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Guo X, Wang F, Fang D, Lin Q, Sahu SK, Luo L, Li J, Chen Y, Dong S, Chen S, Liu Y, Luo S, Guo Y, Liu H. The genome of Acorus deciphers insights into early monocot evolution. Nat Commun 2023; 14:3662. [PMID: 37339966 PMCID: PMC10281966 DOI: 10.1038/s41467-023-38836-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Acorales is the sister lineage to all the other extant monocot plants. Genomic resource enhancement of this genus can help to reveal early monocot genomic architecture and evolution. Here, we assemble the genome of Acorus gramineus and reveal that it has ~45% fewer genes than the majority of monocots, although they have similar genome size. Phylogenetic analyses based on both chloroplast and nuclear genes consistently support that A. gramineus is the sister to the remaining monocots. In addition, we assemble a 2.2 Mb mitochondrial genome and observe many genes exhibit higher mutation rates than that of most angiosperms, which could be the reason leading to the controversies of nuclear genes- and mitochondrial genes-based phylogenetic trees existing in the literature. Further, Acorales did not experience tau (τ) whole-genome duplication, unlike majority of monocot clades, and no large-scale gene expansion is observed. Moreover, we identify gene contractions and expansions likely linking to plant architecture, stress resistance, light harvesting, and essential oil metabolism. These findings shed light on the evolution of early monocots and genomic footprints of wetland plant adaptations.
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Affiliation(s)
- Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Qiongqiong Lin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Liuming Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Jiani Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Sisi Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yalong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, PR China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, Heilongjiang, 150040, PR China.
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Chen LY, Lu B, Morales-Briones DF, Moody ML, Liu F, Hu GW, Huang CH, Chen JM, Wang QF. Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments. Mol Biol Evol 2022; 39:msac079. [PMID: 35438770 PMCID: PMC9070837 DOI: 10.1093/molbev/msac079] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptations to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptations, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the three main clades that was best explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light- or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and WGDs using phylogenomics.
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Affiliation(s)
- Ling-Yun Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Bei Lu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Diego F. Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
- Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 Munich, Germany
| | - Michael L. Moody
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA
| | - Fan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jin-Ming Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Severova EE, Rudall PJ, Macfarlane TD, Krasnova ED, Sokoloff DD. Pollen in water of unstable salinity: Evolution and function of dynamic apertures in monocot aquatics. AMERICAN JOURNAL OF BOTANY 2022; 109:500-513. [PMID: 35244214 DOI: 10.1002/ajb2.1835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
PREMISE The sporoderm of seed-plant pollen grains typically has apertures in which the outer sporopollenin-bearing layer is relatively sparse. The apertures allow regulation of the internal volume of the pollen grain during desiccation and rehydration (harmomegathy) and also serve as sites of pollen germination. A small fraction of angiosperms undergo pollination in water or at the water surface, where desiccation is unlikely. Their pollen grains commonly lack apertures, though with some notable exceptions. We tested a hypothesis that in some angiosperm aquatics that inhabit water of unstable salinity, the pollen apertures accommodate osmotic effects that occur during pollination in such conditions. METHODS Pollen grains of the tepaloid clade of the monocot order Alismatales, which contains ecologically diverse aquatic and marshy plants, were examined using light microscopy and scanning electron microscopy. We used Ruppia as a model to test pollen grain response in water of various salinities. Pollen aperture evolution was also analyzed using molecular tree topologies. RESULTS Phylogenetic optimizations demonstrated an evolutionary loss and two subsequent regains of the aperturate condition in the tepaloid clade of Alismatales. Both of the taxa that have reverted to aperturate pollen (Ruppia, Ruppiaceae; Althenia, Potamogetonaceae) are adapted to changeable water salinity. Direct experiments with Ruppia showed that the pollen apertures have a role in a harmomegathic response to differences in water salinity. CONCLUSIONS Our results showed that the inferred regain of pollen apertures represents an adaptation to changeable water salinity. We invoke a loss-and-regain scenario, prompting questions that are testable using developmental genetics and plant physiology.
