1
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Nishio H, Cano-Ramirez DL, Muranaka T, de Barros Dantas LL, Honjo MN, Sugisaka J, Kudoh H, Dodd AN. Circadian and environmental signal integration in a natural population of Arabidopsis. Proc Natl Acad Sci U S A 2024; 121:e2402697121. [PMID: 39172785 DOI: 10.1073/pnas.2402697121] [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: 02/13/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
Plants sense and respond to environmental cues during 24 h fluctuations in their environment. This requires the integration of internal cues such as circadian timing with environmental cues such as light and temperature to elicit cellular responses through signal transduction. However, the integration and transduction of circadian and environmental signals by plants growing in natural environments remains poorly understood. To gain insights into 24 h dynamics of environmental signaling in nature, we performed a field study of signal transduction from the nucleus to chloroplasts in a natural population of Arabidopsis halleri. Using several modeling approaches to interpret the data, we identified that the circadian clock and temperature are key regulators of this pathway under natural conditions. We identified potential time-delay steps between pathway components, and diel fluctuations in the response of the pathway to temperature cues that are reminiscent of the process of circadian gating. We found that our modeling framework can be extended to other signaling pathways that undergo diel oscillations and respond to environmental cues. This approach of combining studies of gene expression in the field with modeling allowed us to identify the dynamic integration and transduction of environmental cues, in plant cells, under naturally fluctuating diel cycles.
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Affiliation(s)
- Haruki Nishio
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
- Data Science and AI Innovation Research Promotion Center, Shiga University, Hikone, Shiga 522-8522, Japan
| | - Dora L Cano-Ramirez
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Tomoaki Muranaka
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-0814, Japan
| | | | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Jiro Sugisaka
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Antony N Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7RU, United Kingdom
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2
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Tabara M, Uraguchi S, Kiyono M, Watanabe I, Takeda A, Takahashi H, Fukuhara T. A resilient mutualistic interaction between cucumber mosaic virus and its natural host to adapt to an excess zinc environment and drought stress. JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01573-w. [PMID: 39190237 DOI: 10.1007/s10265-024-01573-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024]
Abstract
A perennial pseudometallophyte Arabidopsis halleri is frequently infected with cucumber mosaic virus (CMV) in its natural habitat. The purpose of this study was to characterize the effect of CMV infection on the environmental adaptation of its natural host A. halleri. The CMV(Ho) strain isolated from A. halleri was inoculated into clonal virus-free A. halleri plants, and a unique plant-virus system consisting of CMV(Ho) and its natural wild plant host was established. In a control environment with ambient zinc supplementation, CMV(Ho) infection retarded growth in the above-ground part of host plants but conferred strong drought tolerance. On the other hand, in an excess zinc environment, simulating a natural edaphic environment of A halleri, host plants hyperaccumulated zinc and CMV(Ho) infection did not cause any symptoms to host plants while conferring mild drought tolerance. We also demonstrated in Nicotiana benthamiana as another host that similar effects were induced by the combination of excess zinc and CMV(Ho) infection. Transcriptomic analysis indicated that the host plant recognized CMV(Ho) as a mutualistic symbiont rather than a parasitic pathogen. These results suggest a resilient mutualistic interaction between CMV(Ho) and its natural host A. halleri in its natural habitat.
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Affiliation(s)
- Midori Tabara
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, 1-1-1, Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Shimpei Uraguchi
- Department of Public Health, School of Pharmacy, Kitasato University, Tokyo, 108-8641, Japan
| | - Masako Kiyono
- Department of Public Health, School of Pharmacy, Kitasato University, Tokyo, 108-8641, Japan
| | - Izumi Watanabe
- Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Atsushi Takeda
- College of Life Sciences, Ritsumeikan University, 1-1-1, Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, Aramaki-Aza-Aoba, 468-1, Sendai, 980-0845, Japan
| | - Toshiyuki Fukuhara
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
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3
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Yumoto G, Nishio H, Muranaka T, Sugisaka J, Honjo MN, Kudoh H. Seasonal switching of integrated leaf senescence controls in an evergreen perennial Arabidopsis. Nat Commun 2024; 15:4719. [PMID: 38849351 PMCID: PMC11161623 DOI: 10.1038/s41467-024-48814-z] [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: 07/22/2023] [Accepted: 05/10/2024] [Indexed: 06/09/2024] Open
Abstract
Evergreeness is a substantial strategy for temperate and boreal plants and is as common as deciduousness. However, whether evergreen plants switch foliage functions between seasons remains unknown. We conduct an in natura study of leaf senescence control in the evergreen perennial, Arabidopsis halleri. A four-year census of leaf longevity of 102 biweekly cohorts allows us to identify growth season (GS) and overwintering (OW) cohorts characterised by short and extended longevity, respectively, and to recognise three distinct periods in foliage functions, i.e., the growth, overwintering, and reproductive seasons. Photoperiods during leaf expansion separate the GS and OW cohorts, providing primal control of leaf senescence depending on the season, with leaf senescence being shut down during winter. Phenotypic and transcriptomic responses in field experiments indicate that shade-induced and reproductive-sink-triggered senescence are active during the growth and reproductive seasons, respectively. These secondary controls of leaf senescence cause desynchronised and synchronised leaf senescence during growth and reproduction, respectively. Conclusively, seasonal switching of leaf senescence optimises resource production, storage, and translocation for the season, making the evergreen strategy adaptively relevant.
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Affiliation(s)
- Genki Yumoto
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan.
| | - Haruki Nishio
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
- Data Science and AI Innovation Research Promotion Center, Shiga University, Banba 1-1-1, Hikone, 522-8522, Japan
| | - Tomoaki Muranaka
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-0814, Japan
| | - Jiro Sugisaka
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan.
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4
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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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5
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Zhang ZB, Xiong T, Wang XJ, Chen YR, Wang JL, Guo CL, Ye ZY. Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae. PLoS One 2024; 19:e0302292. [PMID: 38626181 PMCID: PMC11020792 DOI: 10.1371/journal.pone.0302292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.
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Affiliation(s)
- Zai-Bao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Xiao-Jia Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Yu-Rui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Jing-Lei Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Cong-Li Guo
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Zi-Yi Ye
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
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6
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Seki M, Kuze Y, Zhang X, Kurotani KI, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y. An improved method for the highly specific detection of transcription start sites. Nucleic Acids Res 2024; 52:e7. [PMID: 37994784 PMCID: PMC10810191 DOI: 10.1093/nar/gkad1116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Precise detection of the transcriptional start site (TSS) is a key for characterizing transcriptional regulation of genes and for annotation of newly sequenced genomes. Here, we describe the development of an improved method, designated 'TSS-seq2.' This method is an iterative improvement of TSS-seq, a previously published enzymatic cap-structure conversion method to detect TSSs in base sequences. By modifying the original procedure, including by introducing split ligation at the key cap-selection step, the yield and the accuracy of the reaction has been substantially improved. For example, TSS-seq2 can be conducted using as little as 5 ng of total RNA with an overall accuracy of 96%; this yield a less-biased and more precise detection of TSS. We then applied TSS-seq2 for TSS analysis of four plant species that had not yet been analyzed by any previous TSS method.
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Affiliation(s)
- Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yuta Kuze
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Xiang Zhang
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Nagoya, Japan
| | - Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Takuya Suzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Ibaraki, Japan
| | - Satoko Yoshida
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Sumio Sugano
- Institute of Kashiwa-no-ha Omics Gate, Chiba, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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7
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Komoto H, Nagahama A, Miyawaki-Kuwakado A, Hata Y, Kyozuka J, Kajita Y, Toyama H, Satake A. The transcriptional changes underlying the flowering phenology shift of Arabidopsis halleri in response to climate warming. PLANT, CELL & ENVIRONMENT 2024; 47:174-186. [PMID: 37691326 DOI: 10.1111/pce.14716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
Climate warming is causing shifts in key life-history events, including flowering time. To assess the impacts of increasing temperature on flowering phenology, it is crucial to understand the transcriptional changes of genes underlying the phenological shifts. Here, we conducted a comprehensive investigation of genes contributing to the flowering phenology shifts in response to increasing temperature by monitoring the seasonal expression dynamics of 293 flowering-time genes along latitudinal gradients in the perennial herb, Arabidopsis halleri. Through transplant experiments at northern, southern and subtropical study sites in Japan, we demonstrated that the flowering period was shortened as latitude decreased, ultimately resulting in the loss of flowering opportunity in subtropical climates. The key transcriptional changes underlying the shortening of the flowering period and the loss of flowering opportunity were the diminished expression of floral pathway integrator genes and genes in the gibberellin synthesis and aging pathways, all of which are suppressed by increased expression of FLOWERING LOCUS C, a central repressor of flowering. These results suggest that the upper-temperature limit of reproduction is governed by a relatively small number of genes that suppress reproduction in the absence of winter cold.
