1
|
Fu YB. Polycotyly: How Little Do We Know? PLANTS (BASEL, SWITZERLAND) 2024; 13:1054. [PMID: 38674463 PMCID: PMC11054791 DOI: 10.3390/plants13081054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
Polycotyly, an interesting characteristic of seed-bearing dicotyledonous plants with more than two cotyledons, represents one of the least explored plant characters for utilization, even though cotyledon number was used to classify flowering plants in 1682. Gymnosperm and angiosperm species are generally known to have one or two cotyledons, but scattered reports exist on irregular cotyledon numbers in many plant species, and little is known about the extent of polycotyly in plant taxa. Here, we attempt to update the documentation of reports on polycotyly in plant species and highlight some lines of research for a better understanding of polycotyly. This effort revealed 342 angiosperm species of 237 genera in 80 (out of 416) families and 160 gymnosperm species of 26 genera in 6 (out of 12) families with reported or cited polycotyly. The most advanced research included the molecular-based inference of the phylogeny of flowering plants, showing a significant departure from the cotyledon-based classification of angiosperm plants, and the application of genetic cotyledon mutants as tools to clone and characterize the genes regulating cotyledon development. However, there were no reports on breeding lines with a 100% frequency of polycotyly. Research is needed to discover plant species with polycotyly and to explore the nature, development, genetics, evolution, and potential use of polycotyly.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| |
Collapse
|
2
|
Fangel JU, Sørensen KM, Jacobsen N, Mravec J, Ahl LI, Bakshani C, Mikkelsen MD, Engelsen SB, Willats W, Ulvskov P. The legacy of terrestrial plant evolution on cell wall fine structure. PLANT, CELL & ENVIRONMENT 2024; 47:1238-1254. [PMID: 38173082 DOI: 10.1111/pce.14785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/15/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024]
Abstract
The evolution of land flora was an epochal event in the history of planet Earth. The success of plants, and especially flowering plants, in colonizing all but the most hostile environments required multiple mechanisms of adaptation. The mainly polysaccharide-based cell walls of flowering plants, which are indispensable for water transport and structural support, are one of the most important adaptations to life on land. Thus, development of vasculature is regarded as a seminal event in cell wall evolution, but the impact of further refinements and diversification of cell wall compositions and architectures on radiation of flowering plant families is less well understood. We approached this from a glyco-profiling perspective and, using carbohydrate microarrays and monoclonal antibodies, studied the cell walls of 287 plant species selected to represent important evolutionary dichotomies and adaptation to a variety of habitats. The results support the conclusion that radiation of flowering plant families was indeed accompanied by changes in cell wall fine structure and that these changes can obscure earlier evolutionary events. Convergent cell wall adaptations identified by our analyses do not appear to be associated with plants with similar lifestyles but that are taxonomically distantly related. We conclude that cell wall structure is linked to phylogeny more strongly than to habitat or lifestyle and propose that there are many approaches of adaptation to any given ecological niche.
Collapse
Affiliation(s)
- Jonatan U Fangel
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Niels Jacobsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Louise Isager Ahl
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Cassie Bakshani
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | | | | | - William Willats
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
3
|
Kraehmer H, Bonsels-Klein K, Claßen-Bockhoff R. Rhizome architecture, development and vascularization in the water lily Nymphaea alba. ANNALS OF BOTANY 2023; 131:851-866. [PMID: 36976535 PMCID: PMC10184447 DOI: 10.1093/aob/mcad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/24/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Water lilies are of particular interest with regard to the evolution of angiosperms. They live in an aquatic environment and have been regarded as links to the monocots by some authors. Vascular bundles are sometimes described as scattered or atactostelar as in monocots. However, this view needs to be clarified as the morphology and vascularization of Nymphaea rhizomes remain to be understood. METHODS The rhizome of Nymphaea alba was re-investigated morphologically and histologically. Developmental studies were conducted using scanning electron microscopy. Comprehensive histological analyses, including hand and microtome sections and a variety of specific staining procedures, were conducted to re-evaluate the composition of longitudinal and transverse tissue. KEY RESULTS The rhizome is covered by parenchymatous nodal cushions each bearing a leaf and several adventitious roots. Internodes are extremely short. The apex is flat and early overtopped by developing leaf primordia and cushions. The phyllotaxis is spiral and passes alternately through vegetative and reproductive phases. Flowers appear in the leaf spiral, and lack a subtending bract and a cushion below the peduncle. The reproductive phase includes two or three flowers which alternate with a single leaf. The rhizome is histologically subdivided into a central core, an aerenchymatic cortex, and a parenchymatic exocortex formed to a great extent by the nodal cushions. The core contains strands of vascular bundles united to a complex vascular plexus. Vascular elements continuously anastomose and change shape and direction. Provascular strands originating from leaf primordia merge with the outer core vascular tissue whereas the flower strands run into the centre of the core. Roots originating from the parenchymatous cushions show the characteristic actinostelic pattern, which changes into a collateral pattern inside the rhizome. Several root traces merge and form one strand leading to the central core. Early cell divisions below the apical meristem dislocate leaf, flower and root primordia and their provascular strands outwards. Consequently, fully developed vascular strands insert horizontally into the vascular plexus at advanced rhizome stages. CONCLUSIONS The absence of bracts and cushions below the flowers, the alternate leaf-flower sequence and the course of the peduncle strand suggest that the rhizome is sympodially instead of monopodially organized. The spiral phyllotaxis extends in this case over several shoot orders, masking the branching pattern. The vascular strands in the central plexus differ considerably from vascular bundles in monocots, confirming the unique vascularization in Nymphaea. Sclerenchymatic bundle sheaths are lacking, and vascular bundles continuously split and anastomose throughout the rhizome. Though vascular bundles in petioles and peduncles of N. alba show similarities with some Alismatales, the vascular system of N. alba in general has little in common with that of monocots.
Collapse
Affiliation(s)
| | - Kornelia Bonsels-Klein
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Anselm-Franz-von-Bentzel-Weg 2, D-55099 Mainz, Germany
| | - Regine Claßen-Bockhoff
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Anselm-Franz-von-Bentzel-Weg 2, D-55099 Mainz, Germany
| |
Collapse
|
4
|
Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
Collapse
Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
| |
Collapse
|
5
|
Meseguer AS, Carrillo R, Graham SW, Sanmartín I. Macroevolutionary dynamics in the transition of angiosperms to aquatic environments. THE NEW PHYTOLOGIST 2022; 235:344-355. [PMID: 35292979 PMCID: PMC9320795 DOI: 10.1111/nph.18100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Angiosperm lineages in aquatic environments are characterized by high structural and functional diversity, and wide distributions. A long-standing evolutionary riddle is what processes have caused the relatively low diversity of aquatic angiosperms compared to their terrestrial relatives. We use diversification and ancestral reconstruction models with a comprehensive > 10 000 genus angiosperm phylogeny to elucidate the macroevolutionary dynamics associated with transitions of terrestrial plants to water. Our study reveals that net diversification rates are significantly lower in aquatic than in terrestrial angiosperms due to lower speciation and higher extinction. Shifts from land to water started early in angiosperm evolution, but most events were concentrated during the last c. 25 million years. Reversals to a terrestrial habitat started only 40 million years ago, but occurred at much higher rates. Within aquatic angiosperms, the estimated pattern is one of gradual accumulation of lineages, and relatively low and constant diversification rates throughout the Cenozoic. Low diversification rates, together with infrequent water transitions, account for the low diversity of aquatic angiosperms today. The stressful conditions and small global surface of the aquatic habitat available for angiosperms are hypothesized to explain this pattern.
Collapse
Affiliation(s)
| | - Rubén Carrillo
- Real Jardín Botánico de Madrid (RJB)CSIC28014MadridSpain
| | - Sean W. Graham
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
| | | |
Collapse
|
6
|
Shi T, Huneau C, Zhang Y, Li Y, Chen J, Salse J, Wang Q. The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution. NATURE PLANTS 2022; 8:764-777. [PMID: 35835857 PMCID: PMC9300462 DOI: 10.1038/s41477-022-01187-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/30/2022] [Indexed: 05/03/2023]
Abstract
Monocots are one of the most diverse groups of flowering plants, and tracing the evolution of their ancestral genome into modern species is essential for understanding their evolutionary success. Here, we report a high-quality assembly of the Acorus tatarinowii genome, a species that diverged early from all the other monocots. Genome-wide comparisons with a range of representative monocots characterized Acorus as a slowly evolved genome with one whole-genome duplication. Our inference of the ancestral monocot karyotypes provides new insights into the chromosomal evolutionary history assigned to modern species and reveals the probable molecular functions and processes related to the early adaptation of monocots to wetland or aquatic habitats (that is, low levels of inorganic phosphate, parallel leaf venation and ephemeral primary roots). The evolution of ancestral gene order in monocots is constrained by gene structural and functional features. The newly obtained Acorus genome offers crucial evidence for delineating the origin and diversification of monocots, including grasses.
