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Li M, Pu J, Jia C, Luo D, Zhou Q, Fang X, Nie B, Liu W, Nan Z, Searle IR, Fang L, Liu Z. The genome of Vicia sativa ssp. amphicarpa provides insights into the role of terpenoids in antimicrobial resistance within subterranean fruits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39039964 DOI: 10.1111/tpj.16939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024]
Abstract
Vicia sativa ssp. amphicarpa is a unique forage crop capable of simultaneously producing fruits above and below ground, representing a typical amphicarpic plant. In this study, we sequenced and assembled seven pseudo-chromosomes of the genome of V. sativa ssp. amphicarpa (n = 7) yielding a genome size of 1.59 Gb, with a total annotation of 48 932 protein-coding genes. Long terminal repeat (LTR) elements constituted 62.28% of the genome, significantly contributing to the expansion of genome size. Phylogenetic analysis revealed that the divergence between V. sativa ssp. amphicarpa and V. sativa was around 0.88 million years ago (MYA). Comparative transcriptomic and metabolomic analysis of aerial and subterranean pod shells showed biosynthesis of terpenoids in the subterranean pod shells indicating a correlation between the antimicrobial activity of subterranean pod shells and the biosynthesis of terpenoids. Furthermore, functional validation indicates that overexpression of VsTPS5 and VsTPS16 enhances terpenoid biosynthesis for antibacterial activity. Metabolomic analysis suggests the involvement of terpenoids in the antimicrobial properties of subterranean pod shells. Deciphering the genome of V. sativa ssp. amphicarpa elucidated the molecular mechanisms behind the antimicrobial properties of subterranean fruits in amphicarpic plants, providing valuable insights for the study of amphicarpic plant biology.
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Affiliation(s)
- Mingyu Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jun Pu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Chenglin Jia
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Dong Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Qiang Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xiangling Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Bin Nie
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Wenxian Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Iain Robert Searle
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
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Meyer EM, Swift JF, Bassüner B, Smith SA, Menges ES, Oberle B, Edwards CE. Understanding how an amphicarpic species with a mixed mating system responds to fire: a population genetic approach. AOB PLANTS 2021; 13:plab067. [PMID: 34858568 PMCID: PMC8633637 DOI: 10.1093/aobpla/plab067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Amphicarpic plants produce both above-ground and below-ground seeds. Because below-ground seeds are protected in the soil and may maintain viability when above-ground conditions are stressful, they were proposed as an adaptation to recolonize a site after disturbance. However, whether below-ground seeds are the main colonizers after a disturbance remains unknown. Our goal was to understand whether recolonization by an amphicarpic species after fire was accomplished primarily through germination of seeds produced above-ground or below-ground. We investigated Polygala lewtonii, an amphicarpic, perennial species endemic to fire-prone Florida sandhill and scrub, where fire kills plants but subsequently increases recruitment and population sizes. Polygala lewtonii produces three flower types: above-ground chasmogamous flowers and above-ground and below-ground cleistogamous flowers, with previous research demonstrating chasmogamous flowers produce a much greater proportion of seeds than cleistogamous flowers. We quantified outcrossing in seeds produced by chasmogamous flowers to determine whether it differed from the 100 % self-fertilized below-ground seeds. Approximately 25 % of seeds from chasmogamous flowers showed evidence of cross-pollination. Assuming that chasmogamous flowers produce the majority of the above-ground seeds, as was shown previously, this indicates it is possible to differentiate between germination by above-ground versus below-ground seeds in post-fire colonization. We next compared genetic diversity, admixture, inbreeding and population genetic structure pre- and post-fire. If fire promoted germination of chasmogamous seeds, heterozygosity and admixture would increase, and genetic structure and inbreeding would decrease. Instead, inbreeding and genetic structure increased and admixture decreased, suggesting that the below-ground selfed seeds (with limited dispersal ability) increased their contribution to the population after fire, possibly because fire reduced above-ground seed viability. Additionally, new alleles not found previously in range-wide analyses emerged from the seed bank post-fire. These results suggest that amphicarpy is a powerful adaptation to preserve genetic variation, maintain adaptive potential and promote rapid post-fire colonization.