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Affiliation(s)
- Elena E Severova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, Moscow, 119234, Russia
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Terry D Macfarlane
- Western Australian Herbarium, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, WA, 6983, Australia
| | - Elena D Krasnova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, Moscow, 119234, Russia
| | - Dmitry D Sokoloff
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, Moscow, 119234, Russia
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Li ZZ, Lehtonen S, Martins K, Wang QF, Chen JM. Complete genus-level plastid phylogenomics of Alismataceae with revisited historical biogeography. Mol Phylogenet Evol 2021; 166:107334. [PMID: 34715331 DOI: 10.1016/j.ympev.2021.107334] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/19/2022]
Abstract
Alismataceae, an ancient lineage of monocots, has attracted attention due to its complex evolutionary history, ornamental value, and ecological role. However, the phylogenetic relationships and evolutionary history of the family have not been conclusively resolved. Here, we constructed the first complete genus-level plastid phylogeny of Alismataceae by using 78 genes and updated the historical biogeography based on the phylogenomic tree. Our results divide the Alismataceae into three major clades with robust support values; one clade comprises the former Limnocharitaceae, and the second clade includes the mainly temperate genera Alisma, Baldellia, Damasonium and Luronium, and the monotypic African genus Burnatia as a sister of the temperate genera. The remaining genera are either tropical or have some temperate species in addition to tropical ones, and they constitute the third major clade. Molecular dating and biogeographic analyses suggest that Alismataceae arose in Neotropical, West Palearctic, and Afrotropical regions during the Cretaceous, followed by the split into three main clades due to a combination of vicariance and dispersal events. Unlike earlier studies, we inferred that the mainly temperate clade likely originated from Afrotropical and West Palearctic regions during the Eocene. The most recent common ancestor of the other two clades lived in the Neotropical area during the Late Cretaceous. Long-distance dispersal and vicariance together seem to contribute to the transoceanic distribution of this family.
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Affiliation(s)
- Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Samuli Lehtonen
- Herbarium, Biodiversity Unit, University of Turku, Turku 20014, Finland
| | - Karina Martins
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba 18052-780, Brazil
| | - Qing-Feng Wang
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jin-Ming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.
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Chen J, Zang Y, Shang S, Liang S, Zhu M, Wang Y, Tang X. Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass. FRONTIERS IN PLANT SCIENCE 2021; 12:741152. [PMID: 34630493 PMCID: PMC8495015 DOI: 10.3389/fpls.2021.741152] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/23/2021] [Indexed: 05/29/2023]
Abstract
Seagrasses are marine flowering plants found in tropical and sub-tropical areas that live in coastal regions between the sea and land. All seagrass species evolved from terrestrial monocotyledons, providing the opportunity to study plant adaptation to sea environments. Here, we sequenced the chloroplast genomes (cpGenomes) of three Zostera species, then analyzed and compared their cpGenome structures and sequence variations. We also performed a phylogenetic analysis using published seagrass chloroplasts and calculated the selection pressure of 17 species within seagrasses and nine terrestrial monocotyledons, as well as estimated the number of shared genes of eight seagrasses. The cpGenomes of Zosteraceae species ranged in size from 143,877 bp (Zostera marina) to 152,726 bp (Phyllospadix iwatensis), which were conserved and displayed similar structures and gene orders. Additionally, we found 17 variable hotspot regions as candidate DNA barcodes for Zosteraceae species, which will be helpful for studying the phylogenetic relationships and interspecies differences between seagrass species. Interestingly, nine genes had positive selection sites, including two ATP subunit genes (atpA and atpF), two ribosome subunit genes (rps4 and rpl20), two DNA-dependent RNA polymerase genes (rpoC1 and rpoC2), as well as accD, clpP, and ycf2. These gene regions may have played key roles in the seagrass adaptation to diverse environments. The Branch model analysis showed that seagrasses had a higher rate of evolution than terrestrial monocotyledons, suggesting that seagrasses experienced greater environmental pressure. Moreover, a branch-site model identified positively selected sites (PSSs) in ccsA, suggesting their involvement in the adaptation to sea environments. These findings are valuable for further investigations on Zosteraceae cpGenomes and will serve as an excellent resource for future studies on seagrass adaptation to sea environments.