Collapse
Affiliation(s)
- Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Cécile Huneau
- UCA, INRAE, UMR 1095 GDEC (Genetics, Diversity & Ecophysiology of Cereals), Clermont-Ferrand, France
| | - Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
| | - Jérôme Salse
- UCA, INRAE, UMR 1095 GDEC (Genetics, Diversity & Ecophysiology of Cereals), Clermont-Ferrand, France.
| | - Qingfeng Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
| |
Collapse
|
7
|
Odintsova AV, Fishchuk OS, Scrypec KI, Danylyk IM. Systematic treatment of morphological fruit types in plants of the class Liliopsida of the flora of Ukraine. REGULATORY MECHANISMS IN BIOSYSTEMS 2021. [DOI: 10.15421/022151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In this review, the scope of morphological diversity of fruits within the class Liliopsida belonging to the flora of Ukraine compared to the world flora diversity was analyzed. For the first time, the taxonomic diversity of monocot plants of the flora of Ukraine was analyzed, which includes 235 genera and about 1050 species, and the distribution of fruit types in the largest monocot families revealed. It was found that among monocot plants of the world flora, as also of the Ukrainian flora, more than 70% of generic and species diversity is taken up by the Orchidaceae, Poaceae, and Cyperaceae families having dry uniform fruits: inferior capsule (Orchidaceae) and one-seeded enveloped fruit (Poaceae and Cyperaceae). An annotated list of morphological fruit types was compiled for all 38 families of the natural and cultural flora of monocot plants of Ukraine. Among 12 families of the subclass Alismatidae, apocarpous polymerous or trimerous fruits, mostly with one-seeded fruitlets, occur in six families (Alismataceae, Butomaceae, Potamogetonaceae, Ruppiaceae, Scheuchzeriaceae, Zannichelliaceae). In 12 of 16 families of the subclass Liliidae, trimerous capsules are the most common (Agapanthaceae, Agavaceae, Alliaceae, Amaryllidaceae, Asphodelaceae, Colchicaceae, Hemerocallidacae, Hyacinthaceae, Iridaceae, Liliасеае, Melanthiaceae, Orchidaceae), while in six families berry-like fruit occurs in all members or in the single genus (Asparagaceae, Ruscaceae, Dioscoreaceae, Melanthiaceae (Paris), Liliасеае (Streptopus), Smilacaceae). Among 10 families of the subclass Commelinidae, in four families superior dry one-seeded fruits occur (Cyperaceae, Poaceae, Sparganiaceae, Typhaceae), while another four families have trimerous capsules (Cannaceae, Commelinaceae, Juncaceae, Pontederiaceae). In general, the most typical fruit on the familial taxonomical level is the capsule (17 families), berries occur in 10 families, aggregate fruits and one-seeded fruits are represented each in seven families, while the rarest fruit type is the schizocarp (Juncaginaceae). No monomerous follicles, poricide and operculate capsules, winged fruits and loments were found. The most controversial fruit types are found in two groups of families, for both of them the problem is the gynoecium type. These are families with one-seeded fruit (Аrасеае (Lemna), Cyperaceae, Hydrocharitaceae (Najas), Poaceae, Sparganiaceae, Typhaceae, Zosteraceae) and families with initial carpel fusion (Hydrocharitaceae (Stratiotes), Juncaginaceae, Melanthiaceae (Veratrum), Scheuchzeriaceae, Tofieldiaceae). As a result of our work, the key and the most relevant areas of carpological studies in Ukraine were defined, particularly, unifying the terminology, examination of the anatomical structure of the pericarp, revealing of the evolutionary and ecological aspects of fruit morphology.
Collapse
|
8
|
Vos D, Stafford R, Jenkins EL, Garrard A. A model based on Bayesian confirmation and machine learning algorithms to aid archaeological interpretation by integrating incompatible data. PLoS One 2021; 16:e0248261. [PMID: 33788845 PMCID: PMC8011785 DOI: 10.1371/journal.pone.0248261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/23/2021] [Indexed: 11/18/2022] Open
Abstract
The interpretation of archaeological features often requires a combined methodological approach in order to make the most of the material record, particularly from sites where this may be limited. In practice, this requires the consultation of different sources of information in order to cross validate findings and combat issues of ambiguity and equifinality. However, the application of a multiproxy approach often generates incompatible data, and might therefore still provide ambiguous results. This paper explores the potential of a simple digital framework to increase the explanatory power of multiproxy data by enabling the incorporation of incompatible, ambiguous datasets in a single model. In order to achieve this, Bayesian confirmation was used in combination with decision trees. The results of phytolith and geochemical analyses carried out on soil samples from ephemeral sites in Jordan are used here as a case study. The combination of the two datasets as part of a single model enabled us to refine the initial interpretation of the use of space at the archaeological sites by providing an alternative identification for certain activity areas. The potential applications of this model are much broader, as it can also help researchers in other domains reach an integrated interpretation of analysis results by combining different datasets.
Collapse
Affiliation(s)
- Daniella Vos
- Department of Archaeology and Anthropology, Faculty of Science and Technology, Bournemouth University, Poole, United Kingdom
- * E-mail:
| | - Richard Stafford
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, United Kingdom
| | - Emma L. Jenkins
- Department of Archaeology and Anthropology, Faculty of Science and Technology, Bournemouth University, Poole, United Kingdom
| | - Andrew Garrard
- Institute of Archaeology, University College London, London, United Kingdom
| |
Collapse
|
9
|
Li H, Ma Y, Hu H, Song X, Ma Y, Yan H. Novel ammonium dichloroacetates with enhanced herbicidal activity for weed control. RSC Adv 2020; 10:44512-44521. [PMID: 35517127 PMCID: PMC9058436 DOI: 10.1039/d0ra08707f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/23/2020] [Indexed: 12/29/2022] Open
Abstract
Dichloroacetic acid (DCA) exhibits great potential as an herbicide (nontoxic, easily biodegradable), but its application in agriculture has scarcely been investigated. Since DCA readily undergoes photolysis when exposed to natural light or UV irradiation, there is a large activity loss in controlling weeds. To improve the activity of DCA, we proposed the transformation of DCA into an ionic salt form by using an herbicidal ionic liquids (HILs) strategy. Herein, fifteen novel ammonium dichloroacetates were designed and achieved for the first time. When compared to the anionic precursor DCA, three salts with longer alkyl chains ranging from dodecyl to hexadecyl chains were found to enhance not only the post emergence herbicidal activity but also the rates of activity against some broadleaf weeds under greenhouse conditions. The enhancement was due to the synergistic effect of structural factors, such as the surface activity, solubility and stability arising from their ionic nature. In addition, IL 13 possesses a low phytotoxicity to cotton plants with a favorable selectivity index above 2. This study will be useful for the design of new, high-performance herbicidal formulations.
Collapse
Affiliation(s)
- Huanhuan Li
- Plant Protection Department, State Key Laboratory of Cotton Biology, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences Henan Anyang 455000 China +86-372-2562294 +86-372-2562294
| | - Yajie Ma
- Plant Protection Department, State Key Laboratory of Cotton Biology, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences Henan Anyang 455000 China +86-372-2562294 +86-372-2562294
| | - Hongyan Hu
- Plant Protection Department, State Key Laboratory of Cotton Biology, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences Henan Anyang 455000 China +86-372-2562294 +86-372-2562294
| | - Xianpeng Song
- Plant Protection Department, State Key Laboratory of Cotton Biology, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences Henan Anyang 455000 China +86-372-2562294 +86-372-2562294
| | - Yan Ma
- Plant Protection Department, State Key Laboratory of Cotton Biology, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences Henan Anyang 455000 China +86-372-2562294 +86-372-2562294
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| |
Collapse
|
10
|
Coiffard C, Kardjilov N, Manke I, Bernardes-de-Oliveira MEC. Fossil evidence of core monocots in the Early Cretaceous. NATURE PLANTS 2019; 5:691-696. [PMID: 31285562 DOI: 10.1038/s41477-019-0468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/04/2019] [Indexed: 05/11/2023]
Abstract
All the major clades of angiosperms have a fossil record that extends back to more than 100 million years ago (Early Cretaceous), mostly in agreement with molecular dating. However, the Early Cretaceous record of monocots is very poor compared to other angiosperms. Their herbaceous nature has been invoked to explain this rarity, but biogeography could also be an explanation. Unfortunately, most of the Early Cretaceous angiosperm record comes from northern mid-latitudes. The Crato plattenkalk limestone offers a unique window into the Early Cretaceous vegetation of the tropics and has already yielded monocot fossils. Here, we describe a whole monocotyledonous plant from root to reproductive organs that is anatomically preserved. The good preservation of the fossils allowed the evaluation of reproductive, vegetative and anatomical characteristics of monocots, leading to a robust identification of this fossil as a crown monocot. Its occurrence in Northern Gondwana supports the possibility of an early radiation of monocots in the tropics.
