1
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Meng K, Liao W, Wei S, Chen S, Li M, Ma Y, Fan Q. Chromosome-scale genome assembly and annotation of Cotoneaster glaucophyllus. Sci Data 2024; 11:406. [PMID: 38649372 PMCID: PMC11035681 DOI: 10.1038/s41597-024-03246-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Cotoneaster glaucophyllus is a semi-evergreen plant that blossoms in late summer, producing dense, attractive, fragrant white flowers with significant ornamental and ecological value. Here, a chromosome-scale genome assembly was obtained by integrating PacBio and Illumina sequencing data with the aid of Hi-C technology. The genome assembly was 563.3 Mb in length, with contig N50 and scaffold N50 values of ~6 Mb and ~31 Mb, respectively. Most (95.59%) of the sequences were anchored onto 17 pseudochromosomes (538.4 Mb). We predicted 35,856 protein-coding genes, 1,401 miRNAs, 655 tRNAs, 425 rRNAs, and 795 snRNAs. The functions of 34,967 genes (97.52%) were predicted. The availability of this chromosome-level genome will provide valuable resources for molecular studies of this species, facilitating future research on speciation, functional genomics, and comparative genomics within the Rosaceae family.
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Affiliation(s)
- Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Guangxi Key Laboratory of Quality and Safety Control for Subtropical Fruits, Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shaolong Wei
- Guangxi Key Laboratory of Quality and Safety Control for Subtropical Fruits, Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mingwan Li
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yongpeng Ma
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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2
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Liu Q, Xiong G, Wang Z, Wu Y, Tu T, Schwarzacher T, Heslop-Harrison JS. Chromosome-level genome assembly of the diploid oat species Avena longiglumis. Sci Data 2024; 11:412. [PMID: 38649380 PMCID: PMC11035610 DOI: 10.1038/s41597-024-03248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Diploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate the conservation of gene order and equal expansion of all syntenic blocks among three genome assemblies. Two recent whole-genome duplication events were characterized in genomes of diploid Avena species. These findings provide new knowledge for the genomic features of A. longiglumis, give information about the species diversity, and will accelerate the functional genomics and breeding studies in oat and related cereal crops.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, China.
| | - Gui Xiong
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziwei Wang
- School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Yongxing Wu
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Tieyao Tu
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, China
| | - Trude Schwarzacher
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, China
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester, UK
| | - John Seymour Heslop-Harrison
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, China.
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester, UK.
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3
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Sakamoto T, Ikematsu S, Nakayama H, Mandáková T, Gohari G, Sakamoto T, Li G, Hou H, Matsunaga S, Lysak MA, Kimura S. A chromosome-level genome assembly for the amphibious plant Rorippa aquatica reveals its allotetraploid origin and mechanisms of heterophylly upon submergence. Commun Biol 2024; 7:431. [PMID: 38637665 PMCID: PMC11026429 DOI: 10.1038/s42003-024-06088-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
The ability to respond to varying environments is crucial for sessile organisms such as plants. The amphibious plant Rorippa aquatica exhibits a striking type of phenotypic plasticity known as heterophylly, a phenomenon in which leaf form is altered in response to environmental factors. However, the underlying molecular mechanisms of heterophylly are yet to be fully understood. To uncover the genetic basis and analyze the evolutionary processes driving heterophylly in R. aquatica, we assembled the chromosome-level genome of the species. Comparative chromosome painting and chromosomal genomics revealed that allopolyploidization and subsequent post-polyploid descending dysploidy occurred during the speciation of R. aquatica. Based on the obtained genomic data, the transcriptome analyses revealed that ethylene signaling plays a central role in regulating heterophylly under submerged conditions, with blue light signaling acting as an attenuator of ethylene signal. The assembled R. aquatica reference genome provides insights into the molecular mechanisms and evolution of heterophylly.
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Affiliation(s)
- Tomoaki Sakamoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Shuka Ikematsu
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Hokuto Nakayama
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Science Build. #2, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA, USA
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, Masaryk University, CZ-625 00, Brno, Czech Republic
| | - Gholamreza Gohari
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
- Faculty of Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa, Japan
| | - Gaojie Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hongwei Hou
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, Masaryk University, CZ-625 00, Brno, Czech Republic
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan.