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Affiliation(s)
- Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Shuai Shang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Shuo Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiling Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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6
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Stockey RA, Hoffman GL, Rothwell GW. Fossil evidence for Paleocene diversification of Araceae: Bognerospadix gen. nov. and Orontiophyllum grandifolium comb. nov. AMERICAN JOURNAL OF BOTANY 2021; 108:1417-1440. [PMID: 34431509 DOI: 10.1002/ajb2.1707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/28/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Nearly 200 araceous leaves and two spadices have been identified among Paleocene fossils from the Blindman River locality near Blackfalds, Alberta, Canada. Although not found in attachment, these probably represent parts of the same extinct plant species. METHODS Specimens were studied using light microscopy. Phylogenetic analyses using a morphological matrix of living and fossil Araceae were performed using TNT version 1.5 to help establish relationships of the fossil leaves and spadices within Araceae and to each other. RESULTS Leaves are simple with a broad petiole, entire margin, and elliptic to ovate or oblong blade with an acute to slightly rounded apex. A multi-veined midrib extends into the basal region of the blade. Parallelodromous primary veins of two orders diverge at acute angles, converging with a submarginal vein or at the apex. Transverse veins are opposite percurrent, producing rectangular to polygonal areoles. Higher-order veins are mixed opposite/alternate. Spadices are cylindrical, with helically arranged, bisexual, perigoniate flowers, each with six free tepals and a protruding style. Fruits are trilocular, with axile placentation and one seed per locule. CONCLUSIONS Leaves are assignable to the fossil genus Orontiophyllum J. Kvaček & S.Y. Sm. as O. grandifolium comb. nov. Spadices are described as Bognerospadix speirsiae gen. et sp. nov. Leaves and spadices each conform to an early-diverging lineage of Araceae, increasing the known diversity of Proto-Araceae (viz., subfamilies Gymnostachydoideae and Orontioideae). Together, they provide strong evidence for extinct Proto-Araceae with novel combinations of characters shortly after the Cretaceous-Paleogene floral transition.
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Affiliation(s)
- Ruth A Stockey
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Georgia L Hoffman
- G. Hoffman Consulting Services, 1914 5th St. SW, Calgary, Alberta T2S 2B3, Canada
| | - Gar W Rothwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701, USA
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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.
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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
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Lee H, Golicz AA, Bayer PE, Severn-Ellis AA, Chan CKK, Batley J, Kendrick GA, Edwards D. Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3689-3702. [PMID: 29912443 PMCID: PMC6022596 DOI: 10.1093/jxb/ery147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 04/12/2018] [Indexed: 05/06/2023]
Abstract
Seagrasses are marine angiosperms that live fully submerged in the sea. They evolved from land plant ancestors, with multiple species representing at least three independent return-to-the-sea events. This raises the question of whether these marine angiosperms followed the same adaptation pathway to allow them to live and reproduce under the hostile marine conditions. To compare the basis of marine adaptation between seagrass lineages, we generated genomic data for Halophila ovalis and compared this with recently published genomes for two members of Zosteraceae, as well as genomes of five non-marine plant species (Arabidopsis, Oryza sativa, Phoenix dactylifera, Musa acuminata, and Spirodela polyrhiza). Halophila and Zosteraceae represent two independent seagrass lineages separated by around 30 million years. Genes that were lost or conserved in both lineages were identified. All three species lost genes associated with ethylene and terpenoid biosynthesis, and retained genes related to salinity adaptation, such as those for osmoregulation. In contrast, the loss of the NADH dehydrogenase-like complex is unique to H. ovalis. Through comparison of two independent return-to-the-sea events, this study further describes marine adaptation characteristics common to seagrass families, identifies species-specific gene loss, and provides molecular evidence for convergent evolution in seagrass lineages.
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Affiliation(s)
- HueyTyng Lee
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, WA, Australia
| | | | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - Gary A Kendrick
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, WA, Australia
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9
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Tobe H, Huang YL, Kadokawa T, Tamura MN. Floral structure and development in Nartheciaceae (Dioscoreales), with special reference to ovary position and septal nectaries. JOURNAL OF PLANT RESEARCH 2018; 131:411-428. [PMID: 29569170 DOI: 10.1007/s10265-018-1026-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
We present a comparative study of the floral structure and development of Nartheciaceae, a small dioscorealean family consisting of five genera (Aletris, Lophiola, Metanarthecium, Narthecium, and Nietneria). A noticeable diversity existed in nine floral characters. Analyses of their respective character states in the light of a phylogenetic context revealed that the flowers of Nartheciaceae, whose plesiomorphies occur in Aletris and Metanarthecium, have evolved toward in all or part of Lophiola, Narthecium, and Nietneria: (1) loss of a perianth tube; (2) stamen insertion at the perianth base; (3) congenital carpel fusion; (4) loss of the septal nectaries; (5) unilocular style; (6) unfused lateral carpellary margins in the style; (7) flower with the median outer tepal on the abaxial side; (8) flower with moniliform hairs; and (9) flower with weak monosymmetry. We further found that, as the flowers developed, the ovary shifted its position from inferior to superior. As a whole, their structure changes suggest that the Nartheciaceae flowers have evolved in close association with pollination and seed dispersal. By considering inferior ovaries and the presence of septal nectaries as plesiomorphies of Nartheciaceae, we discussed evolution of the ovary position and septal nectaries in all the monocots.