Collapse
Affiliation(s)
- Clément Coiffard
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.
| | - Nikolay Kardjilov
- Helmholtz-Center Berlin for Materials and Energy, Institute of Applied Materials, Berlin, Germany
| | - Ingo Manke
- Helmholtz-Center Berlin for Materials and Energy, Institute of Applied Materials, Berlin, Germany
| | | |
Collapse
|
11
|
Liu H, Wei J, Yang T, Mu W, Song B, Yang T, Fu Y, Wang X, Hu G, Li W, Zhou H, Chang Y, Chen X, Chen H, Cheng L, He X, Cai H, Cai X, Wang M, Li Y, Sahu SK, Yang J, Wang Y, Mu R, Liu J, Zhao J, Huang Z, Xu X, Liu X. Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden. Gigascience 2019; 8:giz007. [PMID: 30689836 PMCID: PMC6441391 DOI: 10.1093/gigascience/giz007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/30/2018] [Accepted: 01/11/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in southwest China. Of these, we sequenced 761 samples and collected voucher specimens stored in the Herbarium of China National GeneBank. RESULTS The 761 sequenced samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 to the family level, using specimen and chloroplast sequences. In total, we generated 54 Tb of sequencing data, with an average sequencing depth of 60X per species, as estimated from genome sizes. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and other possible applications. CONCLUSIONS The large dataset of vascular plant genomes generated in this study, which includes both high-depth whole-genome sequencing data and associated voucher specimens, is valuable for plant genome research and other applications. This project also provides insight into the feasibility and technical requirements for "planetary-scale" projects such as the 10,000 Plant Genomes Project and the Earth BioGenome Project.
Collapse
Affiliation(s)
- Huan Liu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinpu Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Ting Yang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Weixue Mu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Tuo Yang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Yuan Fu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Xuebing Wang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Guohai Hu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Wangsheng Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Hongcheng Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Yue Chang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Xiaoli Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hongyun Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Le Cheng
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, Yunnan 650106, China
| | - Xuefei He
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Hechen Cai
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Xianchu Cai
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Mei Wang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yang Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinlong Yang
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, Yunnan 650106, China
| | - Yu Wang
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, Yunnan 650106, China
| | - Ranchang Mu
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China
| | - Jie Liu
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China
| | - Jianming Zhao
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China
| | - Ziheng Huang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Liu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| |
Collapse
|
12
|
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. AMERICAN JOURNAL OF BOTANY 2018; 105:1888-1910. [PMID: 30368769 DOI: 10.1002/ajb2.1178] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [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).
Collapse
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
| |
Collapse
|
13
|
Schwinn KE, Ngo H, Kenel F, Brummell DA, Albert NW, McCallum JA, Pither-Joyce M, Crowhurst RN, Eady C, Davies KM. The Onion ( Allium cepa L.) R2R3-MYB Gene MYB1 Regulates Anthocyanin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2016; 7:1865. [PMID: 28018399 PMCID: PMC5146992 DOI: 10.3389/fpls.2016.01865] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/25/2016] [Indexed: 05/18/2023]
Abstract
Bulb color is an important consumer trait for onion (Allium cepa L., Allioideae, Asparagales). The bulbs accumulate a range of flavonoid compounds, including anthocyanins (red), flavonols (pale yellow), and chalcones (bright yellow). Flavonoid regulation is poorly characterized in onion and in other plants belonging to the Asparagales, despite being a major plant order containing many important crop and ornamental species. R2R3-MYB transcription factors associated with the regulation of distinct branches of the flavonoid pathway were isolated from onion. These belonged to sub-groups (SGs) that commonly activate anthocyanin (SG6, MYB1) or flavonol (SG7, MYB29) production, or repress phenylpropanoid/flavonoid synthesis (SG4, MYB4, MYB5). MYB1 was demonstrated to be a positive regulator of anthocyanin biosynthesis by the induction of anthocyanin production in onion tissue when transiently overexpressed and by reduction of pigmentation when transiently repressed via RNAi. Furthermore, ectopic red pigmentation was observed in garlic (Allium sativum L.) plants stably transformed with a construct for co-overexpression of MYB1 and a bHLH partner. MYB1 also was able to complement the acyanic petal phenotype of a defined R2R3-MYB anthocyanin mutant in Antirrhinum majus of the asterid clade of eudicots. The availability of sequence information for flavonoid-related MYBs from onion enabled phylogenetic groupings to be determined across monocotyledonous and dicotyledonous species, including the identification of characteristic amino acid motifs. This analysis suggests that divergent evolution of the R2R3-MYB family has occurred between Poaceae/Orchidaceae and Allioideae species. The DNA sequences identified will be valuable for future analysis of classical flavonoid genetic loci in Allium crops and will assist the breeding of these important crop species.
Collapse
Affiliation(s)
- Kathy E. Schwinn
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Hanh Ngo
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Fernand Kenel
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - David A. Brummell
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - John A. McCallum
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Meeghan Pither-Joyce
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Ross N. Crowhurst
- The New Zealand Institute for Plant & Food Research LimitedAuckland, New Zealand
| | - Colin Eady
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Kevin M. Davies
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| |
Collapse
|
14
|
Li QQ, Zhou SD, Huang DQ, He XJ, Wei XQ. Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera. AOB PLANTS 2016; 8:plw041. [PMID: 27339054 PMCID: PMC4976397 DOI: 10.1093/aobpla/plw041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/11/2016] [Indexed: 05/20/2023]
Abstract
A primary aim of historical biogeography is to identify the causal factors or processes that have shaped the composition and distribution of biotas over time. Another is to infer the evolution of geographic ranges of species and clades in a phylogenetic context. To this end, historical biogeography addresses important questions such as: Where were ancestors distributed? Where did lineages originate? Which processes cause geographic ranges to evolve through time? Allium subgenus Anguinum comprises approximately twelve taxa with a disjunct distribution in the high mountains from south-western Europe to eastern Asia and in northeastern North America. Although both the systematic position and the geographical limits of Anguinum have been identified, to date no molecular systematic study has been performed utilizing a comprehensive sampling of these species. With an emphasis on the Anguinum eastern Asian geographical group, the goals of the present study were: (i) to infer species-level phylogenetic relationships within Anguinum, (ii) to assess molecular divergence and estimated the times of the major splits in Anguinum and (iii) to trace the biogeographic history of the subgenus. Four DNA sequences (ITS, matK, trnH-psbA, rps16) were used to reconstruct the phylogeny of Allium subgen. Anguinum RbcL sequences were used to estimate divergences time for Allium, and sequences of ITS were used to estimate the divergence times for Anguinum and its main lineages and to provide implications for the evolutionary history of the subgenus. Phylogenetic analyses for all Allium corroborate that Anguinum is monophyletic and indicate that Anguinum is composed of two sister groups: one with a Eurasian-American distribution, and the other restricted to eastern Asia. In the eastern Asian geographical group, incongruence between gene trees and morphology-based taxonomies was recovered as was incongruence between data from plastid and nuclear sequences. This incongruence is likely due to the combined effects of a recent radiation, incomplete lineage sorting, and hybridization/introgression. Divergence time estimates suggest that the crown group of Anguinum originated during the late Miocene (ca. 7.16 Mya) and then diverged and dispersed. Biogeographic analyses using statistical dispersal-vicariance analysis (S-DIVA) and a likelihood method support an eastern Asia origin of Anguinum It is inferred that in the late Pliocene/Early Pleistocene, with cooling climates and the uplift of the Himalayas and Hengduan Mountains, the ancestor of the eastern Asian alliance clade underwent a very recent radiation.
Collapse
Affiliation(s)
- Qin-Qin Li
- Key Laboratory of Bio-Resources and Eco-Environment, MOE, College of Life Sciences, Sichuan University, Chengdu 610064, China Sichuan College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, China Inner Mongolia
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment, MOE, College of Life Sciences, Sichuan University, Chengdu 610064, China Sichuan
| | - De-Qing Huang
- Key Laboratory of Bio-Resources and Eco-Environment, MOE, College of Life Sciences, Sichuan University, Chengdu 610064, China Sichuan
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment, MOE, College of Life Sciences, Sichuan University, Chengdu 610064, China Sichuan
| | - Xian-Qin Wei
- Key Laboratory of Bio-Resources and Eco-Environment, MOE, College of Life Sciences, Sichuan University, Chengdu 610064, China Sichuan
| |
Collapse
|
15
|
Structural Modifications of Fructans in Aloe barbadensis Miller (Aloe Vera) Grown under Water Stress. PLoS One 2016; 11:e0159819. [PMID: 27454873 PMCID: PMC4959688 DOI: 10.1371/journal.pone.0159819] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/09/2016] [Indexed: 11/19/2022] Open
Abstract
Aloe barbadensis Miller (Aloe vera) has a Crassulaceae acid metabolism which grants the plant great tolerance to water restrictions. Carbohydrates such as acemannans and fructans are among the molecules responsible for tolerating water deficit in other plant species. Nevertheless, fructans, which are prebiotic compounds, have not been described nor studied in Aloe vera, whose leaf gel is known to possess beneficial pharmaceutical, nutritional and cosmetic properties. As Aloe vera is frequently cultivated in semi-arid conditions, like those found in northern Chile, we investigated the effect of water deficit on fructan composition and structure. For this, plants were subjected to different irrigation regimes of 100%, 75%, 50% and 25% field capacity (FC). There was a significant increase in the total sugars, soluble sugars and oligo and polyfructans in plants subjected to water deficit, compared to the control condition (100% FC) in both leaf tips and bases. The amounts of fructans were also greater in the bases compared to the leaf tips in all water treatments. Fructans also increase in degree of polymerization with increasing water deficit. Glycosidic linkage analyses by GC-MS, led to the conclusion that there are structural differences between the fructans present in the leaves of control plants with respect to plants irrigated with 50% and 25% FC. Therefore, in non-stressed plants, the inulin, neo-inulin and neo-levan type of fructans predominate, while in the most stressful conditions for the plant, Aloe vera also synthesizes fructans with a more branched structure, the neofructans. To our knowledge, the synthesis and the protective role of neo-fructans under extreme water deficit has not been previously reported.