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Affiliation(s)
- Hideyuki Komoto
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Ai Nagahama
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | | | - Yuki Hata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yui Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hironori Toyama
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
- College of Arts and Sciences, J. F. Oberlin University, Machida, Tokyo, Japan
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
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8
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Otto M, Wiehe T. The structured coalescent in the context of gene copy number variation. Theor Popul Biol 2023; 154:67-78. [PMID: 37657649 DOI: 10.1016/j.tpb.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023]
Abstract
The Structured Coalescent was introduced to describe the coalescent process in spatially subdivided populations with migration. Here, we re-interpret migration routes of individuals in the original model as "migration routes" of single genes in tandemly arranged gene arrays. A gene copy may change its position within the array via unequal recombination. Hence, in a coalescent framework, two copies sampled from two chromosomes may coalesce only if they are at exactly homologous positions. Otherwise, one or multiple recombination events have to occur before they can coalesce, thereby increasing mean coalescence time and expected genetic diversity among the copies in a gene array. We explicitly calculate the transition probabilities on these routes backward in time. We simulate the structured coalescent with migration and coalescence rates informed by the unequal recombination process of gene copies. With this novel interpretation of population structure models we determine coalescence times and expected genetic diversity in samples of orthologous and paralogous copies from a gene family. As a case study, we discuss the site frequency spectrum of a small gene family in the two scenarios of high and of no gene copy number variation among individuals. These examples underline the significance of our model, since standard test-statistics may lead to misinterpretations when analyzing sequence data of multi-copy genes due to their different expected genetic diversity.
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Affiliation(s)
- Moritz Otto
- University of Cologne, Institute for Genetics, Zuelpicher Str. 47a, Cologne, 50674, Germany
| | - Thomas Wiehe
- University of Cologne, Institute for Genetics, Zuelpicher Str. 47a, Cologne, 50674, Germany.
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9
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Bramsiepe J, Krabberød AK, Bjerkan KN, Alling RM, Johannessen IM, Hornslien KS, Miller JR, Brysting AK, Grini PE. Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:942-961. [PMID: 37517071 DOI: 10.1111/tpj.16401] [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: 01/22/2023] [Revised: 05/24/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023]
Abstract
Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome-wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea, suggesting a genetic cause for the endosperm-based hybridization barrier between A. arenosa and A. lyrata ssp. petraea.
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Affiliation(s)
- Jonathan Bramsiepe
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Anders K Krabberød
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Katrine N Bjerkan
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Renate M Alling
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Ida M Johannessen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Karina S Hornslien
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Jason R Miller
- College of STEM, Shepherd University, Shepherdstown, West Virginia, 25443-5000, USA
| | - Anne K Brysting
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Paul E Grini
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
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10
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Akiyama R, Goto T, Tameshige T, Sugisaka J, Kuroki K, Sun J, Akita J, Hatakeyama M, Kudoh H, Kenta T, Tonouchi A, Shimahara Y, Sese J, Kutsuna N, Shimizu-Inatsugi R, Shimizu KK. Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation. Nat Commun 2023; 14:5792. [PMID: 37737204 PMCID: PMC10517152 DOI: 10.1038/s41467-023-41260-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/29/2023] [Indexed: 09/23/2023] Open
Abstract
Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software that extracts leaf color by detecting plant individuals automatically. As a case study, we applied PlantServation to examine environmental and genotypic effects on the pigment anthocyanin content estimated from leaf color. We processed >4 million images of small individuals of four Arabidopsis species in the field, where the plant shape, color, and background vary over months. Past radiation, coldness, and precipitation significantly affected the anthocyanin content. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation facilitates the study of plant responses to complex environments termed "in natura".
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Affiliation(s)
- Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Takao Goto
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192, Japan
| | - Jiro Sugisaka
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Ken Kuroki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Jianqiang Sun
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8517, Japan
| | - Junichi Akita
- Department of Electric and Computer Engineering, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Tanaka Kenta
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-kogen, Ueda, 386-2204, Japan
| | - Aya Tonouchi
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yuki Shimahara
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Humanome Lab, Inc., L-HUB 3F, 1-4, Shumomiyabi-cho, Shinjuku, Tokyo, 162-0822, Japan
- AIST-Tokyo Tech RWBC-OIL, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Natsumaro Kutsuna
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan.
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11
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Kolesnikova UK, Scott AD, Van de Velde JD, Burns R, Tikhomirov NP, Pfordt U, Clarke AC, Yant L, Seregin AP, Vekemans X, Laurent S, Novikova PY. Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes. Mol Biol Evol 2023; 40:msad122. [PMID: 37432770 PMCID: PMC10335350 DOI: 10.1093/molbev/msad122] [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] [Indexed: 07/13/2023] Open
Abstract
A transition to selfing can be beneficial when mating partners are scarce, for example, due to ploidy changes or at species range edges. Here, we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and how it contributed to the establishment of allotetraploid Arabidopsis kamchatica. First, we provide chromosome-level genome assemblies for two self-fertilizing diploid A. lyrata accessions, one from North America and one from Siberia, including a fully assembled S-locus for the latter. We then propose a sequence of events leading to the loss of self-incompatibility in Siberian A. lyrata, date this independent transition to ∼90 Kya, and infer evolutionary relationships between Siberian and North American A. lyrata, showing an independent transition to selfing in Siberia. Finally, we provide evidence that this selfing Siberian A. lyrata lineage contributed to the formation of the allotetraploid A. kamchatica and propose that the selfing of the latter is mediated by the loss-of-function mutation in a dominant S-allele inherited from A. lyrata.
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Affiliation(s)
- Uliana K Kolesnikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Alison Dawn Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jozefien D Van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Robin Burns
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nikita P Tikhomirov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Ursula Pfordt
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrew C Clarke
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
| | - Levi Yant
- Future Food Beacon of Excellence and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alexey P Seregin
- Herbarium (MW), Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Xavier Vekemans
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille, France
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Polina Yu Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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12
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Leal JL, Milesi P, Salojärvi J, Lascoux M. Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences. Syst Biol 2023; 72:372-390. [PMID: 36932679 PMCID: PMC10275558 DOI: 10.1093/sysbio/syad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 10/14/2022] [Accepted: 03/10/2023] [Indexed: 03/19/2023] Open
Abstract
Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing-to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid-while vastly simplifying its implementation by reducing a complex multistage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods-usually an expensive, complex, and/or time-consuming endeavor-phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization that, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read and short-read high-throughput sequencing data and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS) and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and Arabidopsis suecica, two allopolyploids whose ancestry has been well documented. [Allopolyploidy; Arabidopsis; genomic polarization; homoeologs; incomplete lineage sorting; phasing; polyploid phylogenetics; reticulate evolution.].
