyr
- Department of Biology, University of Idaho, Moscow, ID 83844-3051, USA.
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25
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Abstract
Garden asparagus (Asparagus officinalis L.) belongs to the monocot family Asparagaceae in the order Asparagales. Onion (Allium cepa L.) and Asparagus officinalis are 2 of the most economically important plants of the core Asparagales, a well supported monophyletic group within the Asparagales. Coding regions in onion have lower GC contents than the grasses. We compared the GC content of 3374 unique expressed sequence tags (ESTs) from A. officinalis with Lycoris longituba and onion (both members of the core Asparagales), Acorus americanus (sister to all other monocots), the grasses, and Arabidopsis. Although ESTs in A. officinalis and Acorus had a higher average GC content than Arabidopsis, Lycoris, and onion, all were clearly lower than the grasses. The Asparagaceae have the smallest nuclear genomes among all plants in the core Asparagales, which typically have huge genomes. Within the Asparagaceae, European Asparagus species have approximately twice the nuclear DNA of that of southern African Asparagus species. We cloned and sequenced 20 genomic amplicons from European A. officinalis and the southern African species Asparagus plumosus and observed no clear evidence for a recent genome doubling in A. officinalis relative to A. plumosus. These results indicate that members of the genus Asparagus with smaller genomes may be useful genomic models for plants in the core Asparagales.
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Affiliation(s)
- Joseph C Kuhl
- Department of Horticulture, Michigan State University, East Lansing 48824, USA
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26
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Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol 2006; 6:77. [PMID: 17020608 PMCID: PMC1626487 DOI: 10.1186/1471-2148-6-77] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 10/04/2006] [Indexed: 11/20/2022] Open
Abstract
Background The magnoliids with four orders, 19 families, and 8,500 species represent one of the largest clades of early diverging angiosperms. Although several recent angiosperm phylogenetic analyses supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence resulted in phylogenetic reconstructions supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. We sequenced the plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other angiosperm plastid genomes to assess phylogenetic relationships among magnoliids and to examine patterns of variation of GC content. Results The Drimys, Liriodendron, and Piper plastid genomes are very similar in size at 160,604, 159,886 bp, and 160,624 bp, respectively. Gene content and order are nearly identical to many other unrearranged angiosperm plastid genomes, including Calycanthus, the other published magnoliid genome. Overall GC content ranges from 34–39%, and coding regions have a substantially higher GC content than non-coding regions. Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd codon, and it varies by functional group with photosynthetic genes having the highest percentage and NADH genes the lowest. Phylogenetic analyses using parsimony and likelihood methods and sequences of 61 protein-coding genes provided strong support for the monophyly of magnoliids and two strongly supported groups were identified, the Canellales/Piperales and the Laurales/Magnoliales. Strong support is reported for monocots and eudicots as sister clades with magnoliids diverging before the monocot-eudicot split. The trees also provided moderate or strong support for the position of Amborella as sister to a clade including all other angiosperms. Conclusion Evolutionary comparisons of three new magnoliid plastid genome sequences, combined with other published angiosperm genomes, confirm that GC content is unevenly distributed across the genome by location, codon position, and functional group. Furthermore, phylogenetic analyses provide the strongest support so far for the hypothesis that the magnoliids are sister to a large clade that includes both monocots and eudicots.