Collapse
|
16
|
Amarasinghe S, Watson-Haigh NS, Gilliham M, Roy S, Baumann U. The evolutionary origin of CIPK16: A gene involved in enhanced salt tolerance. Mol Phylogenet Evol 2016; 100:135-147. [DOI: 10.1016/j.ympev.2016.03.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/30/2016] [Accepted: 03/31/2016] [Indexed: 12/26/2022]
|
17
|
Zhang L, Chen F, Zhang GQ, Zhang YQ, Niu S, Xiong JS, Lin Z, Cheng ZMM, Liu ZJ. Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:175-85. [PMID: 26959080 DOI: 10.1111/tpj.13159] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 05/20/2023]
Abstract
Crassulacean acid metabolism (CAM) is a CO2 fixation pathway that maximizes water-use efficiency (WUE), compared with the C3/C4 CO2 pathway, which permits CAM plants to adapt to arid environments. The CAM pathway provides excellent opportunities to genetically design plants, especially bioenergy crops, with a high WUE and better photosynthetic performance than C3/C4 in arid environments. The information available on the origin and evolution of CAM is scant, however. Here, we analyzed transcriptomes from 13 orchid species and two existing orchid genomes, covering CAM and C3 plants, with an emphasis on comparing 13 gene families involved in the complete carbon fixation pathway. The dosage of the core photosynthesis-related genes plays no substantial role in the evolution of CAM in orchids; however, CAM may have evolved primarily by changes at the transcription level of key carbon fixation pathway genes. We proposed that in both dark and light, CO2 is primarily fixed and then released through two metabolic pathways via known genes, such as PPC1, PPDK and PPCK. This study reports a comprehensive comparison of carbon fixation pathway genes across different photosynthetic plants, and reveals the importance of the level of expression of key genes in the origin and evolution of CAM.
Collapse
Affiliation(s)
- Liangsheng Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Shance Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jin-Song Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| |
Collapse
|
18
|
Alves M, Trovó M, Forzza RC, Viana P. Overview of the systematics and diversity of Poales in the Neotropics with emphasis on the Brazilian flora. RODRIGUÉSIA 2015. [DOI: 10.1590/2175-7860201566203] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
19
|
Hinchliff CE, Smith SA. Some limitations of public sequence data for phylogenetic inference (in plants). PLoS One 2014; 9:e98986. [PMID: 24999823 PMCID: PMC4085032 DOI: 10.1371/journal.pone.0098986] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 05/09/2014] [Indexed: 11/24/2022] Open
Abstract
The GenBank database contains essentially all of the nucleotide sequence data generated for published molecular systematic studies, but for the majority of taxa these data remain sparse. GenBank has value for phylogenetic methods that leverage data–mining and rapidly improving computational methods, but the limits imposed by the sparse structure of the data are not well understood. Here we present a tree representing 13,093 land plant genera—an estimated 80% of extant plant diversity—to illustrate the potential of public sequence data for broad phylogenetic inference in plants, and we explore the limits to inference imposed by the structure of these data using theoretical foundations from phylogenetic data decisiveness. We find that despite very high levels of missing data (over 96%), the present data retain the potential to inform over 86.3% of all possible phylogenetic relationships. Most of these relationships, however, are informed by small amounts of data—approximately half are informed by fewer than four loci, and more than 99% are informed by fewer than fifteen. We also apply an information theoretic measure of branch support to assess the strength of phylogenetic signal in the data, revealing many poorly supported branches concentrated near the tips of the tree, where data are sparse and the limiting effects of this sparseness are stronger. We argue that limits to phylogenetic inference and signal imposed by low data coverage may pose significant challenges for comprehensive phylogenetic inference at the species level. Computational requirements provide additional limits for large reconstructions, but these may be overcome by methodological advances, whereas insufficient data coverage can only be remedied by additional sampling effort. We conclude that public databases have exceptional value for modern systematics and evolutionary biology, and that a continued emphasis on expanding taxonomic and genomic coverage will play a critical role in developing these resources to their full potential.
Collapse
Affiliation(s)
- Cody E. Hinchliff
- Department of Ecology and Evolutionary Biology, University of Michigan. Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Stephen Andrew Smith
- Department of Ecology and Evolutionary Biology, University of Michigan. Ann Arbor, Michigan, United States of America
| |
Collapse
|
20
|
Kim JS, Kim JH. Comparative genome analysis and phylogenetic relationship of order Liliales insight from the complete plastid genome sequences of two Lilies (Lilium longiflorum and Alstroemeria aurea). PLoS One 2013; 8:e68180. [PMID: 23950788 PMCID: PMC3688979 DOI: 10.1371/journal.pone.0068180] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/27/2013] [Indexed: 11/18/2022] Open
Abstract
Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Lilium longiflorum (Liliaceae) and 155,510bp in Alstroemeria aurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium.
Collapse
Affiliation(s)
- Jung Sung Kim
- Department of Life Science, Gacheon University, Seongnam, Gyeonggi-do, South Korea.
| | | |
Collapse
|
21
|
Rivière C, Pawlus AD, Mérillon JM. Natural stilbenoids: distribution in the plant kingdom and chemotaxonomic interest in Vitaceae. Nat Prod Rep 2013; 29:1317-33. [PMID: 23014926 DOI: 10.1039/c2np20049j] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Stilbenoids, a family of polyphenols known for the complexity of their structure and for their diverse biological activities, occur with a limited but heterogeneous distribution in the plant kingdom. The most prominent stilbene containing plant family, the Vitaceae, represented by the famous wine producing grape vines Vitis vinifera L., is one of the richest sources of novel stilbenes currently known, together with other families, such as Dipterocarpaceae, Gnetaceae and Fabaceae. This review focuses on the distribution of stilbenes and 2-arylbenzofuran derivatives in the plant kingdom, the chemical structure of stilbenes in the Vitaceae family and their taxonomic implication.
Collapse
Affiliation(s)
- Céline Rivière
- Université de Bordeaux, Groupe d'Etude des Substances Végétales à Activité Biologique (GESVAB), EA 3675, Institut des Sciences de la Vigne et du Vin, 210 Chemin de Leysotte, CS 50008, F-33882 Villenave d'Ornon Cedex, France.
| | | | | |
Collapse
|
22
|
Nazareno AG, Reis MSD. Linking phenology to mating system: exploring the reproductive biology of the threatened palm species Butia eriospatha. ACTA ACUST UNITED AC 2012; 103:842-52. [PMID: 23077230 DOI: 10.1093/jhered/ess070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The reproductive biology of the vulnerable palm species Butia eriospatha was studied to provide important information that contributes to our understanding and conservation of the species. In order to determine when and how B. erisopatha reproduces, we combined data from 7 nuclear microsatellite loci with ecological data on flowering and fruiting phenology collected between 2009 and 2011 from a population (N = 515) in the Atlantic Rainforest, Southern Brazil. Periods of flowering and fruit production were seasonal and variable across reproductive events. Mating system analyses indicate that B. eriospatha is a predominantly outcrossing species, ((m) = 0.961), since a certain degree of biparental inbreeding does occur. The species is self-compatible and reproduction may also occur by geitonogamy, indicating the ability of isolated populations to survive and persist. Open-pollinated seeds varied in relatedness, including mainly half-sibs and full-sibs. The effective population size was lower than that expected for panmictic populations. Hence, seeds for conservation programs must be collected from a large number of seed-trees to ensure an adequate effective population in the sample. The collection of germplasm is a high-priority strategy that should be employed to maintain the genetic variability that remains.
Collapse
Affiliation(s)
- Alison Gonçalves Nazareno
- Núcleo de Pesquisas em Florestas Tropicais, Federal University of Santa Catarina, CP 476, 88040-900, Florianópolis, Santa Catarina, Brazil.
| | | |
Collapse
|
23
|
Huotari T, Korpelainen H. Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes. Gene 2012; 508:96-105. [PMID: 22841789 DOI: 10.1016/j.gene.2012.07.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/13/2012] [Accepted: 07/15/2012] [Indexed: 02/02/2023]
|
24
|
Garay-Arroyo A, Piñeyro-Nelson A, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER. When ABC becomes ACB. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2377-2395. [PMID: 22442416 DOI: 10.1093/jxb/ers024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Understanding how the information contained in genes is mapped onto the phenotypes, and deriving formal frameworks to search for generic aspects of developmental constraints and evolution remains one of the main challenges of contemporary biological research. The Mexican endemic triurid Lacandonia schismatica (Lacandoniaceae), a mycoheterotrophic monocotyledonous plant with hermaphroditic reproductive axes is alone among 250,000 species of angiosperms, as it has central stamens surrounded by a peripheral gynoecium, representing a natural instance of a homeotic mutant. Based on the classical ABC model of flower development, it has recently been shown that the B-function gene APETALA3 (AP3), essential for stamen identity, was displaced toward the flower centre in L. schismatica (ABC to ACB) from the early stages of flower development. A functional conservation of B-function genes from L. schismatica through the rescue of B-gene mutants in Arabidopsis thaliana, as well as conserved protein interactions, has also been demonstrated. Thus, it has been shown that relatively simple genetic alterations may underlie large morphological shifts fixed in extant natural populations. Nevertheless, critical questions remain in order to have a full and sufficient explanation of the molecular genetic mechanisms underlying L. schismatica's unique floral arrangement. Evolutionary approaches to developmental mechanisms and systems biology, including high-throughput functional genomic studies and models of complex developmental gene regulatory networks, constitute two main approaches to meet such a challenge. In this review, the aim is to address some of the pending questions with the ultimate goal of investigating further the mechanisms of L. schismatica's unique homeotic flower arrangement and its evolution.