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Affiliation(s)
- Hiroshi Tobe
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
| | - Yu-Ling Huang
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
- National Museum of Natural Science, Guancian Rd., Taichung, 404, Taiwan
| | - Tomoki Kadokawa
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Minoru N Tamura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
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10
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Iwamoto A, Nakamura A, Kurihara S, Otani A, Ronse De Craene LP. Floral development of petaloid Alismatales as an insight into the origin of the trimerous Bauplan in monocot flowers. JOURNAL OF PLANT RESEARCH 2018; 131:395-407. [PMID: 29549525 DOI: 10.1007/s10265-018-1022-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Monocots are remarkably homogeneous in sharing a common trimerous pentacyclic floral Bauplan. A major factor affecting monocot evolution is the unique origin of the clade from basal angiosperms. The origin of the floral Bauplan of monocots remains controversial, as no immediate sister groups with similar structure can be identified among basal angiosperms, and there are several possibilities for an ancestral floral structure, including more complex flowers with higher stamen and carpel numbers, or strongly reduced flowers. Additionally, a stable Bauplan is only established beyond the divergence of Alismatales. Here, we observed the floral development of five members of the three 'petaloid' Alismatales families Butomaceae, Hydrocharitaceae, and Alismataceae. Outer stamen pairs can be recognized in mature flowers of Alismataceae and Butomaceae. Paired stamens always arise independently, and are either shifted opposite the sepals or close to the petals. The position of stamen pairs is related to the early development of the petals. In Butomaceae, the perianth is not differentiated and the development of the inner tepals is not delayed; the larger inner tepals (petals) only permit the initiation of stamens in antesepalous pairs. Alismataceae has delayed petals and the stamens are shifted close to the petals, leading to an association of stamen pairs with petals in so-called stamen-petal complexes. In the studied Hydrocharitaceae species, which have the monocot floral Bauplan, paired stamens are replaced by larger single stamens and the petals are not delayed. These results indicate that the origin of the floral Bauplan, at least in petaloid Alismatales, is closely linked to the position of stamen pairs and the rate of petal development. Although the petaloid Alismatales are not immediately at the base of monocot divergence, the floral evolution inferred from the results should be a key to elucidate the origin of the floral Bauplan of monocots.
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Affiliation(s)
- Akitoshi Iwamoto
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukui Kita-machi, Koganei-shi, Tokyo, 184-8501, Japan.
| | - Ayaka Nakamura
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukui Kita-machi, Koganei-shi, Tokyo, 184-8501, Japan
| | - Shinichi Kurihara
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukui Kita-machi, Koganei-shi, Tokyo, 184-8501, Japan
| | - Ayumi Otani
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukui Kita-machi, Koganei-shi, Tokyo, 184-8501, Japan
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Tian N, Han L, Chen C, Wang Z. The complete chloroplast genome sequence of Epipremnum aureum and its comparative analysis among eight Araceae species. PLoS One 2018. [PMID: 29529038 PMCID: PMC5846728 DOI: 10.1371/journal.pone.0192956] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epipremnum aureum is an important foliage plant in the Araceae family. In this study, we have sequenced the complete chloroplast genome of E. aureum by using Illumina Hiseq sequencing platforms. This genome is a double-stranded circular DNA sequence of 164,831 bp that contains 35.8% GC. The two inverted repeats (IRa and IRb; 26,606 bp) are spaced by a small single-copy region (22,868 bp) and a large single-copy region (88,751 bp). The chloroplast genome has 131 (113 unique) functional genes, including 86 (79 unique) protein-coding genes, 37 (30 unique) tRNA genes, and eight (four unique) rRNA genes. Tandem repeats comprise the majority of the 43 long repetitive sequences. In addition, 111 simple sequence repeats are present, with mononucleotides being the most common type and di- and tetranucleotides being infrequent events. Positive selection pressure on rps12 in the E. aureum chloroplast has been demonstrated via synonymous and nonsynonymous substitution rates and selection pressure sites analyses. Ycf15 and infA are pseudogenes in this species. We constructed a Maximum Likelihood phylogenetic tree based on the complete chloroplast genomes of 38 species from 13 families. Those results strongly indicated that E. aureum is positioned as the sister of Colocasia esculenta within the Araceae family. This work may provide information for further study of the molecular phylogenetic relationships within Araceae, as well as molecular markers and breeding novel varieties by chloroplast genetic-transformation of E. aureum in particular.