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Affiliation(s)
- J Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
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13
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Yoshida N, Morinaga SI, Wakamiya T, Ishii Y, Kubota S, Hikosaka K. Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient. JOURNAL OF PLANT RESEARCH 2023; 136:183-199. [PMID: 36547771 DOI: 10.1007/s10265-022-01429-1] [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: 07/03/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Adaptive divergence occurs even between insufficiently isolated populations when there is a great difference in environments between their habitats. Individuals present in an intermediate zone of the two divergent populations are expected to have an admixed genetic structure due to gene flow. A selective pressure that acts on the genetically admixed individuals may limit the gene flow and maintain the adaptive divergence. Here, we addressed a question whether selection occurs in the genetically admixed individuals between two divergent populations. Arabidopsis halleri is a perennial montane plant, which has clear phenotypic dimorphisms between highland and lowland habitats in Mt. Ibuki, central Japan. We obtained the whole-genome sequences of Arabidopsis halleri plants along an altitudinal gradient of 359-1,317 m with a high spatial resolution (mean altitudinal interval of 20 m). We found a zone where the highland and lowland genes were mixing (intermediate subpopulation). In the intermediate subpopulation, we identified 5 and 13 genome regions, which included 3 and 8 genes, that had a high frequency of alleles that are accumulated in highland and lowland subpopulations, respectively. In addition, we also found that the frequency of highland alleles of these selected genome regions was smaller in the lowland subpopulation compared with that of the non-selected regions. These results suggest that the selection in the intermediate subpopulation might limit the gene flow and contribute to the adaptive divergence between altitudes. We also identified 7 genome regions that had low heterozygote frequencies in the intermediate subpopulation. We conclude that different types of selection in addition to gene flow occur at the intermediate altitude and shape the genetic structure across altitudes.
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Affiliation(s)
- Naofumi Yoshida
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan.
| | - Shin-Ichi Morinaga
- Faculty of Life and Environmental Sciences, Teikyo University of Science, 120-0045, Adachi, Tokyo, Japan
| | - Takeshi Wakamiya
- Graduate School of Integrated Sciences for Life, Hiroshima University, 739-8528, Kagamiyama, Hiroshima, Higashi, Japan
| | - Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan
| | | | - Kouki Hikosaka
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan
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14
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Microbiome engineering for bioremediation of emerging pollutants. Bioprocess Biosyst Eng 2023; 46:323-339. [PMID: 36029349 DOI: 10.1007/s00449-022-02777-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.
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15
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Bai S, Han X, Feng D. Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1139744. [PMID: 36890896 PMCID: PMC9987563 DOI: 10.3389/fpls.2023.1139744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.
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Affiliation(s)
- Shiyan Bai
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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16
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Nishio H, Kudoh H. Distinct responses to autumn and spring temperatures by the key flowering-time regulator FLOWERING LOCUS C. Curr Opin Genet Dev 2023; 78:102016. [PMID: 36549195 DOI: 10.1016/j.gde.2022.102016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/10/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
Despite the similarity in temperature regimes between late autumn and early spring, plants exhibit distinct developmental responses that result in distinct morphologies, that is, overwintering and reproductive forms. In Arabidopsis, the control of autumn-spring distinction involves the transcriptional regulation of the floral repressor FLOWERING LOCUS C (FLC). The memory of winter cold is registered as epigenetic silencing of FLC. Recent studies on A. thaliana FLC revealed detailed and additional mechanisms of silencing in response to autumn and winter cold. Studies on perennial Arabidopsis FLC revealed that its expression responds to spring warmth and is robustly upregulated, ignoring cold. These new studies provide mechanistic insights into the distinct regulation of FLC under autumn and spring temperature regimes.
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Affiliation(s)
- Haruki Nishio
- Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan; Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga 522-8522, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan.
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17
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Shimizu-Inatsugi R, Morishima A, Mourato B, Shimizu KK, Sato Y. Phenotypic variation of a new synthetic allotetraploid Arabidopsis kamchatica enhanced in natural environment. FRONTIERS IN PLANT SCIENCE 2023; 13:1058522. [PMID: 36684772 PMCID: PMC9846130 DOI: 10.3389/fpls.2022.1058522] [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: 09/30/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The phenotypic variation of vegetative organs and reproductive organs of newly synthesized and natural Arabidopsis kamchatica genotypes was investigated in both a controlled environment and a natural environment in an experimental garden. When we compared the variation of their leaf shape as a vegetative organ, the synthetic A. kamchatica individuals grown in the garden showed larger variation compared with the individuals incubated in a growth chamber, suggesting enhanced phenotypic variation in a natural fluctuating environment. In contrast, the natural A. kamchatica genotypes did not show significant change in variation by growth condition. The phenotypic variation of floral organs by growth condition was much smaller in both synthetic and natural A. kamchatica genotypes, and the difference in variation width between the growth chamber and the garden was not significant in each genotype as well as among genotypes. The higher phenotypic variation in synthetic leaf may imply flexible transcriptomic regulation of a newly synthesized polyploid compared with a natural polyploid.
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Affiliation(s)
- Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Aki Morishima
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Beatriz Mourato
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Yasuhiro Sato
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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18
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Rahman MU, Zulfiqar S, Raza MA, Ahmad N, Zhang B. Engineering Abiotic Stress Tolerance in Crop Plants through CRISPR Genome Editing. Cells 2022; 11:cells11223590. [PMID: 36429019 PMCID: PMC9688763 DOI: 10.3390/cells11223590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental abiotic stresses challenge food security by depressing crop yields often exceeding 50% of their annual production. Different methods, including conventional as well as genomic-assisted breeding, mutagenesis, and genetic engineering have been utilized to enhance stress resilience in several crop species. Plant breeding has been partly successful in developing crop varieties against abiotic stresses owning to the complex genetics of the traits as well as the narrow genetic base in the germplasm. Irrespective of the fact that genetic engineering can transfer gene(s) from any organism(s), transgenic crops have become controversial mainly due to the potential risk of transgene-outcrossing. Consequently, the cultivation of transgenic crops is banned in certain countries, particularly in European countries. In this scenario, the discovery of the CRISPR tool provides a platform for producing transgene-free genetically edited plants-similar to the mutagenized crops that are not extensively regulated such as genetically modified organisms (GMOs). Thus, the genome-edited plants without a transgene would likely go into the field without any restriction. Here, we focused on the deployment of CRISPR for the successful development of abiotic stress-tolerant crop plants for sustaining crop productivity under changing environments.
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Affiliation(s)
- Mehboob-ur Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
- Correspondence: (M.-u.R.); (B.Z.)
| | - Sana Zulfiqar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Muhammad Ahmad Raza
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Niaz Ahmad
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
- Correspondence: (M.-u.R.); (B.Z.)
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19
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Shimizu KK. Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution? CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102292. [PMID: 36063635 DOI: 10.1016/j.pbi.2022.102292] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/01/2022] [Accepted: 07/27/2022] [Indexed: 05/26/2023]
Abstract
The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages and disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide changes termed "genome shock," as well as ancient polyploidy. Recent bioinformatics advances and empirical studies of Arabidopsis and wheat relatives are filling a research gap: the functional evolutionary study of polyploid species using RNA-seq, DNA polymorphism, and epigenomics. Polyploid species can become generalists in natura through environmental robustness by inheriting and merging parental stress responses. Their evolvability is enhanced by mutational robustness working on inherited standing variation. The identification of key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer polyploid advantages to other species.
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Affiliation(s)
- Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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20
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Di Marsico M, Paytuvi Gallart A, Sanseverino W, Aiese Cigliano R. GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. Nucleic Acids Res 2022; 50:D1442-D1447. [PMID: 34723326 PMCID: PMC8728176 DOI: 10.1093/nar/gkab1014] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 02/04/2023] Open
Abstract
The Green Non-Coding Database (GreeNC) is one of the reference databases for the study of plant long non-coding RNAs (lncRNAs). Here we present our most recent update where 16 species have been updated, while 78 species have been added, resulting in the annotation of more than 495 000 lncRNAs. Moreover, sequence clustering was applied providing information about sequence conservation and gene families. The current version of the database is available at: http://greenc.sequentiabiotech.com/wiki2/Main_Page.
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Affiliation(s)
- Marco Di Marsico
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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21
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Chen H, Wang T, He X, Cai X, Lin R, Liang J, Wu J, King G, Wang X. BRAD V3.0: an upgraded Brassicaceae database. Nucleic Acids Res 2022; 50:D1432-D1441. [PMID: 34755871 PMCID: PMC8728314 DOI: 10.1093/nar/gkab1057] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.