Collapse
Affiliation(s)
- Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México
| | | | | | | | | |
Collapse
|
25
|
|
26
|
Lemaire B, Huysmans S, Smets E, Merckx V. Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms. JOURNAL OF PLANT RESEARCH 2011; 124:561-76. [PMID: 21188459 PMCID: PMC3159761 DOI: 10.1007/s10265-010-0395-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 10/25/2010] [Indexed: 05/08/2023]
Abstract
Rate variation in genes from all three genomes has been observed frequently in plant lineages with a parasitic and mycoheterotrophic mode of life. While the loss of photosynthetic ability leads to a relaxation of evolutionary constraints in genes involved in the photosynthetic apparatus, it remains to be determined how prevalent increased substitution rates are in nuclear DNA of non-photosynthetic angiosperms. In this study we infer rates of molecular evolution of 18S rDNA of all parasitic and mycoheterotorphic plant families (except Lauraceae and Polygalaceae) using relative rate tests. In several holoparasitic and mycoheterotrophic plant lineages extremely high substitution rates are observed compared to other photosynthetic angiosperms. The position and frequency of these substitutions have been identified to understand the mutation dynamics of 18S rRNA in achlorophyllous plants. Despite the presence of significantly elevated substitution rates, very few mutations occur in major functional and structural regions of the small ribosomal molecule, providing evidence that the efficiency of the translational apparatus in non-photosynthetic plants has not been affected.
Collapse
Affiliation(s)
- Benny Lemaire
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, K.U. Leuven, Kasteelpark Arenberg, Belgium.
| | | | | | | |
Collapse
|
27
|
Fucile G, Garcia C, Carlsson J, Sunnerhagen M, Christendat D. Structural and biochemical investigation of two Arabidopsis shikimate kinases: the heat-inducible isoform is thermostable. Protein Sci 2011; 20:1125-36. [PMID: 21520319 PMCID: PMC3149186 DOI: 10.1002/pro.640] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 04/08/2011] [Accepted: 04/08/2011] [Indexed: 11/12/2022]
Abstract
The expression of plant shikimate kinase (SK; EC 2.7.1.71), an intermediate step in the shikimate pathway to aromatic amino acid biosynthesis, is induced under specific conditions of environmental stress and developmental requirements in an isoform-specific manner. Despite their important physiological role, experimental structures of plant SKs have not been determined and the biochemical nature of plant SK regulation is unknown. The Arabidopsis thaliana genome encodes two SKs, AtSK1 and AtSK2. We demonstrate that AtSK2 is highly unstable and becomes inactivated at 37 °C whereas the heat-induced isoform, AtSK1, is thermostable and fully active under identical conditions at this temperature. We determined the crystal structure of AtSK2, the first SK structure from the plant kingdom, and conducted biophysical characterizations of both AtSK1 and AtSK2 towards understanding this mechanism of thermal regulation. The crystal structure of AtSK2 is generally conserved with bacterial SKs with the addition of a putative regulatory phosphorylation motif forming part of the adenosine triphosphate binding site. The heat-induced isoform, AtSK1, forms a homodimer in solution, the formation of which facilitates its relative thermostability compared to AtSK2. In silico analyses identified AtSK1 site variants that may contribute to AtSK1 stability. Our findings suggest that AtSK1 performs a unique function under heat stress conditions where AtSK2 could become inactivated. We discuss these findings in the context of regulating metabolic flux to competing downstream pathways through SK-mediated control of steady state concentrations of shikimate.
Collapse
Affiliation(s)
- Geoffrey Fucile
- Department of Cell and Systems Biology, University of TorontoOntario, Canada
| | - Christel Garcia
- Department of Cell and Systems Biology, University of TorontoOntario, Canada
| | - Jonas Carlsson
- Department of Physics, Chemistry and Biology, Linköping UniversityLinköping, Sweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping UniversityLinköping, Sweden
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of TorontoOntario, Canada
- Center for the Analysis of Genome Evolution and Function, University of TorontoOntario, Canada
| |
Collapse
|
28
|
Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, dePamphilis CW, Graham SW, Pires JC, Stevenson DW, Zomlefer WB, Briggs BG, Duvall MR, Moore MJ, Heaney JM, Soltis DE, Soltis PS, Thiele K, Leebens-Mack JH. Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales 1. ANNALS OF THE MISSOURI BOTANICAL GARDEN 2010. [PMID: 0 DOI: 10.3417/2010023] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
|
29
|
Vaughton G, Ramsey M, Johnson SD. Pollination and late-acting self-incompatibility in Cyrtanthus breviflorus (Amaryllidaceae): implications for seed production. ANNALS OF BOTANY 2010; 106:547-55. [PMID: 20647225 PMCID: PMC2944973 DOI: 10.1093/aob/mcq149] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 06/01/2010] [Accepted: 06/18/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Animal pollination is typically an uncertain process that interacts with self-incompatibility status to determine reproductive success. Seed set is often pollen-limited, but species with late-acting self-incompatibility (SI) may be particularly vulnerable, if self-pollen deposition results in ovule discounting. Pollination is examined and the occurrence of late-acting SI and ovule discounting assessed in Cyrtanthus breviflorus. METHODS The pollination system was characterized by observing floral visitors and assessing nectar production and spectral reflectance of flowers. To assess late-acting SI and ovule discounting, growth of self- and cross-pollen tubes, and seed set following open pollination or hand pollination with varying proportions of self- and cross-pollen, were examined. KEY RESULTS Native honeybees Apis mellifera scutellata pollinated flowers as they actively collected pollen. Most flowers (≥70 %) did not contain nectar, while the rest produced minute volumes of dilute nectar. The flowers which are yellow to humans are visually conspicuous to bees with a strong contrast between UV-reflecting tepals and UV-absorbing anthers and pollen. Plants were self-incompatible, but self-rejection was late-acting and both self- and cross-pollen tubes penetrated ovules. Seed set of open-pollinated flowers was pollen-limited, despite pollen deposition exceeding ovule number by 6-fold. Open-pollinated seed set was similar to that of the cross + self-pollen treatment, but was less than that of the cross-pollen-only treatment. CONCLUSIONS Flowers of C. breviflorus are pollinated primarily by pollen-collecting bees and possess a late-acting SI system, previously unknown in this clade of the Amaryllidaceae. Pollinators of C. breviflorus deposit mixtures of cross- and self-pollen and, because SI is late-acting, self-pollen disables ovules, reducing female fertility. This study thus contributes to growing evidence that seed production in plants with late-acting SI systems is frequently limited by pollen quality, even when pollinators are abundant.
Collapse
Affiliation(s)
- Glenda Vaughton
- Botany, University of New England, Armidale, NSW 2351, Australia.
| | | | | |
Collapse
|
30
|
Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK. Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae. J Mol Evol 2010; 70:149-66. [PMID: 20091301 PMCID: PMC2825539 DOI: 10.1007/s00239-009-9317-3] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 12/16/2009] [Indexed: 11/21/2022]
Abstract
Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes.
Collapse
Affiliation(s)
- Mary M Guisinger
- Section of Integrative Biology, University of Texas, Austin, TX 78712, USA.
| | | | | | | | | |
Collapse
|
31
|
Nunes ELP, Bona C, Moço MCDC, Coan AI. Release of developmental constraints on tetrad shape is confirmed in inaperturate pollen of Potamogeton. ANNALS OF BOTANY 2009; 104:1011-1015. [PMID: 19567417 PMCID: PMC2749525 DOI: 10.1093/aob/mcp160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 05/05/2009] [Accepted: 06/01/2009] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Microsporogenesis in monocots is often characterized by successive cytokinesis with centrifugal cell plate formation. Pollen grains in monocots are predominantly monosulcate, but variation occurs, including the lack of apertures. The aperture pattern can be determined by microsporogenesis features such as the tetrad shape and the last sites of callose deposition among the microspores. Potamogeton belongs to the early divergent Potamogetonaceae and possesses inaperturate pollen, a type of pollen for which it has been suggested that there is a release of the constraint on tetrad shape. This study aimed to investigate the microsporogenesis and the ultrastructure of pollen wall in species of Potamogeton in order to better understand the relationship between microsporogenesis features and the inaperturate condition. METHODS The microsporogenesis was investigated using both light and epifluorescence microscopy. The ultrastructure of the pollen grain was studied using transmission electron microscopy. KEY RESULTS The cytokinesis is successive and formation of the intersporal callose wall is achieved by centrifugal cell plates, as a one-step process. The microspore tetrads were tetragonal, decussate, T-shaped and linear, except in P. pusillus, which showed less variation. This species also showed a callose ring in the microsporocyte, and some rhomboidal tetrads. In the mature pollen, the thickening observed in a broad area of the intine was here interpreted as an artefact. CONCLUSIONS The data support the view that there is a correlation between the inaperturate pollen production and the release of constraint on tetrad shape. However, in P. pusillus the tetrad shape may be constrained by a callose ring. It is also suggested that the lack of apertures in the pollen of Potamogeton may be due to the lack of specific sites on which callose deposition is completed. Moreover, inaperturate pollen of Potamogeton would be better classified as omniaperturate.