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan.
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4
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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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5
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Peng Z, Jia KH, Meng J, Wang J, Zhang J, Li X, Wan S. Transcriptome profiling of aerial and subterranean peanut pod development. Sci Data 2024; 11:364. [PMID: 38605113 PMCID: PMC11009330 DOI: 10.1038/s41597-024-03205-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Peanut (Arachis hypogaea) showcases geocarpic behavior, transitioning from aerial flowering to subterranean seed development. We recently obtained an atavistic variant of this species, capable of producing aerial and subterranean pods on a single plant. Notably, although these pod types share similar vigor levels, they exhibit distinct differences in their physical aspects, such as pod size, color, and shell thickness. We constructed 63 RNA-sequencing datasets, comprising three biological replicates for each of 21 distinct tissues spanning six developmental stages for both pod types, providing a rich tapestry of the pod development process. This comprehensive analysis yielded an impressive 409.36 Gb of clean bases, facilitating the detection of 42,401 expressed genes. By comparing the transcriptomic data of the aerial and subterranean pods, we identified many differentially expressed genes (DEGs), highlighting their distinct developmental pathways. By providing a detailed workflow from the initial sampling to the final DEGs, this study serves as an important resource, paving the way for future research into peanut pod development and aiding transcriptome-based expression profiling and candidate gene identification.
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Affiliation(s)
- Zhenying Peng
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Kai-Hua Jia
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Jingjing Meng
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jianguo Wang
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jialei Zhang
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xinguo Li
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Shubo Wan
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
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6
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Nousias O, Zheng J, Li T, Meinhardt LW, Bailey B, Gutierrez O, Baruah IK, Cohen SP, Zhang D, Yin Y. Three de novo assembled wild cacao genomes from the Upper Amazon. Sci Data 2024; 11:369. [PMID: 38605066 PMCID: PMC11009333 DOI: 10.1038/s41597-024-03215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. The five cacao genetic clusters were inferred to have diverged in the early and middle Pleistocene period, approximately 1.83-0.69 million years ago. The results shown here serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying genetic diversity and advancing genetic improvement of this species.
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Affiliation(s)
- Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lyndel W Meinhardt
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Bryan Bailey
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Osman Gutierrez
- U.S. Department of Agriculture, Subtropical Horticulture Research Station, Miami, FL, USA
| | - Indrani K Baruah
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Stephen P Cohen
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Dapeng Zhang
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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7
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Tomlin CM, Rajaraman S, Sebesta JT, Scheen AC, Bendiksby M, Low YW, Salojärvi J, Michael TP, Albert VA, Lindqvist C. Allopolyploid origin and diversification of the Hawaiian endemic mints. Nat Commun 2024; 15:3109. [PMID: 38600100 PMCID: PMC11006916 DOI: 10.1038/s41467-024-47247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.
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Affiliation(s)
- Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, New York, USA
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - Mika Bendiksby
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, New York, USA.
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8
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Kfoury B, Rodrigues WFC, Kim SJ, Brandizzi F, Del-Bem LE. Multiple horizontal gene transfer events have shaped plant glycosyl hydrolase diversity and function. New Phytol 2024; 242:809-824. [PMID: 38417454 DOI: 10.1111/nph.19595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 01/15/2024] [Indexed: 03/01/2024]
Abstract
Plant glycosyl hydrolases (GHs) play a crucial role in selectively breaking down carbohydrates and glycoconjugates during various cellular processes, such as reserve mobilization, pathogen defense, and modification/disassembly of the cell wall. In this study, we examined the distribution of GH genes in the Archaeplastida supergroup, which encompasses red algae, glaucophytes, and green plants. We identified that the GH repertoire expanded from a few tens of genes in early archaeplastidians to over 400 genes in modern angiosperms, spanning 40 GH families in land plants. Our findings reveal that major evolutionary transitions were accompanied by significant changes in the GH repertoire. Specifically, we identified at least 23 GH families acquired by green plants through multiple horizontal gene transfer events, primarily from bacteria and fungi. We found a significant shift in the subcellular localization of GH activity during green plant evolution, with a marked increase in extracellular-targeted GH proteins associated with the diversification of plant cell wall polysaccharides and defense mechanisms against pathogens. In conclusion, our study sheds light on the macroevolutionary processes that have shaped the GH repertoire in plants, highlighting the acquisition of GH families through horizontal transfer and the role of GHs in plant adaptation and defense mechanisms.