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Affiliation(s)
- Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Tianpeng Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Xiaoning He
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Graham King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
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22
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Tello-Ruiz MK, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol 2022; 2443:101-131. [PMID: 35037202 DOI: 10.1007/978-1-0716-2067-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end-users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.
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Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, USA.
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23
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Fasani E, DalCorso G, Zorzi G, Vitulo N, Furini A. Comparative analysis identifies micro-RNA associated with nutrient homeostasis, development and stress response in Arabidopsis thaliana upon high Zn and metal hyperaccumulator Arabidopsis halleri. PHYSIOLOGIA PLANTARUM 2021; 173:920-934. [PMID: 34171137 PMCID: PMC8597110 DOI: 10.1111/ppl.13488] [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: 01/11/2021] [Accepted: 06/21/2021] [Indexed: 05/05/2023]
Abstract
miRNAs have been found to be key players in mineral homeostasis, both in the control of nutrient balance and in the response to toxic trace elements. However, the effect of Zn excess on miRNAs has not been elucidated; moreover, no data are present regarding miRNAs in hyperaccumulator species, where metal homeostasis is tightly regulated. Therefore, expression levels of mature miRNAs were measured by RNA-Seq in Zn-sensitive Arabidopsis thaliana grown in control conditions and upon high Zn, in soil and in Zn-hyperaccumulator Arabidopsis halleri grown in control conditions. Differential expression of notable miRNAs and their targets was confirmed by real-time RT-PCR. The comparison in A. thaliana revealed a small subset modulated upon Zn treatment that is associated with stress response and nutrient homeostasis. On the other hand, a more consistent group of miRNAs was differentially expressed in A. halleri compared with A. thaliana, reflecting inherent differences in nutritional requirements and response to stresses and plant growth and development. Overall, these results confirm the involvement of miRNAs in Zn homeostasis and support the hypothesis of distinct regulatory pathways in hyperaccumulator species.
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Affiliation(s)
- Elisa Fasani
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | | | - Gianluca Zorzi
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | - Nicola Vitulo
- Department of BiotechnologyUniversity of VeronaVeronaItaly
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24
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Lee G, Ahmadi H, Quintana J, Syllwasschy L, Janina N, Preite V, Anderson JE, Pietzenuk B, Krämer U. Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress-adapted Arabidopsis halleri. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:896-911. [PMID: 34669984 DOI: 10.1111/tpj.15544] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Heavy metal-rich toxic soils and ordinary soils are both natural habitats of Arabidopsis halleri, a diploid perennial and obligate outcrosser in the sister clade of the genetic model plant Arabidopsis thaliana. The molecular divergence underlying survival in sharply contrasting environments is unknown. Here we comparatively address metal physiology and transcriptomes of A. halleri originating from the most highly heavy metal-contaminated soil in Europe, Ponte Nossa, Italy (Noss), and from non-metalliferous (NM) soils. Plants from Noss exhibit enhanced hypertolerance and attenuated accumulation of cadmium (Cd), and their transcriptomic Cd responsiveness is decreased, compared to plants of NM soil origin. Among the condition-independent transcriptome characteristics of Noss, the most highly overrepresented functional class of 'meiotic cell cycle' comprises 21 transcripts with elevated abundance in vegetative tissues, in particular Argonaute 9 (AGO9) and the synaptonemal complex transverse filament protein-encoding ZYP1a/b. Increased AGO9 transcript levels in Noss are accompanied by decreased long terminal repeat retrotransposon expression. Similar to Noss, plants from other highly metalliferous sites in Poland and Germany share elevated somatic AGO9 transcript levels in comparison to plants originating from NM soils in their respective geographic regions. Transcript levels of Iron-Regulated Transporter 1 (IRT1) are very low and transcript levels of Heavy Metal ATPase 2 (HMA2) are strongly elevated in Noss, which can account for its altered Cd handling. We conclude that in plants adapted to the most extreme abiotic stress, broadly enhanced functions comprise genes with likely roles in somatic genome integrity maintenance, accompanied by few alterations in stress-specific functional networks.
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Affiliation(s)
- Gwonjin Lee
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Hassan Ahmadi
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Julia Quintana
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Lara Syllwasschy
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Nadežda Janina
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Veronica Preite
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Justin E Anderson
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Björn Pietzenuk
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
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25
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Jiang X, Song Q, Ye W, Chen ZJ. Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids. Nat Ecol Evol 2021; 5:1382-1393. [PMID: 34413505 PMCID: PMC8484014 DOI: 10.1038/s41559-021-01523-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/24/2021] [Indexed: 02/06/2023]
Abstract
During evolution successful allopolyploids must overcome 'genome shock' between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsis thaliana (TT) and Arabidopsis arenosa (AA). A. suecica shows conserved gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F1 to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inherited from F1 to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution.
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Affiliation(s)
- Xinyu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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26
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Kuo TCY, Hatakeyama M, Tameshige T, Shimizu KK, Sese J. Homeolog expression quantification methods for allopolyploids. Brief Bioinform 2021; 21:395-407. [PMID: 30590436 PMCID: PMC7299288 DOI: 10.1093/bib/bby121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/21/2018] [Indexed: 12/19/2022] Open
Abstract
Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (>10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (<1% using EAGLE-RC, <2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method in wheat. In general, disagreement in low-expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision.
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Affiliation(s)
- Tony C Y Kuo
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan.,AIST-Tokyo Tech RWBC-OIL, 2-12-1 Okayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland.,Functional Genomics Center Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, Lausanne 1015, Switzerland
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research, Yokohama City University, 641-12, Maioka, Totsuka-ku, Yokohama 244-0813, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland.,Kihara Institute for Biological Research, Yokohama City University, 641-12, Maioka, Totsuka-ku, Yokohama 244-0813, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan.,AIST-Tokyo Tech RWBC-OIL, 2-12-1 Okayama, Meguro-ku, Tokyo 152-8550, Japan
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27
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Milosavljevic S, Kuo T, Decarli S, Mohn L, Sese J, Shimizu KK, Shimizu-Inatsugi R, Robinson MD. ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. BMC Genomics 2021; 22:547. [PMID: 34273949 PMCID: PMC8285871 DOI: 10.1186/s12864-021-07845-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid's parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization. RESULTS We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC's performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO's output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data. CONCLUSIONS The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO .
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Affiliation(s)
- Stefan Milosavljevic
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Tony Kuo
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Samuele Decarli
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Lucas Mohn
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jun Sese
- AIST Artificial Intelligence Research Center, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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28
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Tausta SL, Berbasova T, Peverelli M, Strobel SA. The fluoride transporter FLUORIDE EXPORTER (FEX) is the major mechanism of tolerance to fluoride toxicity in plants. PLANT PHYSIOLOGY 2021; 186:kiab131. [PMID: 33744970 PMCID: PMC8195535 DOI: 10.1093/plphys/kiab131] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/08/2021] [Indexed: 05/13/2023]
Abstract
Fluoride is everywhere in the environment, yet it is toxic to living things. How biological organisms detoxify fluoride has been unknown until recently. Fluoride-specific ion transporters in both prokaryotes (Fluoride channel; Fluc) and fungi (Fluoride Exporter; FEX) efficiently export fluoride to the extracellular environment. FEX homologues have been identified throughout the plant kingdom. Understanding the function of FEX in a multicellular organism will reveal valuable knowledge about reducing toxic effects caused by fluoride. Here we demonstrate the conserved role of plant FEX (FLUORIDE EXPORTER) in conferring fluoride tolerance. Plant FEX facilitates the efflux of toxic fluoride ions from yeast cells and is required for fluoride tolerance in plants. A CRISPR/Cas9-generated mutation in Arabidopsis thaliana FEX renders the plant vulnerable to low concentrations (100 µM) of fluoride at every stage of development. Pollen is particularly affected, failing to develop even at extremely low levels of fluoride in the growth medium. The action of the FEX membrane transport protein is the major fluoride defense mechanism in plants.