Collapse
Affiliation(s)
- Elaine Lopes Pereira Nunes
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, C. Postal 19031, 81531-980, Curitiba, Paraná, Brazil.
| | | | | | | |
Collapse
|
32
|
Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH. The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A 2009; 106:13875-9. [PMID: 19667210 PMCID: PMC2728988 DOI: 10.1073/pnas.0811575106] [Citation(s) in RCA: 708] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Indexed: 11/18/2022] Open
Abstract
Since its discovery in 1907, polyploidy has been recognized as an important phenomenon in vascular plants, and several lines of evidence indicate that most, if not all, plant species ultimately have a polyploid ancestry. However, previous estimates of the frequency of polyploid speciation suggest that the formation and establishment of neopolyploid species is rare. By combining information from the botanical community's vast cytogenetic and phylogenetic databases, we establish that 15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase. These frequency estimates are higher by a factor of four than earlier estimates and lead to a standing incidence of polyploid species within genera of 35% (n = 1,506). Despite this high incidence, we find no direct evidence that polyploid lines, once established, enjoy greater net species diversification. Thus, the widespread occurrence of polyploid taxa appears to result from the substantial contribution of polyploidy to cladogenesis, but not from subsequent increases in diversification rates of polyploid lines.
Collapse
Affiliation(s)
- Troy E Wood
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany.
| | | | | | | | | | | |
Collapse
|
33
|
Miller JS. Generic Revision of the Dioptinae (Lepidoptera: Noctuoidea: Notodontidae) Part 1: Dioptini. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2009. [DOI: 10.1206/321.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
34
|
Miller JS. Generic Revision of the Dioptinae (Lepidoptera: Noctuoidea: Notodontidae) Part 2: Josiini. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2009. [DOI: 10.1206/321.1-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
35
|
Crepet WL, Niklas KJ. Darwin's second 'abominable mystery': Why are there so many angiosperm species? AMERICAN JOURNAL OF BOTANY 2009; 96:366-81. [PMID: 21628194 DOI: 10.3732/ajb.0800126] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The rapid diversification and ecological dominance of the flowering plants beg the question "Why are there so many angiosperm species and why are they so successful?" A number of equally plausible hypotheses have been advanced in response to this question, among which the most widely accepted highlights the mutually beneficial animal-plant relationships that are nowhere better developed nor more widespread than among angiosperm species and their biotic vectors for pollination and dispersal. Nevertheless, consensus acknowledges that there are many other attributes unique to or characteristic of the flowering plants. In addition, the remarkable coevolution of the angiosperms and pollination/dispersal animal agents could be an effect of the intrinsic adaptability of the flowering plants rather than a primary cause of their success, suggesting that the search for underlying causes should focus on an exploration of the genetic and epigenetic mechanisms that might facilitate adaptive evolution and speciation. Here, we explore angiosperm diversity promoting attributes in their general form and draw particular attention to those that, either individually or collectively, have been shown empirically to favor high speciation rates, low extinction rates, or broad ecological tolerances. Among these are the annual growth form, homeotic gene effects, asexual/sexual reproduction, a propensity for hybrid polyploidy, and apparent "resistance" to extinction. Our survey of the literature suggests that no single vegetative, reproductive, or ecological feature taken in isolation can account for the evolutionary success of the angiosperms. Rather, we believe that the answer to Darwin's second "abominable mystery" lies in a confluence of features that collectively make the angiosperms unique among the land plants.
Collapse
Affiliation(s)
- William L Crepet
- Department of Plant Biology, Cornell University, Ithaca, New York 14853 USA
| | | |
Collapse
|
36
|
Meng Y, Wen J, Nie ZL, Sun H, Yang YP. Phylogeny and biogeographic diversification of Maianthemum (Ruscaceae: Polygonatae). Mol Phylogenet Evol 2008; 49:424-34. [DOI: 10.1016/j.ympev.2008.07.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Revised: 06/26/2008] [Accepted: 07/26/2008] [Indexed: 11/15/2022]
|
37
|
Yishay M, Burdman S, Valverde A, Luzzatto T, Ophir R, Yedidia I. Differential pathogenicity and genetic diversity among Pectobacterium carotovorum ssp. carotovorum isolates from monocot and dicot hosts support early genomic divergence within this taxon. Environ Microbiol 2008; 10:2746-59. [PMID: 18681897 DOI: 10.1111/j.1462-2920.2008.01694.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The capability of Pectobacterium carotovorum isolates to infect monocotyledonous plants has been previously reported; however, no full consideration was given to characterize the association between such isolates and their monocot hosts. To assess differences in aggressiveness among P. carotovorum ssp. carotovorum isolates originating from monocotyledonous or dicotyledonous plants, we used as model plants two susceptible monocot hosts, the ornamentals Zantedeschia aethiopica and Ornithogalum dubium, as well as two common dicot hosts, Solanum tuberosum and Brassica oleracea. Using virulence assays and different genetic analyses we characterized P. carotovorum ssp. carotovorum isolates from diverse geographical locations which originated from plants belonging to four unrelated orders of monocots and five orders of dicots. Invariably, isolates originating from monocots exhibited higher virulence towards the tested monocot plants than dicot isolates, independently of their geographical source. Moreover, monocot and dicot isolates were clearly differentiated by various genetic analyses, such as 16S rRNA sequence clustering, intergenic transcribed spacer-PCR (ITS-PCR) banding pattern and amplified fragment length polymorphism (AFLP). We propose that the observed relationship between pathogenicity and genetic diversity among P. carotovorum ssp. carotovorum isolates reveals a co-evolutionary specialization trend in the interaction between this pathogen and its hosts.
Collapse
Affiliation(s)
- Moran Yishay
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, PO Box 6, Bet-Dagan 50250, Israel
| | | | | | | | | | | |
Collapse
|
38
|
North GB, Brinton EK, Garrett TY. Contractile roots in succulent monocots: convergence, divergence and adaptation to limited rainfall. PLANT, CELL & ENVIRONMENT 2008; 31:1179-1189. [PMID: 18507804 DOI: 10.1111/j.1365-3040.2008.01832.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Contractile roots (CRs) that pull shoots further down in the soil are a possible example of convergent evolution in two monocot families, the Agavaceae and the Asphodelaceae. The association between CRs, water uptake and habitat aridity was investigated for agaves, yuccas and aloes by assessing the occurrence of CRs and the amount of root contraction for glasshouse-grown plants with respect to mean annual rainfall of their native habitats. Structural features of CRs as well as root hydraulic conductance were compared with those of non-contractile roots (NCRs). CRs occurred in 55% of the 73 species examined, including 64% of the agaves and 85% of the yuccas, but in none of the aloes despite the occurrence of CRs in related genera. The phylogenetic distribution of CRs was consistent with multiple acquisitions or losses of the trait. The amount of root contraction showed a highly significant negative relationship with mean annual rainfall, although other environmental factors may also be important. Radial hydraulic conductance of the basal (contractile) zone exceeded that of the midroot zone for CRs; for NCRs, the opposite was true. Thus, CRs in the species examined may provide a mechanism for greater water uptake near the soil surface in regions with limited rainfall.
Collapse
Affiliation(s)
- Gretchen B North
- Department of Biology, Occidental College, Los Angeles, CA 90041, USA.
| | | | | |
Collapse
|
39
|
Merckx V, Chatrou LW, Lemaire B, Sainge MN, Huysmans S, Smets EF. Diversification of myco-heterotrophic angiosperms: evidence from Burmanniaceae. BMC Evol Biol 2008; 8:178. [PMID: 18573195 PMCID: PMC2492876 DOI: 10.1186/1471-2148-8-178] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 06/23/2008] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Myco-heterotrophy evolved independently several times during angiosperm evolution. Although many species of myco-heterotrophic plants are highly endemic and long-distance dispersal seems unlikely, some genera are widely dispersed and have pantropical distributions, often with large disjunctions. Traditionally this has been interpreted as evidence for an old age of these taxa. However, due to their scarcity and highly reduced plastid genomes our understanding about the evolutionary histories of the angiosperm myco-heterotrophic groups is poor. RESULTS We provide a hypothesis for the diversification of the myco-heterotrophic family Burmanniaceae. Phylogenetic inference, combined with biogeographical analyses, molecular divergence time estimates, and diversification analyses suggest that Burmanniaceae originated in West Gondwana and started to diversify during the Late Cretaceous. Diversification and migration of the species-rich pantropical genera Burmannia and Gymnosiphon display congruent patterns. Diversification began during the Eocene, when global temperatures peaked and tropical forests occurred at low latitudes. Simultaneous migration from the New to the Old World in Burmannia and Gymnosiphon occurred via boreotropical migration routes. Subsequent Oligocene cooling and breakup of boreotropical flora ended New-Old World migration and caused a gradual decrease in diversification rate in Burmanniaceae. CONCLUSION Our results indicate that extant diversity and pantropical distribution of myco-heterotrophic Burmanniaceae is the result of diversification and boreotropical migration during the Eocene when tropical rain forest expanded dramatically.