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Affiliation(s)
- Beatriz Kfoury
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Wenderson Felipe Costa Rodrigues
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Graduate Program in Plant Biology, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Sang-Jin Kim
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Luiz-Eduardo Del-Bem
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Graduate Program in Plant Biology, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
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9
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Park S, Kwak M, Park S. Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data. Sci Rep 2024; 14:7636. [PMID: 38561351 PMCID: PMC10985005 DOI: 10.1038/s41598-024-58253-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Abies koreana E.H.Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history. Using the Illumina NovaSeq 6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from A. koreana. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking conserved gene clusters. In the plastome, the ONT reads revealed two structural conformations of A. koreana. The short inverted repeats (1186 bp) of the A. koreana plastome are associated with different structural types. Transcriptomic sequencing revealed 1356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using A. koreana as a reference, we additionally produced nuclear and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (Balsamea, Momi, and Pseudopicea) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization. The obtained data illustrate that phylogenomic analyses based on sequences from differently inherited organelle genomes have resulted in conflicting trees. Organelle capture, organelle genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within Abies and new insights into the phylogenomic complexity of this genus.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - Myounghai Kwak
- National Institute of Biological Resources, Incheon, 22689, South Korea.
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
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10
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Fang C, Jiang N, Teresi SJ, Platts AE, Agarwal G, Niederhuth C, Edger PP, Jiang J. Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry. Nat Commun 2024; 15:2491. [PMID: 38509076 PMCID: PMC10954716 DOI: 10.1038/s41467-024-46861-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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11
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Elshamly AMS, Iqbal R, Elshikh MS, Alwasel YA, Chaudhary T. Chitosan combined with humic applications during sensitive growth stages to drought improves nutritional status and water relations of sweet potato. Sci Rep 2024; 14:6351. [PMID: 38491017 PMCID: PMC10943102 DOI: 10.1038/s41598-024-55904-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
The current decline in freshwater resources presents a significant global challenge to crop production, a situation expected to intensify with ongoing climate change. This underscores the need for extensive research to enhance crop yields under drought conditions, a priority for scientists given its vital role in global food security. Our study explores the effects of using humic and chitosan treatments to alleviate drought stress during critical growth phases and their impact on crop yield and water efficiency. We employed four different irrigation strategies: full irrigation, 70% irrigation at the early vine development stage, 70% irrigation during the storage root bulking stage, and 85% irrigation across both stages, complemented by full irrigation in other periods. The plants received either humic treatments through foliar spray or soil application, or chitosan foliar applications, with tap water serving as a control. Our findings highlight that the early vine development stage is particularly vulnerable to drought, with a 42.0% decrease in yield observed under such conditions. In normal growth scenarios, foliar application of humic substances significantly improved growth parameters, resulting in a substantial increase in yield and water efficiency by 66.9% and 68.4%, respectively, compared to the control treatment under full irrigation. For sweet potatoes irrigated with 70% water at the storage root bulking stage, ground application of humic substances outperformed both foliar applications of chitosan and humic in terms of yield results. The highest tuber yield and water efficiency were attained by combining chitosan and humic ground applications, regardless of whether 70% irrigation was used at the storage root bulking stage or 85% irrigation during both the early vine development and storage root bulking stages.
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Affiliation(s)
- Ayman M S Elshamly
- Water Studies and Research Complex, National Water Research Center, Cairo, Egypt.
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Yasmeen A Alwasel
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Talha Chaudhary
- Faculty of Agricultural and Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Godollo, 2100, Hungary.