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Affiliation(s)
- S. Lori Tausta
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510
| | - Tanya Berbasova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510
| | - Martin Peverelli
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510
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29
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Genete M, Castric V, Vekemans X. Genotyping and De Novo Discovery of Allelic Variants at the Brassicaceae Self-Incompatibility Locus from Short-Read Sequencing Data. Mol Biol Evol 2021; 37:1193-1201. [PMID: 31688901 DOI: 10.1093/molbev/msz258] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinarily high levels of polymorphism, both in terms of the number of functionally distinct S-alleles that segregate in SI species and in terms of their nucleotide sequence divergence. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological challenges that have so far largely prevented the comprehensive analysis of complete allelic series in natural populations, and also precluded the obtention of complete genic sequences for many S-alleles. Here, we develop a powerful methodological approach based on a computationally optimized comparison of short Illumina sequencing reads from genomic DNA to a database of known nucleotide sequences of the extracellular domain of SRK (eSRK). By examining mapping patterns along the reference sequences, we obtain highly reliable predictions of S-genotypes from individuals collected from natural populations of Arabidopsis halleri. Furthermore, using a de novo assembly approach of the filtered short reads, we obtain full-length sequences of eSRK even when the initial sequence in the database was only partial, and we discover putative new SRK alleles that were not initially present in the database. When including those new alleles in the reference database, we were able to resolve the complete diploid SI genotypes of all individuals. Beyond the specific case of Brassicaceae S-alleles, our approach can be readily applied to other polymorphic loci, given reference allelic sequences are available.
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Affiliation(s)
- Mathieu Genete
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Vincent Castric
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Xavier Vekemans
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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30
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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31
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Bhardwaj E, Lal M, Anand S, Das S. Independent recurrent evolution of MICRORNA genes converging onto similar non-canonical organisation across green plant lineages is driven by local and segmental duplication events in species, family and lineages. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110661. [PMID: 33218629 DOI: 10.1016/j.plantsci.2020.110661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
The relationship between evolutionary history, organisation and transcriptional regulation of genes are intrinsically linked. These have been well studied in canonically organised protein-coding genes but not of MIRNAs. In the present study, we investigated the non-canonical arrangement of MIRNAs across taxonomic boundaries from algae to angiosperms employing a combination of genome organization, phylogeny and synteny. We retrieved the complete dataset of MIRNA from twenty-five species to identify and classify based on organisational patterns. The median size of cluster was between 2-5 kb and between 1-20 % of all MIRNAs are organized in head-to-head (with bidirectional promoter), head-to-tail (tandem), and overlapping manner. Although majority of the clusters are composed of MIRNA homologs, 25% of all clusters comprises of non-homologous genes with a potential of generating functional and regulatory complexity. A comparison of phylogeny and organizational patterns revealed that multiple independent events, some of which are species-specific, and some ancient, in different lineages, are responsible for non-canonical organization. Detailed investigation of MIR395 family across the plants revealed a complex origin of non-canonical arrangement through ancient and recent, segmental and local duplications; analysis of MIR399 family revealed major expansion occurred prior to monocot-dicot split, with few lineage-specific events. Evolution of "convergent" organization pattern of non-canonical arrangement originating from independent loci through recurrent event highlights our poor understanding of evolutionary process of MIRNA genes. The present investigation thus paves way for comparative functional genomics to understand the role of non-canonical organization on transcriptional regulation and regulatory diversity in MIRNA gene families.
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Affiliation(s)
- Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - S Anand
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110 007, India.
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Szopiński M, Sitko K, Rusinowski S, Zieleźnik-Rusinowska P, Corso M, Rostański A, Rojek-Jelonek M, Verbruggen N, Małkowski E. Different strategies of Cd tolerance and accumulation in Arabidopsis halleri and Arabidopsis arenosa. PLANT, CELL & ENVIRONMENT 2020; 43:3002-3019. [PMID: 32890409 DOI: 10.1111/pce.13883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Pseudometallophytes are commonly used to study the evolution of metal tolerance and accumulation traits in plants. Within the Arabidopsis genus, the adaptation of Arabidopsis halleri to metalliferous soils has been widely studied, which is not the case for the closely related species Arabidopsis arenosa. We performed an in-depth physiological comparison between the A. halleri and A. arenosa populations from the same polluted site, together with the geographically close non-metallicolous (NM) populations of both species. The ionomes, growth, photosynthetic parameters and pigment content were characterized in the plants that were growing on their native site and in a hydroponic culture under Cd treatments. In situ, the metallicolous (M) populations of both species hyperaccumulated Cd and Zn. The NM population of A. halleri hyperaccumulated Cd and Zn while the NM A. arenosa did not. In the hydroponic experiments, the NM populations of both species accumulated more Cd in their shoots than the M populations. Our research suggests that the two Arabidopsis species evolved different strategies of adaptation to extreme metallic environments that involve fine regulation of metal homeostasis, adjustment of the photosynthetic apparatus and accumulation of flavonols and anthocyanins.
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Affiliation(s)
- Michał Szopiński
- Plant Ecophysiology Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Krzysztof Sitko
- Plant Ecophysiology Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | | | - Paulina Zieleźnik-Rusinowska
- Plant Ecophysiology Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Massimiliano Corso
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Adam Rostański
- Botany and Nature Protection Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Magdalena Rojek-Jelonek
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Eugeniusz Małkowski
- Plant Ecophysiology Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Manara A, Fasani E, Furini A, DalCorso G. Evolution of the metal hyperaccumulation and hypertolerance traits. PLANT, CELL & ENVIRONMENT 2020; 43:2969-2986. [PMID: 32520430 DOI: 10.1111/pce.13821] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/20/2020] [Accepted: 06/05/2020] [Indexed: 05/21/2023]
Abstract
To succeed in life, living organisms have to adapt to the environmental issues to which they are subjected. Some plants, defined as hyperaccumulators, have adapted to metalliferous environments, acquiring the ability to tolerate and accommodate high amounts of toxic metal into their shoot, without showing symptoms of toxicity. The determinants for these traits and their mode of action have long been the subject of research, whose attention lately moved to the evolution of the hypertolerance and hyperaccumulation traits. Genetic evidence indicates that the evolution of both traits includes significant evolutionary events that result in species-wide tolerant and accumulating backgrounds. Different edaphic environments are responsible for subsequent refinement, by local adaptive processes, leading to specific strategies and various degrees of hypertolerance and hyperaccumulation, which characterize metallicolous from non-metallicolous ecotypes belonging to the same genetic unit. In this review, we overview the most updated concepts regarding the evolution of hyperaccumulation and hypertolerance, highlighting also the ecological context concerning the plant populations displaying this fascinating phenomenon.
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Affiliation(s)
- Anna Manara
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Elisa Fasani
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Antonella Furini
- Department of Biotechnology, University of Verona, Verona, Italy
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Agarwal P, Giri BS, Rani R. Unravelling the Role of Rhizospheric Plant-Microbe Synergy in Phytoremediation: A Genomic Perspective. Curr Genomics 2020; 21:334-342. [PMID: 33093797 PMCID: PMC7536802 DOI: 10.2174/1389202921999200623133240] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 12/27/2022] Open
Abstract
Background Accretion of organic and inorganic contaminants in soil interferes in the food chain, thereby posing a serious threat to the ecosystem and adversely affecting crop productivity and human life. Both endophytic and rhizospheric microbial communities are responsible for the biodegradation of toxic organic compounds and have the capability to enhance the uptake of heavy metals by plants via phytoremediation approaches. The diverse set of metabolic genes encoding for the production of biosurfactants and biofilms, specific enzymes for degrading plant polymers, modification of cell surface hydrophobicity and various detoxification pathways for the organic pollutants, plays a significant role in bacterial driven bioremediation. Various genetic engineering approaches have been demonstrated to modulate the activity of specific microbial species in order to enhance their detoxification potential. Certain rhizospheric bacterial communities are genetically modified to produce specific enzymes that play a role in degrading toxic pollutants. Few studies suggest that the overexpression of extracellular enzymes secreted by plant, fungi or rhizospheric microbes can improve the degradation of specific organic pollutants in the soil. Plants and microbes dwell synergistically, where microbes draw benefit by nutrient acquisition from root exudates whereas they assist in plant growth and survival by producing certain plant growth promoting metabolites, nitrogen fixation, phosphate solubilization, auxin production, siderophore production, and inhibition or suppression of plant pathogens. Thus, the plant-microbe interaction establishes the foundation of the soil nutrient cycle as well as decreases soil toxicity by the removal of harmful pollutants. Conclusion The perspective of integrating genetic approach with bioremediation is crucial to evaluate connexions among microbial communities, plant communities and ecosystem processes with a focus on improving phytoremediation of contaminated sites.