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Affiliation(s)
- Zhengqiu Cai
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
| | - Cynthia Penaflor
- Biology Department, 373 WIDB, Brigham Young University, Provo, UT 84602, USA
| | - Jennifer V Kuehl
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
| | | | - John E Carlson
- School of Forest Resources and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Claude W dePamphilis
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jeffrey L Boore
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
| | - Robert K Jansen
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
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Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006; 313:1596-604. [PMID: 16973872 DOI: 10.1126/science.1128691] [Citation(s) in RCA: 2575] [Impact Index Per Article: 143.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
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Affiliation(s)
- G A Tuskan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Althoff DM, Segraves KA, Leebens-Mack J, Pellmyr O. Patterns of Speciation in the Yucca Moths: Parallel Species Radiations within the Tegeticula yuccasella Species Complex. Syst Biol 2006; 55:398-410. [PMID: 16684719 DOI: 10.1080/10635150600697325] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The interaction between yuccas and yucca moths has been central to understanding the origin and loss of obligate mutualism and mutualism reversal. Previous systematic research using mtDNA sequence data and characters associated with genitalic morphology revealed that a widespread pollinator species in the genus Tegeticula was in fact a complex of pollinator species that differed in host use and the placement of eggs into yucca flowers. Within this mutualistic clade two nonpollinating "cheater" species evolved. Cheaters feed on yucca seeds but lack the tentacular mouthparts necessary for yucca pollination. Previous work suggested that the species complex formed via a rapid radiation within the last several million years. In this study, we use an expanded mtDNA sequence data set and AFLP markers to examine the phylogenetic relationships among this rapidly diverging clade of moths and compare these relationships to patterns in genitalic morphology. Topologies obtained from analyses of the mtDNA and AFLP data differed significantly. Both data sets, however, corroborated the hypothesis of a rapid species radiation and suggested that there were likely two independent species radiations. Morphological analyses based on oviposition habit produced species groupings more similar to the AFLP topology than the mtDNA topology and suggested the two radiations coincided with differences in oviposition habit. The evolution of cheating was reaffirmed to have evolved twice and the closest pollinating relative for one cheater species was identified by both mtDNA and AFLP markers. For the other cheater species, however, the closest pollinating relative remains ambiguous, and mtDNA, AFLP, and morphological data suggest this cheater species may be diverged based on host use. Much of the divergence in the species complex can be explained by geographic isolation associated with the evolution of two oviposition habits.
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Affiliation(s)
- David M Althoff
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844-3051, USA.
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Zahn LM, Leebens-Mack J, DePamphilis CW, Ma H, Theissen G. To B or Not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. ACTA ACUST UNITED AC 2005; 96:225-40. [PMID: 15695551 DOI: 10.1093/jhered/esi033] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
DEFICIENS (DEF) and GLOBOSA (GLO) function in petal and stamen organ identity in Antirrhinum and are orthologs of APETALA3 and PISTILLATA in Arabidopsis. These genes are known as B-function genes for their role in the ABC genetic model of floral organ identity. Phylogenetic analyses show that DEF and GLO are closely related paralogs, having originated from a gene duplication event after the separation of the lineages leading to the extant gymnosperms and the extant angiosperms. Several additional gene duplications followed, providing multiple potential opportunities for functional divergence. In most angiosperms studied to date, genes in the DEF/GLO MADS-box subfamily are expressed in the petals and stamens during flower development. However, in some angiosperms, the expression of DEF and GLO orthologs are occasionally observed in the first and fourth whorls of flowers or in nonfloral organs, where their function is unknown. In this article we review what is known about function, phylogeny, and expression in the DEF/GLO subfamily to examine their evolution in the angiosperms. Our analyses demonstrate that although the primary role of the DEF/GLO subfamily appears to be in specifying the stamens and inner perianth, several examples of potential sub- and neofunctionalization are observed.
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Affiliation(s)
- L M Zahn
- Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA.
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Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L. Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol 2005; 395:348-84. [PMID: 15865976 DOI: 10.1016/s0076-6879(05)95020-9] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
During the past decade, there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. There are 45 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next 5 years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important developments that enhance our ability to generate whole chloroplast genome sequences involve the generation of pure fractions of chloroplast genomes by whole genome amplification using rolling circle amplification, cloning genomes into Fosmid or bacterial artificial chromosome (BAC) vectors, and the development of an organellar annotation program (Dual Organellar GenoMe Annotator [DOGMA]). In addition to providing details of these methods, we provide an overview of methods for analyzing complete plastid genome sequences for repeats and gene content, as well as approaches for using gene order and sequence data for phylogeny reconstruction. This explosive increase in the number of sequenced plastid genomes and improved computational tools will provide many insights into the evolution of these genomes and much new data for assessing relationships at deep nodes in plants and other photosynthetic organisms.