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12
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Coiro M, Seyfullah LJ. Disparity of cycad leaves dispels the living fossil metaphor. Commun Biol 2024; 7:328. [PMID: 38485767 PMCID: PMC10940627 DOI: 10.1038/s42003-024-06024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists. Here, we use a recent phylogenetic framework and an improved character matrix to reconstruct the Disparity Through Time for cycad leaves using a Principal Coordinate Analysis and employing Pre-Ordination Ancestral State Reconstruction to test the impact of sampling on the results. Our analysis shows that the cycad leaf morsphospace expanded up to the present, with numerous shifts in its general positioning, independently of sampling biases. Moreover, they also show that Zamiaceae expanded rapidly in the Early Cretaceous and continued to expand up to the present, while now-extinct clades experienced a slow contraction from their peak in the Triassic. We also show that rates of evolution were constantly high up to the Early Cretaceous, and then experienced a slight decrease in the Paleogene, followed by a Neogene acceleration. These results show a much more dynamic history for cycads, and suggest that the 'living fossil' metaphor is actually a hindrance to our understanding of their macroevolution.
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Affiliation(s)
- Mario Coiro
- Department of Palaeontology, University of Vienna, Vienna, Austria.
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA.
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13
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Maruta T, Tanaka Y, Yamamoto K, Ishida T, Hamada A, Ishikawa T. Evolutionary insights into strategy shifts for the safe and effective accumulation of ascorbate in plants. J Exp Bot 2024:erae062. [PMID: 38452239 DOI: 10.1093/jxb/erae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Indexed: 03/09/2024]
Abstract
Plants accumulate high concentrations of ascorbate, commonly in their leaves, as a redox buffer. While ascorbate levels have increased during plant evolution, the mechanisms behind this phenomenon are unclear. Moreover, has the increase in ascorbate concentration been achieved without imposing any detrimental effects on the plants? In this review, we focus on potential transitions in two regulatory mechanisms related to ascorbate biosynthesis and the availability of cellular dehydroascorbate (DHA) during plant evolution. The first transition might be that the trigger for the transcriptional induction of VTC2, which encodes the rate-limiting enzyme in ascorbate biosynthesis, has shifted from oxidative stress (in green algae) to light/photosynthesis (in land plants), probably enabling the continuous accumulation of ascorbate under illumination. This could serve as a preventive system against the unpredictable occurrence of oxidative stress. The second transition might be that DHA-degrading enzymes, which protect cells from the highly reactive DHA in green algae and mosses, have been lost in ferns or flowering plants. Instead, flowering plants may have increased glutathione concentrations to reinforce the DHA reduction capacity, possibly allowing ascorbate accumulation and avoiding the toxicity of DHA. These potential transitions may have contributed to strategies for plants' safe and effective accumulation of ascorbate.
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Affiliation(s)
- Takanori Maruta
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Yasuhiro Tanaka
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
| | - Kojiro Yamamoto
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Tetsuya Ishida
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Akane Hamada
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Takahiro Ishikawa
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
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14
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Zhou H, Zhang X, Liu H, Ma J, Hao F, Ye H, Wang Y, Zhang S, Yue M, Zhao P. Chromosome-level genome assembly of Platycarya strobilacea. Sci Data 2024; 11:269. [PMID: 38443357 PMCID: PMC10914804 DOI: 10.1038/s41597-024-03107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
Platycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases. This new high-quality assembly of P. strobilacea provide valuable resource for the phylogenetic and evolutionary analysis of the walnut family and angiosperm.
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Affiliation(s)
- Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Xuedong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Fan Hao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yaling Wang
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ming Yue
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China.
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15
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Lim I, Park YJ, Ha J. Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies. Sci Rep 2024; 14:5226. [PMID: 38433262 PMCID: PMC10909864 DOI: 10.1038/s41598-024-55581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024] Open
Abstract
The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.
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Affiliation(s)
- Insu Lim
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Yong-Jin Park
- Department of Plant Sciences, Kongju National University, Yesan, 340-702, Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea.
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16
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Feng X, Chen Q, Wu W, Wang J, Li G, Xu S, Shao S, Liu M, Zhong C, Wu CI, Shi S, He Z. Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication. Nat Commun 2024; 15:1635. [PMID: 38388712 PMCID: PMC10884412 DOI: 10.1038/s41467-024-46080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. To elucidate the role of ploidy changes in genome evolution, we improve a model of the polyploidization-rediploidization process based on genomic evidence, contributing to the understanding of adaptive evolution during climate change.