Collapse
Affiliation(s)
- Vincent Merckx
- Laboratory of Plant Systematics, K.U. Leuven, Kasteelpark Arenberg 31, P.O. Box 2437, BE-3001 Leuven, Belgium
| | - Lars W Chatrou
- National Herbarium of the Netherlands, Wageningen University Branch, Generaal Foulkesweg 37, NL-6703 BL Wageningen, The Netherlands
| | - Benny Lemaire
- Laboratory of Plant Systematics, K.U. Leuven, Kasteelpark Arenberg 31, P.O. Box 2437, BE-3001 Leuven, Belgium
| | - Moses N Sainge
- Centre for Tropical Forest Sciences (CTFS), University of Buea, Department of Plant & Animal Sciences, P.O. Box 63, Buea, Cameroon
| | - Suzy Huysmans
- Laboratory of Plant Systematics, K.U. Leuven, Kasteelpark Arenberg 31, P.O. Box 2437, BE-3001 Leuven, Belgium
| | - Erik F Smets
- Laboratory of Plant Systematics, K.U. Leuven, Kasteelpark Arenberg 31, P.O. Box 2437, BE-3001 Leuven, Belgium
- National Herbarium of the Netherlands, Leiden University Branch, P.O. Box 9514, NL-2300 RA, Leiden, The Netherlands
| |
Collapse
|
40
|
Merckx V, Bidartondo MI. Breakdown and delayed cospeciation in the arbuscular mycorrhizal mutualism. Proc Biol Sci 2008; 275:1029-35. [PMID: 18270159 PMCID: PMC2600904 DOI: 10.1098/rspb.2007.1622] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/24/2008] [Accepted: 01/25/2008] [Indexed: 11/12/2022] Open
Abstract
The ancient arbuscular mycorrhizal association between the vast majority of plants and the fungal phylum Glomeromycota is a dominant nutritional mutualism worldwide. In the mycorrhizal mutualism, plants exchange photosynthesized carbohydrates for mineral nutrients acquired by fungi from the soil. This widespread cooperative arrangement is broken by 'cheater' plant species that lack the ability to photosynthesize and thus become dependent upon three-partite linkages (cheater-fungus-photosynthetic plant). Using the first fine-level coevolutionary analysis of mycorrhizas, we show that extreme fidelity towards fungi has led cheater plants to lengthy evolutionary codiversification. Remarkably, the plants' evolutionary history closely mirrors that of their considerably older mycorrhizal fungi. This demonstrates that one of the most diffuse mutualistic networks is vulnerable to the emergence, persistence and speciation of highly specific cheaters.
Collapse
Affiliation(s)
- Vincent Merckx
- Laboratory of Plant Systematics, K. U. Leuven, Kasteelpark Arenberg 31, PO Box 2437, 3001 Leuven, Belgium.
| | | |
Collapse
|
41
|
Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CMR, D'Hont A, Garsmeur O, Vilarinhos AD, Kanamori H, Matsumoto T, Ronning CM, Cheung F, Haas BJ, Althoff R, Arbogast T, Hine E, Pappas GJ, Sasaki T, Souza MT, Miller RNG, Glaszmann JC, Town CD. Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 2008; 9:58. [PMID: 18234080 PMCID: PMC2270835 DOI: 10.1186/1471-2164-9-58] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 01/30/2008] [Indexed: 01/10/2023] Open
Abstract
Background Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.
Collapse
Affiliation(s)
- Magali Lescot
- French Agricultural Research Center for International Development, UMR 1096, Avenue Agropolis, TA40/03, FR-34398, Montpellier, Cedex 5, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Vaughan DA, Ge S, Kaga A, Tomooka N. Phylogeny and Biogeography of the Genus Oryza. RICE BIOLOGY IN THE GENOMICS ERA 2008. [DOI: 10.1007/978-3-540-74250-0_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
43
|
Luzzatto T, Golan A, Yishay M, Bilkis I, Ben-Ari J, Yedidia I. Priming of antimicrobial phenolics during induced resistance response towards Pectobacterium carotovorum in the ornamental monocot calla lily. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:10315-22. [PMID: 17994692 DOI: 10.1021/jf072037+] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Calla lilies are herbaceous monocotyledonous plants that are highly sensitive to Pectobacterium carotovorum, the causal agent of soft-rot disease. Results demonstrate that, in response to elicitation using plant defense activators, the calla lily produces elevated levels of antimicrobial phenolics and that these compounds contribute to increased resistance against P. carotovorum, as shown by reduced bacterial proliferation in elicited leaves. The polyphenolic nature of the induced compounds was supported by autofluorescence, absorbance spectra, and reaction with Folin-Ciocalteu reagent. Two plant defense activators, Bion and methyl jasmonate, differed in both their capacity to induce accumulation of polyphenols and their resistance against the pathogen. Methyl jasmonate elicitation brought about higher accumulation of free phenolics relative to Bion, suggesting priming of bioactive polyphenols as a principal factor in the calla lily defense against P. carotovorum. To further characterize the nature of induced compounds, two major compounds were collected and identified as swertisin and isovitexin by mass and nuclear magnetic resonance spectroscopies.
Collapse
Affiliation(s)
- Tal Luzzatto
- Department of Ornamental Horticulture, ARO, The Volcani Center, Derech Hamacabim 20, P.O. Box 6, Bet-Dagan, 50250, Israel
| | | | | | | | | | | |
Collapse
|
44
|
Estavillo GM, Rao SK, Reiskind JB, Bowes G. Characterization of the NADP malic enzyme gene family in the facultative, single-cell C4 monocot Hydrilla verticillata. PHOTOSYNTHESIS RESEARCH 2007; 94:43-57. [PMID: 17638114 DOI: 10.1007/s11120-007-9212-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 06/05/2007] [Indexed: 05/16/2023]
Abstract
Hydrilla verticillata has a facultative single-cell system that changes from C3 to C4 photosynthesis. A NADP+-dependent malic enzyme (NADP-ME) provides a high [CO2] for Rubisco fixation in the C4 leaf chloroplasts. Of three NADP-ME genes identified, only hvme1 was up-regulated in the C4 leaf, during the light period, and it possessed a putative transit peptide. Unlike obligate C4 species, H. verticillata exhibited only one plastidic isoform that may perform housekeeping functions, but is up-regulated as the photosynthetic decarboxylase. Of the two cytosolic forms, hvme2 and hvme3, the latter exhibited the greatest expression, but was not light-regulated. The mature isoform of hvme1 had a pI of 6.0 and a molecular mass of 64 kD, as did the recombinant rHVME1m, and it formed a tetramer in the chloroplast. The recombinant photosynthetic isoform showed intermediate characteristics between isoforms in terrestrial C3 and C4 species. The catalytic efficiency of rHVME1m was four-fold higher than the cytosolic rHVME3 and two-fold higher than recombinant cytosolic isoforms of rice, but lower than plastidic forms of maize. The Km (malate) of 0.6 mM for rHVME1 was higher than maize plastid isoforms, but four-fold lower than found with rice. A comprehensive phylogenetic analysis of 25 taxa suggested that chloroplastic NADP-ME isoforms arose from four duplication events, and hvme1 was derived from cytosolic hvme3. The chloroplastic eudicot sequences were a monophyletic group derived from a cytosolic clade after the eudicot and monocot lineages separated, while the monocots formed a polyphyletic group. The findings support the hypothesis that a NADP-ME isoform with specific and unusual regulatory properties facilitates the functioning of the single-cell C4 system in H. verticillata.
Collapse
Affiliation(s)
- Gonzalo M Estavillo
- Department of Botany, University of Florida, 220 Bartram Hall, PO Box 118526, Gainesville, FL 32611-8526, USA.
| | | | | | | |
Collapse
|
45
|
Crisp MD, Cook LG. A congruent molecular signature of vicariance across multiple plant lineages. Mol Phylogenet Evol 2007; 43:1106-17. [PMID: 17434758 DOI: 10.1016/j.ympev.2007.02.030] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Revised: 02/06/2007] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
Explaining disjunct distributions, or why closely related organisms are often separated by apparently severe barriers such as oceans or deserts, is a great challenge for historical biogeography. Competing explanations are long-distance dispersal across a barrier, and vicariance, in which disjunct taxa are descended from an ancestral population that was split by formation of the barrier. Vicariance explanations are testable by their prediction that near-simultaneous speciation should have occurred across multiple lineages of organisms between the disjunct areas because the origin of a barrier would potentially disrupt gene flow within multiple species. To date, there have been few studies providing evidence for multiple synchronous ancient divergences across a barrier whose origin coincides with the timing of the speciation events. Here, we use relaxed molecular-clock dating to investigate the timing of south-western (SW) versus south-eastern (SE) divergences in 23 pairs of plant lineages in southern Australia. Sixteen of the divergences correlate with the origin, 13-14 million years (Myr) ago, of the arid treeless Nullarbor Plain. The Nullarbor Plain currently forms a substantial barrier to SW-SE migration but during the last 45Myr this region has experienced multiple episodes of marine inundation and subaerial exposure. Thus, there have been multiple events that could have caused either isolation and speciation, or secondary contact, among the taxa of southern Australia. The strong molecular signal of coincident speciation in many diverse lineages during a short period provides the best evidence to date linking synchronous speciation to an ancient vicariance event.