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Affiliation(s)
- Robert K Jansen
- Section of Integrative Biology, The University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, Texas 78712-0253, USA
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Abstract
MOTIVATION The gene expression intensity information conveyed by (EST) Expressed Sequence Tag data can be used to infer important cDNA library properties, such as gene number and expression patterns. However, EST clustering errors, which often lead to greatly inflated estimates of obtained unique genes, have become a major obstacle in the analyses. The EST clustering error structure, the relationship between clustering error and clustering criteria, and possible error correction methods need to be systematically investigated. RESULTS We identify and quantify two types of EST clustering error, namely, Type I and II in EST clustering using CAP3 assembling program. A Type I error occurs when ESTs from the same gene do not form a cluster whereas a Type II error occurs when ESTs from distinct genes are falsely clustered together. While the Type II error rate is <1.5% for both 5' and 3' EST clustering, the Type I error in the 5' EST case is approximately 10 times higher than the 3' EST case (30% versus 3%). An over-stringent identity rule, e.g., P >/= 95%, may even inflate the Type I error in both cases. We demonstrate that approximately 80% of the Type I error is due to insufficient overlap among sibling ESTs (ISO error) in 5' EST clustering. A novel statistical approach is proposed to correct ISO error to provide more accurate estimates of the true gene cluster profile.
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Affiliation(s)
- Ji-Ping Z Wang
- Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
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Abstract
Plant-insect associations have served as models for investigations of coevolution and the influence of biotic interactions on diversification. The pollination association between yuccas and yucca moths is a classic example of an obligate mutualism often suggested to have been affected by coevolution. Recent work has shown high host specificity in pollinating yucca moths, and here we use Tegeticula yuccasella, the species with the widest diet breadth, to ask how host specificity and isolation by distance contribute to specialization. Isolation by distance at a regional scale was observed in nucleotide variation within the mitochondrial gene cytochrome oxidase I (COI) (r =.294; P =.003). Host-related genetic structure (F(ct) = 0.08) was found to be slightly lower than the level of structure observed between eastern and western moth populations (F(ct) = 0.096). However, 56% of the COI haplotypes sampled from moths on Yucca filamentosa mapped to a host-specific clade in the haplotype network. Taken together, these results suggest that differentiation among T. yuccasella populations on alternative hosts is slight, but gene flow is influenced by both host association and geographic distance.
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Affiliation(s)
- J Leebens-Mack
- Department of Biology, 612 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA.
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Marr DL, Leebens-Mack J, Elms L, Pellmyr O. Pollen dispersal in Yucca filamentosa (Agavaceae): the paradox of self-pollination behavior by Tegeticula yuccasella (Prodoxidae). Am J Bot 2000. [PMID: 10811791 DOI: 10.2307/2656853] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We investigated pollen dispersal in an obligate pollination mutualism between Yucca filamentosa and Tegeticula yuccasella. Yucca moths are the only documented pollinator of yuccas, and moth larvae feed solely on developing yucca seeds. The quality of pollination by a female moth affects larval survival because flowers receiving small amounts of pollen or self-pollen have a high abscission probability, and larvae die in abscised flowers. We tested the prediction that yucca moths primarily perform outcross pollinations by using fluorescent dye to track pollen dispersal in five populations of Y. filamentosa. Dye transfers within plants were common in all populations (mean ± 1 SE, 55 ± 3.0%), indicating that moths frequently deposit self-pollen. Distance of dye transfers ranged from 0 to 50 m, and the mean number of flowering plants between the pollen donor and recipient was 5 (median = 0), suggesting that most pollen was transferred among near neighbors. A multilocus genetic estimate of outcrossing based on seedlings matured from open-pollinated fruits at one site was 94 ± 6% (mean ± 1 SD). We discuss why moths frequently deposit self-pollen to the detriment of their offspring and compare the yucca-yucca moth interaction with other obligate pollinator mutualisms in which neither pollinator nor plant benefit from self-pollination.
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Affiliation(s)
- D L Marr
- Department of Biology, Box 1812 Station B, Vanderbilt University, Nashville, Tennessee 37235 USA
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Abstract
The obligate mutualism between yuccas and yucca moths is a major model system for the study of coevolving species interactions. Exploration of the processes that have generated current diversity and associations within this mutualism requires robust phylogenies and timelines for both moths and yuccas. Here we establish a molecular clock for the moths based on mtDNA and use it to estimate the time of major life history events within the yucca moths. Colonization of yuccas had occurred by 41.5 +/- 9.8 million years ago (Mya), with rapid life history diversification and the emergence of pollinators within 0-6 My after yucca colonization. A subsequent burst of diversification 3.2 +/- 1.8 Mya coincided with evolution of arid habitats in western North America. Derived nonpollinating cheater yucca moths evolved 1.26 +/- 0.96 Mya. The estimated age of the moths far predates the host fossil record, but is consistent with suggested host age based on paleobotanical, climatological, biogeographical, and geological data, and a tentative estimation from an rbcL-based molecular clock for yuccas. The moth data are used to establish three alternative scenarios of how the moths and plants have coevolved. They yield specific predictions that can be tested once a robust plant phylogeny becomes available.