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Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Jiexin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Guohong Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), 571100, Haikou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
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17
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Leng L, Xu Z, Hong B, Zhao B, Tian Y, Wang C, Yang L, Zou Z, Li L, Liu K, Peng W, Liu J, An Z, Wang Y, Duan B, Hu Z, Zheng C, Zhang S, Li X, Li M, Liu Z, Bi Z, He T, Liu B, Fan H, Song C, Tong Y, Chen S. Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery. Nat Commun 2024; 15:1537. [PMID: 38378731 PMCID: PMC10879537 DOI: 10.1038/s41467-024-45690-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Cepharanthine is a secondary metabolite isolated from Stephania. It has been reported that it has anti-conronaviruses activities including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Here, we assemble three Stephania genomes (S. japonica, S. yunnanensis, and S. cepharantha), propose the cepharanthine biosynthetic pathway, and assess the antiviral potential of compounds involved in the pathway. Among the three genomes, S. japonica has a near telomere-to-telomere assembly with one remaining gap, and S. cepharantha and S. yunnanensis have chromosome-level assemblies. Following by biosynthetic gene mining and metabolomics analysis, we identify seven cepharanthine analogs that have broad-spectrum anti-coronavirus activities, including SARS-CoV-2, Guangxi pangolin-CoV (GX_P2V), swine acute diarrhoea syndrome coronavirus (SADS-CoV), and porcine epidemic diarrhea virus (PEDV). We also show that two other genera, Nelumbo and Thalictrum, can produce cepharanthine analogs, and thus have the potential for antiviral compound discovery. Results generated from this study could accelerate broad-spectrum anti-coronavirus drug discovery.
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Affiliation(s)
- Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Bixia Hong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Binbin Zhao
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, 100730, China
| | - Ya Tian
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Can Wang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Lulu Yang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhongmei Zou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Lingyu Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Ke Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wanjun Peng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, 100730, China
| | - Jiangning Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, 100730, China
| | - Zhoujie An
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yalin Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Chuan Zheng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Sanyin Zhang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xiaodong Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhaoyu Liu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zenghao Bi
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tianxing He
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baimei Liu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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18
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Carruthers T, Moerland MS, Ebersbach J, Favre A, Folk RA, Hawkins JA, Muellner-Riehl AN, Röser M, Soltis DE, Tkach N, Baker WJ, de Vos JM, Eiserhardt WL. Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling. Nat Commun 2024; 15:1100. [PMID: 38321017 PMCID: PMC10847498 DOI: 10.1038/s41467-024-45289-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
Mountains are among the most biodiverse places on Earth, and plant lineages that inhabit them have some of the highest speciation rates ever recorded. Plant diversity within the alpine zone - the elevation above which trees cannot grow-contributes significantly to overall diversity within mountain systems, but the origins of alpine plant diversity are poorly understood. Here, we quantify the processes that generate alpine plant diversity and their changing dynamics through time in Saxifraga (Saxifragaceae), an angiosperm genus that occurs predominantly in mountain systems. We present a time-calibrated molecular phylogenetic tree for the genus that is inferred from 329 low-copy nuclear loci and incorporates 73% (407) of known species. We show that upslope biome shifts into the alpine zone are considerably more prevalent than dispersal of alpine specialists between regions, and that the rate of upslope biome shifts increased markedly in the last 5 Myr, a timeframe concordant with a cooling and fluctuating climate that is likely to have increased the extent of the alpine zone. Furthermore, alpine zone specialists have lower speciation rates than generalists that occur inside and outside the alpine zone, and major speciation rate increases within Saxifraga significantly pre-date increased rates of upslope biome shifts. Specialisation to the alpine zone is not therefore associated with speciation rate increases. Taken together, this study presents a quantified and broad scale perspective of processes underpinning alpine plant diversity.