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Affiliation(s)
- Na Tian
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P.R. China
| | - Limin Han
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P.R. China
- Department of Bioscience and Biotechnology, Shaanxi Xueqian Normal University, Xi’an, Shaanxi, P.R. China
| | - Chen Chen
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P.R. China
- Institute of Botany of Shaanxi Province, Xi’an Botanical Garden of Shaanxi Province, Xi’an, Shaanxi, P.R. China
| | - Zhezhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P.R. China
- * E-mail:
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Matias LQ, Gonzalez HHES, Oliveira WRD. Flora do Ceará: Hydrocharitaceae e as fanerógamas marinhas: Cymodoceaceae, Ruppiaceae. RODRIGUÉSIA 2017. [DOI: 10.1590/2175-7860201768415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Resumo As áreas inundadas continentais e a região costeira do estado do Ceará apresentam comunidades vegetais aquáticas constituídas por Angiospermas. Espécies pertencentes às famílias Hydrocharitaceae, Cymodoceaceae e Ruppiaceae são comumente encontrados nestes ambientes, constituindo relvados marinhos ou de água doce, submersos ou emersos. Este trabalho apresenta o estudo florístico destas famílias, descrevendo representantes dos gêneros Apalanthe, Egeria, Najas, Limnobium, Halophila, Halodule e Ruppia, estes três últimos também reconhecidos pela denominação de "fanerógamas marinhas". Um total de nove táxons pertencentes à Hydrocharitaceae foram registrados para o Ceará: Apalanthe granatensis, Egeria densa, E. najas, Limnobium laevigatum, Najas arguta var. arguta, Najas arguta var. podostemon, N. conferta, N. marina e Halophila decipiens. Além destas, a ocorrência de Halodule wrightii (Cymodoceaceae ) foi registrada em toda a extensão litorânea, enquanto Ruppia maritima (Ruppiaceae) em áreas estuarinas. A maioria das espécies continentais registradas foi encontrada na região central semiárida do Estado do Ceará. Neste trabalho são apresentadas descrições, comentários taxonômicos, chaves de identificação, ilustrações e dados de distribuição geográfica das espécies.
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Petersen G, Cuenca A, Zervas A, Ross GT, Graham SW, Barrett CF, Davis JI, Seberg O. Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes. PLoS One 2017; 12:e0177606. [PMID: 28545148 PMCID: PMC5435185 DOI: 10.1371/journal.pone.0177606] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/28/2017] [Indexed: 11/18/2022] Open
Abstract
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.
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Affiliation(s)
- Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Argelia Cuenca
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Athanasios Zervas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gregory T. Ross
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig F. Barrett
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Cuenca A, Ross TG, Graham SW, Barrett CF, Davis JI, Seberg O, Petersen G. Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome. Genome Biol Evol 2016; 8:2176-89. [PMID: 27435795 PMCID: PMC4987113 DOI: 10.1093/gbe/evw148] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 12/23/2022] Open
Abstract
Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.
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Affiliation(s)
- Argelia Cuenca
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - T Gregory Ross
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W Graham
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles, California
| | - Jerrold I Davis
- L.H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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15
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Ross TG, Barrett CF, Soto Gomez M, Lam VK, Henriquez CL, Les DH, Davis JI, Cuenca A, Petersen G, Seberg O, Thadeo M, Givnish TJ, Conran J, Stevenson DW, Graham SW. Plastid phylogenomics and molecular evolution of Alismatales. Cladistics 2015; 32:160-178. [DOI: 10.1111/cla.12133] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/27/2022] Open
Affiliation(s)
- T. Gregory Ross
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Craig F. Barrett
- Department of Biological Sciences 5151 State University Dr. California State University Los Angeles CA 90032‐8201 USA
| | - Marybel Soto Gomez
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Vivienne K.Y. Lam
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Claudia L. Henriquez
- Evolution, Ecology & Population Biology Division of Biology Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Donald H. Les
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT 06269‐3043 USA
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Section of Plant Biology Cornell University Ithaca NY 14853 USA
| | - Argelia Cuenca
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Ole Seberg
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | | | | | - John Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre School of Biological Sciences Benham Bldg DX 650 312 The University of Adelaide Adelaide SA 5005 Australia
| | | | - Sean W. Graham
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
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