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Affiliation(s)
- O Pellmyr
- Department of Biology, Vanderbilt University, Box 1812, Station B, Nashville, TN 37235, USA
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Leebens-Mack J, Milligan B. Pollination biology in hybridizing Baptisia (Fabaceae) populations. Am J Bot 1998; 85:500. [PMID: 21684932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In their classic study, Alston and Turner (American Journal of Botany, vol. 50, 159-173, 1963) documented extensive hybridization among four morphologically distinct Baptisia species native to East Texas. While Alston and Turner found putative F1 hybrids in great numbers, they found no evidence of backcrossing. In this study prezygotic and postzygotic reproductive barriers between two of these species, B. leucophaea and B. sphaerocarpa, were investigated and found to be quite weak. Flowering times overlap and bumble bees were observed visiting both species and intermediate hybrids. While pollinator constancy in flights between B. leucophaea and B. sphaerocarpa was moderately strong, significant levels of constancy were not observed in flights involving hybrids and either parental species. Thus, backcrossing was not impeded by pollinator behavior. Further, hybrid pollen was highly stainable (93.5%) and able to effectively set seed in crossing experiments with both parental species. Pollinator behavior was compared in experimental populations with and without hybrid ramets and found to differ between these two treatments. Hybrids were found to facilitate pollinator movement between species. In total, these results suggest that reproductive isolation is not responsible for the rarity of backcrossing in naturally hybridizing B. leucophaea and B. sphaerocarpa populations.
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Abstract
While DNA-based markers can provide a wealth of information for the study of plant evolutionary biology, progress is limited by the lack of primers available for PCR. To overcome this limitation, we outline a protocol for developing oligonucleotide primers targeting regions of low copy-number nuclear genes. This protocol is intended to lead to universally useful primer sets. To test our approach, we designed eight primer sets and tested their abilities to amplify targets from representatives of each dicot and one monocot subclass. Five of the eight primer sets amplified targets from at least five of the seven taxa and thus exhibited broad taxonomic usefulness; the remaining primers were rather specific, however, and amplified targets from at most three taxa. In only one primer-taxon combination was a complex multiple-banded amplification produced. Overall, the protocol outlined proved quite useful at identifying broadly applicable primers targeted to low copy-number nuclear genes. Wider application of this approach should be effective at greatly increasing the amount of genetic information available for a diversity of plant nuclear genomes.
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Affiliation(s)
- A E Strand
- Department of Biology, New Mexico State University, Las Cruces 88003, USA.
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Abstract
Interspecific mutualisms are regarded as having evolved from antagonistic or commensalistic interactions, with most mutualisms remaining facultative but some having coevolved into obligate reciprocal dependency. Underlying mutualism is an intrinsic conflict between the parties, in that each is under selection for increased exploitation of the other. Theoretical models suggest that this conflict is a source of evolutionary instability, and that evolution of 'cheating' by one party may lead to reciprocal extinction. Here we present phylogenic evidence for reversal of an obligate mutualism: within the yucca moth complex, distinct cheater species derived from obligate pollinators inflict a heavy cost on their yucca hosts by laying their eggs but not pollinating the yucca. Phylogenetic data show the cheaters to have existed for a long time. Coexisting pollinators and cheaters are not sister taxa, supporting predictions that evolution of cheating within a single pollinator is evolutionarily unstable. Several lines of evidence support a hypothesis that host shifts preceded the reversal of obligate mutualism. Host or partner shifts is a mechanism that can provide a route of evolutionary escape among obligate mutualists in general.
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Affiliation(s)
- O Pellmyr
- Department of Biology, Vanderbilt University, Nashville, Tennessee 37235, USA
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