Collapse
Affiliation(s)
- Michael D Crisp
- School of Botany and Zoology, The Australian National University, Daley Road, Building 44, Canberra, ACT, Australia.
| | | |
Collapse
|
46
|
Hirayama Y, Yamada T, Oya Y, Ito M, Kato M, Imaichi R. Expression patterns of class I KNOX and YABBY genes in Ruscus aculeatus (Asparagaceae) with implications for phylloclade homology. Dev Genes Evol 2007; 217:363-72. [PMID: 17429685 DOI: 10.1007/s00427-007-0149-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2006] [Accepted: 03/14/2007] [Indexed: 10/23/2022]
Abstract
STM (RaSTM) and YAB2 (RaYAB2) homologues were isolated from Ruscus aculeatus (Asparagaceae, monocots), and their expressions were analyzed by real-time polymerase chain reaction (PCR) to assess hypotheses on the evolutionary origin of the phylloclade in the Asparagaceae. In young shoot buds, RaSTM is expressed in the shoot apex, while RaYAB2 is expressed in the scale leaf subtending the shoot bud. This expression pattern is shared by other angiosperms, suggesting that the expression patterns of RaSTM and RaYAB2 are useful as molecular markers to identify the shoot and leaf, respectively. RaSTM and RaYAB2 are expressed concomitantly in phylloclade primordia. These results suggest that the phylloclade is not homologous to either the shoot or leaf, but that it has a double organ identity.
Collapse
Affiliation(s)
- Yumiko Hirayama
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Tokyo 112-8681, Japan
| | | | | | | | | | | |
Collapse
|
47
|
Gómez-Zurita J, Hunt T, Kopliku F, Vogler AP. Recalibrated tree of leaf beetles (Chrysomelidae) indicates independent diversification of angiosperms and their insect herbivores. PLoS One 2007; 2:e360. [PMID: 17426809 PMCID: PMC1832224 DOI: 10.1371/journal.pone.0000360] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 03/19/2007] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The great diversity of the "Phytophaga" (weevils, longhorn beetles and leaf beetles) has been attributed to their co-radiation with the angiosperms based on matching age estimates for both groups, but phylogenetic information and molecular clock calibrations remain insufficient for this conclusion. METHODOLOGY A phylogenetic analysis of the leaf beetles (Chrysomelidae) was conducted based on three partial ribosomal gene markers (mitochondrial rrnL, nuclear small and large subunit rRNA) including over 3000 bp for 167 taxa representing most major chrysomelid lineages and outgroups. Molecular clock calibrations and confidence intervals were based on paleontological data from the oldest (K-T boundary) leaf beetle fossil, ancient feeding traces ascribed to hispoid Cassidinae, and the vicariant split of Nearctic and Palearctic members of the Timarchini. PRINCIPAL FINDINGS The origin of the Chrysomelidae was dated to 73-79 Mya (confidence interval 63-86 Mya), and most subfamilies were post-Cretaceous, consistent with the ages of all confirmed body fossils. Two major monocot feeding chrysomelid lineages formed widely separated clades, demonstrating independent colonization of this ancient (early Cretaceous) angiosperm lineage. CONCLUSIONS Previous calibrations proposing a much older origin of Chrysomelidae were not supported. Therefore, chrysomelid beetles likely radiated long after the origin of their host lineages and their diversification was driven by repeated radiaton on a pre-existing diverse resource, rather than ancient host associations.
Collapse
Affiliation(s)
- Jesús Gómez-Zurita
- Department of Entomology, Natural History Museum, London, United Kindgom.
| | | | | | | |
Collapse
|
48
|
Jouannic S, Collin M, Vidal B, Verdeil JL, Tregear JW. A class I KNOX gene from the palm species Elaeis guineensis (Arecaceae) is associated with meristem function and a distinct mode of leaf dissection. THE NEW PHYTOLOGIST 2007; 174:551-568. [PMID: 17447911 DOI: 10.1111/j.1469-8137.2007.02020.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Class I Knotted-like homeobox (KNOX) transcription factors are important regulators of shoot apical meristem function and leaf morphology by their contribution to dissected leaf development. Palms are of particular interest as they produce dissected leaves generated by a distinct mechanism compared with eudicots. The question addressed here was whether class I KNOX genes might be involved in meristem function and leaf dissection in palms. Here, we characterized the EgKNOX1 gene from oil palm (Elaeis guineensis, Arecaceae) and compared it with available sequences from other plant species using phylogenetic analysis. Gene expression pattern was investigated using reverse transcription-polymerase chain reaction (RT-PCR) and in situ hybridization. Functional analysis was carried out by ectopic expression in Arabidopsis and rice. EgKNOX1 was orthologous to STM from Arabidopsis and to OSH1 from rice. It was expressed in the central zone of both vegetative and reproductive meristems. During leaf development, its expression was associated with plications from which the leaflets originate. Different modes of leaf dissection are seen to involve a similar class of genes to control meristematic activities, which govern the production of dissected morphologies.
Collapse
Affiliation(s)
- Stefan Jouannic
- IRD/CIRAD Palm Group, UMR 1098, Centre IRD Montpellier, 911 avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Myriam Collin
- IRD/CIRAD Palm Group, UMR 1098, Centre IRD Montpellier, 911 avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Benjamin Vidal
- IRD/CIRAD Palm Group, UMR 1098, Centre IRD Montpellier, 911 avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Jean-Luc Verdeil
- Plateau d'Histocytologie et d'Imagerie Cellulaire Végétale, IFR 127, TA/40/02, CIRAD, Avenue Agropolis, F-34398 Montpellier cedex 5, France
| | - James W Tregear
- IRD/CIRAD Palm Group, UMR 1098, Centre IRD Montpellier, 911 avenue Agropolis, 34394 Montpellier cedex 5, France
| |
Collapse
|
49
|
Joung YH, Kamo K. Expression of a polyubiquitin promoter isolated from Gladiolus. PLANT CELL REPORTS 2006; 25:1081-8. [PMID: 16761144 DOI: 10.1007/s00299-006-0185-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Revised: 05/10/2006] [Accepted: 05/17/2006] [Indexed: 05/09/2023]
Abstract
A polyubiquitin promoter (GUBQ1) including its 5'UTR and intron was isolated from the floral monocot Gladiolus because high levels of expression could not be obtained using publicly available promoters isolated from either cereals or dicots. Sequencing of the promoter revealed highly conserved 5' and 3' intron splicing sites for the 1.234 kb intron. The coding sequence of the first two ubiquitin genes showed the highest homology (87 and 86%, respectively) to the ubiquitin genes of Nicotiana tabacum and Oryza sativa RUBQ2. Transient expression following gene gun bombardment showed that relative levels of GUS activity with the GUBQ1 promoter were comparable to the CaMV 35S promoter in gladiolus, tobacco, rose, rice, and the floral monocot freesia. The highest levels of GUS expression with GUBQ1 were attained with Gladiolus. The full-length GUBQ1 promoter including 5'UTR and intron were necessary for maximum GUS expression in Gladiolus. The relative GUS activity for the promoter only was 9%, and the activity for the promoter with 5'UTR and 399 bp of the full-length 1.234 kb intron was 41%. Arabidopsis plants transformed with uidA under GUBQ1 showed moderate GUS expression throughout young leaves and in the vasculature of older leaves. The highest levels of transient GUS expression in Gladiolus have been achieved using the GUBQ1 promoter. This promoter should be useful for genetic engineering of disease resistance in Gladiolus, rose, and freesia, where high levels of gene expression are important.
Collapse
Affiliation(s)
- Young Hee Joung
- School of Biological Science and Technology, Chonnam National University, Gwangju 500-757, Korea
| | | |
Collapse
|
50
|
McKenna DD, Farrell BD. Tropical forests are both evolutionary cradles and museums of leaf beetle diversity. Proc Natl Acad Sci U S A 2006; 103:10947-51. [PMID: 16818884 PMCID: PMC1544154 DOI: 10.1073/pnas.0602712103] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Indexed: 11/18/2022] Open
Abstract
The high extant species diversity of tropical lineages of organisms is usually portrayed as a relatively recent and rapid development or as a consequence of the gradual accumulation or preservation of species over time. These explanations have led to alternative views of tropical forests as evolutionary "cradles" or "museums" of diversity, depending on the organisms under study. However, biogeographic and fossil evidence implies that the evolutionary histories of diversification among tropical organisms may be expected to exhibit characteristics of both cradle and museum models. This possibility has not been explored in detail for any group of terrestrial tropical organisms. From an extensively sampled molecular phylogeny of herbivorous Neotropical leaf beetles in the genus Cephaloleia, we present evidence for (i) comparatively ancient Paleocene-Eocene adaptive radiation associated with global warming and Cenozoic maximum global temperatures, (ii) moderately ancient lineage-specific diversification coincident with the Oligocene adaptive radiation of Cephaloleia host plants in the genus Heliconia, and (iii) relatively recent Miocene-Pliocene diversification coincident with the collision of the Panama arc with South America and subsequent bridging of the Isthmus of Panama. These results demonstrate that, for Cephaloleia and perhaps other lineages of organisms, tropical forests are at the same time both evolutionary cradles and museums of diversity.
Collapse
Affiliation(s)
- Duane D McKenna
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | | |
Collapse
|