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Affiliation(s)
- Priyanka Agarwal
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj-211004, Uttar Pradesh, India; 2Department of Chemical Engineering and Technology, Centre of Advanced Study, Indian Institute of Technology Banaras Hindu University, Varanasi221005, India
| | - Balendu Shekher Giri
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj-211004, Uttar Pradesh, India; 2Department of Chemical Engineering and Technology, Centre of Advanced Study, Indian Institute of Technology Banaras Hindu University, Varanasi221005, India
| | - Radha Rani
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj-211004, Uttar Pradesh, India; 2Department of Chemical Engineering and Technology, Centre of Advanced Study, Indian Institute of Technology Banaras Hindu University, Varanasi221005, India
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35
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Formation and diversification of a paradigm biosynthetic gene cluster in plants. Nat Commun 2020; 11:5354. [PMID: 33097700 PMCID: PMC7584637 DOI: 10.1038/s41467-020-19153-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Numerous examples of biosynthetic gene clusters (BGCs), including for compounds of agricultural and medicinal importance, have now been discovered in plant genomes. However, little is known about how these complex traits are assembled and diversified. Here, we examine a large number of variants within and between species for a paradigm BGC (the thalianol cluster), which has evolved recently in a common ancestor of the Arabidopsis genus. Comparisons at the species level reveal differences in BGC organization and involvement of auxiliary genes, resulting in production of species-specific triterpenes. Within species, the thalianol cluster is primarily fixed, showing a low frequency of deleterious haplotypes. We further identify chromosomal inversion as a molecular mechanism that may shuffle more distant genes into the cluster, so enabling cluster compaction. Antagonistic natural selection pressures are likely involved in shaping the occurrence and maintenance of this BGC. Our work sheds light on the birth, life and death of complex genetic and metabolic traits in plants.
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36
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Rellstab C, Zoller S, Sailer C, Tedder A, Gugerli F, Shimizu KK, Holderegger R, Widmer A, Fischer MC. Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species. Mol Ecol 2020; 29:4350-4365. [PMID: 32969558 PMCID: PMC7756229 DOI: 10.1111/mec.15648] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/26/2020] [Accepted: 09/04/2020] [Indexed: 01/24/2023]
Abstract
It has long been discussed to what extent related species develop similar genetic mechanisms to adapt to similar environments. Most studies documenting such convergence have either used different lineages within species or surveyed only a limited portion of the genome. Here, we investigated whether similar or different sets of orthologous genes were involved in genetic adaptation of natural populations of three related plant species to similar environmental gradients in the Alps. We used whole-genome pooled population sequencing to study genome-wide SNP variation in 18 natural populations of three Brassicaceae (Arabis alpina, Arabidopsis halleri, and Cardamine resedifolia) from the Swiss Alps. We first de novo assembled draft reference genomes for all three species. We then ran population and landscape genomic analyses with ~3 million SNPs per species to look for shared genomic signatures of selection and adaptation in response to similar environmental gradients acting on these species. Genes with a signature of convergent adaptation were found at significantly higher numbers than expected by chance. The most closely related species pair showed the highest relative over-representation of shared adaptation signatures. Moreover, the identified genes of convergent adaptation were enriched for nonsynonymous mutations, suggesting functional relevance of these genes, even though many of the identified candidate genes have hitherto unknown or poorly described functions based on comparison with Arabidopsis thaliana. We conclude that adaptation to heterogeneous Alpine environments in related species is partly driven by convergent evolution, but that most of the genomic signatures of adaptation remain species-specific.
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Affiliation(s)
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Christian Sailer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Andrew Tedder
- Department of Evolutionary Biology and Environmental Studies, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,School of Chemistry & Bioscience, University of Bradford, Bradford, UK
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Rolf Holderegger
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Martin C Fischer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
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37
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Boulc'h PN, Caullireau E, Faucher E, Gouerou M, Guérin A, Miray R, Couée I. Abiotic stress signalling in extremophile land plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5771-5785. [PMID: 32687568 DOI: 10.1093/jxb/eraa336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Plant life relies on complex arrays of environmental stress sensing and signalling mechanisms. Extremophile plants develop and grow in harsh environments with extremes of cold, heat, drought, desiccation, or salinity, which have resulted in original adaptations. In accordance with their polyphyletic origins, extremophile plants likely possess core mechanisms of plant abiotic stress signalling. However, novel properties or regulations may have emerged in the context of extremophile adaptations. Comparative omics of extremophile genetic models, such as Arabidopsis lyrata, Craterostigma plantagineum, Eutrema salsugineum, and Physcomitrella patens, reveal diverse strategies of sensing and signalling that lead to a general improvement in abiotic stress responses. Current research points to putative differences of sensing and emphasizes significant modifications of regulatory mechanisms, at the level of secondary messengers (Ca2+, phospholipids, reactive oxygen species), signal transduction (intracellular sensors, protein kinases, transcription factors, ubiquitin-mediated proteolysis) or signalling crosstalk. Involvement of hormone signalling, especially ABA signalling, cell homeostasis surveillance, and epigenetic mechanisms, also shows that large-scale gene regulation, whole-plant integration, and probably stress memory are important features of adaptation to extreme conditions. This evolutionary and functional plasticity of signalling systems in extremophile plants may have important implications for plant biotechnology, crop improvement, and ecological risk assessment under conditions of climate change.
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Affiliation(s)
- Pierre-Nicolas Boulc'h
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Emma Caullireau
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Elvina Faucher
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Maverick Gouerou
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
- University of Rennes 1, CNRS, ECOBIO (Ecosystems-Biodiversity-Evolution) - UMR, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Amandine Guérin
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Romane Miray
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Ivan Couée
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
- University of Rennes 1, CNRS, ECOBIO (Ecosystems-Biodiversity-Evolution) - UMR, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
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38
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Paape T, Akiyama R, Cereghetti T, Onda Y, Hirao AS, Kenta T, Shimizu KK. Experimental and Field Data Support Range Expansion in an Allopolyploid Arabidopsis Owing to Parental Legacy of Heavy Metal Hyperaccumulation. Front Genet 2020; 11:565854. [PMID: 33193650 PMCID: PMC7554548 DOI: 10.3389/fgene.2020.565854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/04/2020] [Indexed: 01/31/2023] Open
Abstract
Empirical evidence is limited on whether allopolyploid species combine or merge parental adaptations to broaden habitats. The allopolyploid Arabidopsis kamchatica is a hybrid of the two diploid parents Arabidopsis halleri and Arabidopsis lyrata. A. halleri is a facultative heavy metal hyperaccumulator, and may be found in cadmium (Cd) and zinc (Zn) contaminated environments, as well as non-contaminated environments. A. lyrata is considered non-tolerant to these metals, but can be found in serpentine habitats. Therefore, the parents have adaptation to different environments. Here, we measured heavy metals in soils from native populations of A. kamchatica. We found that soil Zn concentration of nearly half of the sampled 40 sites was higher than the critical toxicity level. Many of the sites were near human construction, suggesting adaptation of A. kamchatica to artificially contaminated soils. Over half of the A. kamchatica populations had >1,000 μg g–1 Zn in leaf tissues. Using hydroponic treatments, most genotypes accumulated >3,000 μg g–1 Zn, with high variability among them, indicating substantial genetic variation in heavy metal accumulation. Genes involved in heavy metal hyperaccumulation showed an expression bias in the A. halleri-derived homeolog in widely distributed plant genotypes. We also found that two populations were found growing on serpentine soils. These data suggest that A. kamchatica can inhabit a range of both natural and artificial soil environments with high levels of ions that either of the parents specializes and that it can accumulate varying amount of heavy metals. Our field and experimental data provide a compelling example of combining genetic toolkits for soil adaptations to expand the habitat of an allopolyploid species.