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Affiliation(s)
- Elena M Meyer
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA
- Division of Natural Sciences, New College of Florida, 5800 Bay Shore Road, Sarasota, FL 34243, USA
| | - Joel F Swift
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA
| | - Burgund Bassüner
- Present address: Department of Biology, Saint Louis University, 1008 Spring Avenue, St. Louis, MO 63110, USA
| | - Stacy A Smith
- Plant Ecology Program, Archbold Biological Station, 123 Main Drive, Venus, FL 33960, USA
| | - Eric S Menges
- Plant Ecology Program, Archbold Biological Station, 123 Main Drive, Venus, FL 33960, USA
| | - Brad Oberle
- Division of Natural Sciences, New College of Florida, 5800 Bay Shore Road, Sarasota, FL 34243, USA
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA
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Germinative behaviour of Acacia dealbata Link, Ailanthus altissima (Mill.) Swingle and Robinia pseudoacacia L. in relation to fire and exploration of the regenerative niche of native species for the control of invaders. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Zhang K, Baskin JM, Baskin CC, Cheplick GP, Yang X, Huang Z. Amphicarpic plants: definition, ecology, geographic distribution, systematics, life history, evolution and use in agriculture. Biol Rev Camb Philos Soc 2020; 95:1442-1466. [PMID: 32462729 PMCID: PMC7540684 DOI: 10.1111/brv.12623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022]
Abstract
Although most plants produce all of their fruits (seeds) aboveground, amphicarpic species produce fruits (seeds) both above‐ and belowground. Our primary aims were to determine the number of reported amphicarpic species and their taxonomic, geographic, life form and phylogenetic distribution, to evaluate differences in the life history of plants derived from aerial and subterranean seeds, to discuss the ecological and evolutionary significance of amphicarpy, to explore the use of amphicarpic plants in agriculture, and to suggest future research directions for studies on amphicarpy. Amphicarpy occurs in at least 67 herbaceous species (31 in Fabaceae) in 39 genera and 13 families of angiosperms distributed in various geographical regions of the world and in various habitats. Seeds from aerial and subterranean fruits differ in size/mass, degree of dormancy, dispersal and ability to form a persistent seed bank, with aerial seeds generally being smaller, more dormant and more likely to be dispersed and to form a seed bank than subterranean seeds. In addition, plants produced by aerial and subterranean seeds may differ in survival and growth, competitive ability and biomass allocation to reproduction. Amphicarpic plants may exhibit a high degree of plasticity during reproduction. Subterranean fruits are usually formed earlier than aerial ones, and plants may produce only subterranean propagules under stressful environmental conditions. Differences in the life histories of plants from aerial and subterranean seeds may be an adaptive bet‐hedging strategy.
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Affiliation(s)
- Keliang Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China.,Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, P.R. China
| | - Jerry M Baskin
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | - Carol C Baskin
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA.,Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Gregory P Cheplick
- Department of Biology, City University of New York, Staten Island, NY, 10314, USA
| | - Xuejun Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China
| | - Zhenying Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China
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Guthrie SG, Crandall RM, Knight TM. Fire indirectly benefits fitness in two invasive species. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1064-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Shah V, Shah S, Kambhampati MS, Ambrose J, Smith N, Dowd SE, McDonnell KT, Panigrahi B, Green T. Bacterial and archaea community present in the Pine Barrens Forest of Long Island, NY: unusually high percentage of ammonia oxidizing bacteria. PLoS One 2011; 6:e26263. [PMID: 22028845 PMCID: PMC3197628 DOI: 10.1371/journal.pone.0026263] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 09/23/2011] [Indexed: 12/23/2022] Open
Abstract
Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0-10 cm (Horizon O); 11-25 cm (Horizon A) and 26-40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil.
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Affiliation(s)
- Vishal Shah
- Department of Biology, Dowling College, Oakdale, New York, United States of America.
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Myster RW. Species-specific effects of grass litter mass and type on emergence of three tall grass prairie species. ECOSCIENCE 2006. [DOI: 10.2980/1195-6860(2006)13[95:seoglm]2.0.co;2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Maret MP, Wilson MV. Fire and Litter Effects on Seedling Establishment in Western Oregon Upland Prairies. Restor Ecol 2005. [DOI: 10.1111/j.1526-100x.2005.00071.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Carson WP, Peterson CJ. The role of litter in an old-field community: impact of litter quantity in different seasons on plant species richness and abundance. Oecologia 1990; 85:8-13. [DOI: 10.1007/bf00317337] [Citation(s) in RCA: 158] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/1989] [Accepted: 06/29/1990] [Indexed: 11/28/2022]
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