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Affiliation(s)
- Timothy Paape
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Sugadaira Montane Research Center, University of Tsukuba, Tsukuba, Japan
| | - Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Teo Cereghetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Yoshihiko Onda
- Sugadaira Montane Research Center, University of Tsukuba, Tsukuba, Japan
| | - Akira S Hirao
- Sugadaira Montane Research Center, University of Tsukuba, Tsukuba, Japan.,Faculty of Symbiotic Systems Science, Fukushima University, Fukushima, Japan
| | - Tanaka Kenta
- Sugadaira Montane Research Center, University of Tsukuba, Tsukuba, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
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39
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Nishio H, Nagano AJ, Ito T, Suzuki Y, Kudoh H. Seasonal plasticity and diel stability of H3K27me3 in natural fluctuating environments. NATURE PLANTS 2020; 6:1091-1097. [PMID: 32868888 DOI: 10.1038/s41477-020-00757-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Diel and seasonal oscillations are two major environmental changes in nature. While organisms cope with the former by the well-characterized mechanism of the circadian clock1,2, there is limited information on the molecular mechanisms underlying long-term responses to the latter3-5. Histone H3 lysine 27 trimethylation (H3K27me3), a repressive histone modification, imparts stability and plasticity to gene regulation during developmental transitions6-9. Here we studied the seasonal and diel dynamics of H3K27me3 at the genome-wide level in a natural population of perennial Arabidopsis halleri and compared these dynamics with those of histone H3 lysine 4 trimethylation (H3K4me3), an active histone modification. Chromatin immunoprecipitation sequencing revealed that H3K27me3 exhibits seasonal plasticity and diel stability. Furthermore, we found that the seasonal H3K27me3 oscillation is delayed in phase relative to the H3K4me3 oscillation, particularly for genes associated with environmental memory. Our findings suggest that H3K27me3 monitors past transcriptional activity to create long-term gene expression trends during organismal responses over weeks in natural fluctuating environments.
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Affiliation(s)
- Haruki Nishio
- Center for Ecological Research, Kyoto University, Otsu, Japan.
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Otsu, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Tasuku Ito
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan.
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40
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Simon NML, Sugisaka J, Honjo MN, Tunstad SA, Tunna G, Kudoh H, Dodd AN. Altered stomatal patterning accompanies a trichome dimorphism in a natural population of Arabidopsis. PLANT DIRECT 2020; 4:e00262. [PMID: 32995701 PMCID: PMC7507053 DOI: 10.1002/pld3.262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 07/09/2020] [Accepted: 08/07/2020] [Indexed: 05/27/2023]
Abstract
Trichomes are large epidermal cells on the surface of leaves that are thought to deter herbivores, yet the presence of trichomes can also negatively impact plant growth and reproduction. Stomatal guard cells and trichomes have shared developmental origins, and experimental manipulation of trichome formation can lead to changes in stomatal density. The influence of trichome formation upon stomatal development in natural populations of plants is currently unknown. Here, we show that a natural population of Arabidopsis halleri that includes hairy (trichome-bearing) and glabrous (no trichomes) morphs has differences in stomatal density that are associated with this trichome dimorphism. We found that glabrous morphs had significantly greater stomatal density and stomatal index than hairy morphs. One interpretation is that this arises from a trade-off between the proportions of cells that have trichome and guard cell fates during leaf development. The differences in stomatal density between the two morphs might have impacts upon environmental adaptation, in addition to herbivory deterrence caused by trichome development.
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Affiliation(s)
| | - Jiro Sugisaka
- Center for Ecological Research Kyoto University Otsu Shiga Japan
| | - Mie N Honjo
- Center for Ecological Research Kyoto University Otsu Shiga Japan
| | | | - George Tunna
- School of Biological Sciences University of Bristol Bristol UK
| | - Hiroshi Kudoh
- Center for Ecological Research Kyoto University Otsu Shiga Japan
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41
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Quadrana L. The contribution of transposable elements to transcriptional novelty in plants: the FLC affair. Transcription 2020; 11:192-198. [PMID: 32783496 PMCID: PMC7714446 DOI: 10.1080/21541264.2020.1803031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences with the ability to replicate across genomes and generate mutations with major transcriptional effects. Epigenetic silencing mechanisms that target TEs to limit their activity, including DNA methylation, add to the range of gene expression variants generated by TEs. Here, using the iconic gene flowering locus C (FLC) as a case study I discuss the multiple ways by which TEs can affect the expression of genes and contribute to the adaptation of plants to changing environments
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Affiliation(s)
- Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University , Paris, France
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42
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 PMCID: PMC7042746 DOI: 10.1002/ece3.6002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest ManagementColorado State UniversityFort CollinsCOUSA
- Department of Biological SciencesUniversity of CyprusNicosiaCyprus
| | - Lua Lopez
- Department of BiologyBinghamton University (State University of New York)BinghamtonNYUSA
| | - Adrian E. Platts
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNYUSA
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
| | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
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43
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Corso M, García de la Torre VS. Biomolecular approaches to understanding metal tolerance and hyperaccumulation in plants. Metallomics 2020; 12:840-859. [DOI: 10.1039/d0mt00043d] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Trace metal elements are essential for plant growth but become toxic at high concentrations, while some non-essential elements, such as Cd and As, show toxicity even in traces.
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Affiliation(s)
- Massimiliano Corso
- Institut Jean-Pierre Bourgin
- Université Paris-Saclay
- INRAE
- AgroParisTech
- 78000 Versailles
| | - Vanesa S. García de la Torre
- Molecular Genetics and Physiology of Plants
- Faculty of Biology and Biotechnology
- Ruhr University Bochum
- 44801 Bochum
- Germany
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44
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Hu B, Deng F, Chen G, Chen X, Gao W, Long L, Xia J, Chen ZH. Evolution of Abscisic Acid Signaling for Stress Responses to Toxic Metals and Metalloids. FRONTIERS IN PLANT SCIENCE 2020; 11:909. [PMID: 32765540 PMCID: PMC7379394 DOI: 10.3389/fpls.2020.00909] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/03/2020] [Indexed: 05/02/2023]
Abstract
Toxic heavy metals and metalloids in agricultural ecosystems are crucial factors that limit global crop productivity and food safety. Industrial toxic heavy metals and metalloids such as cadmium, lead, and arsenic have contaminated large areas of arable land in the world and their accumulation in the edible parts of crops is causing serious health risks to humans and animals. Plants have co-evolved with various concentrations of these toxic metals and metalloids in soil and water. Some green plant species have significant innovations in key genes for the adaptation of abiotic stress tolerance pathways that are able to tolerate heavy metals and metalloids. Increasing evidence has demonstrated that phytohormone abscisic acid (ABA) plays a vital role in the alleviation of heavy metal and metalloid stresses in plants. Here, we trace the evolutionary origins of the key gene families connecting ABA signaling with tolerance to heavy metals and metalloids in green plants. We also summarize the molecular and physiological aspects of ABA in the uptake, root-to-shoot translocation, chelation, sequestration, reutilization, and accumulation of key heavy metals and metalloids in plants. The molecular evolution and interaction between the ABA signaling pathway and mechanisms for heavy metal and metalloid tolerance are highlighted in this review. Therefore, we propose that it is promising to manipulate ABA signaling in plant tissues to reduce the uptake and accumulation of toxic heavy metals and metalloids in crops through the application of ABA-producing bacteria or ABA analogues. This may lead to improvements in tolerance of major crops to heavy metals and metalloids.
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Affiliation(s)
- Beibei Hu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, China
| | - Fenglin Deng
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, China
- *Correspondence: Fenglin Deng, ; Zhong-Hua Chen,
| | - Guang Chen
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, China
| | - Xuan Chen
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, China
| | - Wei Gao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Lu Long
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Jixing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- *Correspondence: Fenglin Deng, ; Zhong-Hua Chen,
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45
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Zhong S, Liu M, Wang Z, Huang Q, Hou S, Xu YC, Ge Z, Song Z, Huang J, Qiu X, Shi Y, Xiao J, Liu P, Guo YL, Dong J, Dresselhaus T, Gu H, Qu LJ. Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis. Science 2019; 364:364/6443/eaau9564. [PMID: 31147494 DOI: 10.1126/science.aau9564] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/14/2019] [Accepted: 04/25/2019] [Indexed: 12/21/2022]
Abstract
Reproductive isolation is a prerequisite for speciation. Failure of communication between female tissues of the pistil and paternal pollen tubes imposes hybridization barriers in flowering plants. Arabidopsis thaliana LURE1 (AtLURE1) peptides and their male receptor PRK6 aid attraction of the growing pollen tube to the ovule. Here, we report that the knockout of the entire AtLURE1 gene family did not affect fertility, indicating that AtLURE1-PRK6-mediated signaling is not required for successful fertilization within one Arabidopsis species. AtLURE1s instead function as pollen tube emergence accelerators that favor conspecific pollen over pollen from other species and thus promote reproductive isolation. We also identified maternal peptides XIUQIU1 to -4, which attract pollen tubes regardless of species. Cooperation between ovule attraction and pollen tube growth acceleration favors conspecific fertilization and promotes reproductive isolation.
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Affiliation(s)
- Sheng Zhong
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China.,The National Plant Gene Research Center (Beijing), Beijing 100101, People's Republic of China
| | - Meiling Liu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Zhijuan Wang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Qingpei Huang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Saiying Hou
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zengxiang Ge
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Zihan Song
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jiaying Huang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xinyu Qiu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yihao Shi
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Junyu Xiao
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Pei Liu
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, People's Republic of China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Hongya Gu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China.,The National Plant Gene Research Center (Beijing), Beijing 100101, People's Republic of China
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China. .,The National Plant Gene Research Center (Beijing), Beijing 100101, People's Republic of China
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46
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Honjo MN, Kudoh H. Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation. AOB PLANTS 2019; 11:plz076. [PMID: 31832127 PMCID: PMC6899346 DOI: 10.1093/aobpla/plz076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/26/2019] [Indexed: 05/21/2023]
Abstract
Local adaptation is assumed to occur when populations differ in a phenotypic trait or a set of traits, and such variation has a genetic basis. Here, we introduce Arabidopsis halleri and its life history as a perennial model system to study population differentiation and local adaptation. Studies on altitudinal adaptation have been conducted in two regions: Mt. Ibuki in Japan and the European Alps. Several studies have demonstrated altitudinal adaptation in ultraviolet-B (UV-B) tolerance, leaf water repellency against spring frost and anti-herbivore defences. Studies on population differentiation in A. halleri have also focused on metal hyperaccumulation and tolerance to heavy metal contamination. In these study systems, genome scans to identify candidate genes under selection have been applied. Lastly, we briefly discuss how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms. In conclusion, A. halleri provides us with opportunities to study population differentiation and local adaptation, and relate these to the genetic systems underlying target functional traits.
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Affiliation(s)
- Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
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47
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Vithanage M, Kumarathilaka P, Oze C, Karunatilake S, Seneviratne M, Hseu ZY, Gunarathne V, Dassanayake M, Ok YS, Rinklebe J. Occurrence and cycling of trace elements in ultramafic soils and their impacts on human health: A critical review. ENVIRONMENT INTERNATIONAL 2019; 131:104974. [PMID: 31376597 DOI: 10.1016/j.envint.2019.104974] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 06/10/2023]
Abstract
The transformation of trace metals (TMs) in natural environmental systems has created significant concerns in recent decades. Ultramafic environments lead to potential risks to the agricultural products and, subsequently, to human health. This unique review presents geochemistry of ultramafic soils, TM fractionation (i.e. sequential and single extraction techniques), TM uptake and accumulation mechanisms of ultramafic flora, and ultramafic-associated health risks to human and agricultural crops. Ultramafic soils contain high levels of TMs (i.e. Cr, Ni, Mn, and Co) and have a low Ca:Mg ratio together with deficiencies in essential macronutrients required for the growth of crops. Even though a higher portion of TMs bind with the residual fraction of ultramafic soils, environmental changes (i.e. natural or anthropogenic) may increase the levels of TMs in the bioavailable or extractable fractions of ultramafic soils. Extremophile plants that have evolved to thrive in ultramafic soils present clear examples of evolutionary adaptations to TM resistance. The release of TMs into water sources and accumulation in food crops in and around ultramafic localities increases health risks for humans. Therefore, more focused investigations need to be implemented to understand the mechanisms related to the mobility and bioavailability of TMs in different ultramafic environments. Research gaps and directions for future studies are also discussed in this review. Lastly, we consider the importance of characterizing terrestrial ultramafic soil and its effect on crop plants in the context of multi-decadal plans by NASA and other space agencies to establish human colonies on Mars.
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Affiliation(s)
- Meththika Vithanage
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; School of Civil Engineering and Surveying, Faculty of Health, Engineering and Sciences, University of Southern Queensland, West Street, Toowoomba, Queensland 4350, Australia.
| | - Prasanna Kumarathilaka
- School of Civil Engineering and Surveying, Faculty of Health, Engineering and Sciences, University of Southern Queensland, West Street, Toowoomba, Queensland 4350, Australia
| | - Christopher Oze
- Department of Geology, Occidental College, Los Angeles, CA 90041, USA
| | - Suniti Karunatilake
- Planetary Science Lab, Geology & Geophysics, Louisiana State University, USA
| | - Mihiri Seneviratne
- Department of Botany, The Open University of Sri Lanka, Nawala, Sri Lanka
| | - Zeng-Yei Hseu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Viraj Gunarathne
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | | | - Yong Sik Ok
- Korea Biochar Research Center, O-Jeong Eco-Resilience Institute, Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; University of Sejong, Department of Environment and Energy, Seoul 05006, Republic of Korea.
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48
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Kiefer C, Willing EM, Jiao WB, Sun H, Piednoël M, Hümann U, Hartwig B, Koch MA, Schneeberger K. Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation. NATURE PLANTS 2019; 5:846-855. [PMID: 31358959 DOI: 10.1038/s41477-019-0486-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 06/25/2019] [Indexed: 05/18/2023]
Abstract
Comparative genomics can unravel the genetic basis of species differences; however, successful reports on quantitative traits are still scarce. Here we present genome assemblies of 31 so-far unassembled Brassicaceae plant species and combine them with 16 previously published assemblies to establish the Brassicaceae Diversity Panel. Using a new interspecies association strategy for quantitative traits, we found a so-far unknown association between the unexpectedly high variation in CG to TG substitution rates in genes and the absence of CHROMOMETHYLASE3 (CMT3) orthologues. Low substitution rates were associated with the loss of CMT3, while species with conserved CMT3 orthologues showed high substitution rates. Species without CMT3 also lacked gene-body methylation (gbM), suggesting an evolutionary trade-off between the unknown function of gbM and low substitution rates in Brassicaceae, possibly due to low mutability of non-methylated cytosines.
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Affiliation(s)
- Christiane Kiefer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Eva-Maria Willing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- NEO New Oncology, Cologne, Germany
| | - Wen-Biao Jiao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hequan Sun
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathieu Piednoël
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ulrike Hümann
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Benjamin Hartwig
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- NEO New Oncology, Cologne, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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49
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Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L. Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180243. [PMID: 31154972 PMCID: PMC6560266 DOI: 10.1098/rstb.2018.0243] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 01/09/2023] Open
Abstract
It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Veronica Preite
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Christian Sailer
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Lara Syllwasschy
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Sian Bray
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Hassan Ahmadi
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Levi Yant
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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50
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Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L. Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180243. [PMID: 31154972 DOI: 10.5061/dryad.jg30j4v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Veronica Preite
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Christian Sailer
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
| | - Lara Syllwasschy
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Sian Bray
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
| | - Hassan Ahmadi
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Ute Krämer
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Levi Yant
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
- 3 School of Life Sciences, University of Nottingham , Nottingham NG7 2RD , UK
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