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Affiliation(s)
- Tom Carruthers
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Michelangelo S Moerland
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, RG6 6EX, UK
| | - Jana Ebersbach
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, D-04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103, Leipzig, Germany
| | - Adrien Favre
- Regional Nature Park of the Trient Valley, la Place 24, 1922, Salvan, Switzerland
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
| | - Julie A Hawkins
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, RG6 6EX, UK
| | - Alexandra N Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, D-04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103, Leipzig, Germany
| | - Martin Röser
- Martin Luther University Halle-Wittenberg, Institute of Biology, Geobotany and Botanical Garden, Dept. of Systematic Botany, Neuwerk 21, 06108, Halle, Germany
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Natalia Tkach
- Martin Luther University Halle-Wittenberg, Institute of Biology, Geobotany and Botanical Garden, Dept. of Systematic Botany, Neuwerk 21, 06108, Halle, Germany
| | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Jurriaan M de Vos
- Department of Environmental Sciences-Botany, University of Basel, Schönbeinstrasse 6, 4056, Basel, Switzerland
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.
- Department of Biology, Aarhus University, 8000, Aarhus C, Denmark.
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19
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Evans SE, Franks AE, Bergman ME, Sethna NS, Currie MA, Phillips MA. Plastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway. Nat Commun 2024; 15:1102. [PMID: 38321044 PMCID: PMC10847513 DOI: 10.1038/s41467-024-45384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/20/2024] [Indexed: 02/08/2024] Open
Abstract
The Entner-Doudoroff (ED) pathway provides an alternative to glycolysis. It converts 6-phosphogluconate (6-PG) to glyceraldehyde-3-phosphate and pyruvate in two steps consisting of a dehydratase (EDD) and an aldolase (EDA). Here, we investigate its distribution and significance in higher plants and determine the ED pathway is restricted to prokaryotes due to the absence of EDD genes in eukaryotes. EDDs share a common origin with dihydroxy-acid dehydratases (DHADs) of the branched chain amino acid pathway (BCAA). Each dehydratase features strict substrate specificity. E. coli EDD dehydrates 6-PG to 2-keto-3-deoxy-6-phosphogluconate, while DHAD only dehydrates substrates from the BCAA pathway. Structural modeling identifies two divergent domains which account for their non-overlapping substrate affinities. Coupled enzyme assays confirm only EDD participates in the ED pathway. Plastid ancestors lacked EDD but transferred metabolically promiscuous EDA, which explains the absence of the ED pathway from the Viridiplantae and sporadic persistence of EDA genes across the plant kingdom.
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Affiliation(s)
- Sonia E Evans
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Anya E Franks
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Matthew E Bergman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Nasha S Sethna
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Mark A Currie
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Michael A Phillips
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada.
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20
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Bierenbroodspot MJ, Darienko T, de Vries S, Fürst-Jansen JMR, Buschmann H, Pröschold T, Irisarri I, de Vries J. Phylogenomic insights into the first multicellular streptophyte. Curr Biol 2024; 34:670-681.e7. [PMID: 38244543 PMCID: PMC10849092 DOI: 10.1016/j.cub.2023.12.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).1,2,3,4 Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments-from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)-Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats.5,6 Currently, the lack of a robust phylogenetic framework for the Klebsormidiophyceae hampers our understanding of the evolutionary history of these key traits. Here, we conducted a phylogenomic analysis utilizing advanced models that can counteract systematic biases. We sequenced 24 new transcriptomes of Klebsormidiophyceae and combined them with 14 previously published genomic and transcriptomic datasets. Using an analysis built on 845 loci and sophisticated mixture models, we establish a phylogenomic framework, dividing the six distinct genera of Klebsormidiophyceae in a novel three-order system, with a deep divergence more than 830 million years ago. Our reconstructions of ancestral states suggest (1) an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with stem Klebsormidiales having conquered land earlier than embryophytes, and (2) that the body plan of the last common ancestor of Klebsormidiophyceae was multicellular, with a high probability that it was filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. We provide evidence that the first multicellular streptophytes likely lived about a billion years ago.
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Affiliation(s)
- Maaike J Bierenbroodspot
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Janine M R Fürst-Jansen
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Thomas Pröschold
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Innsbruck, Research Department for Limnology, 5310 Mondsee, Austria
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany.
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany.
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21
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Song Y, Huang JP, Wang YJ, Huang SX. Chromosome level genome assembly of endangered medicinal plant Anisodus tanguticus. Sci Data 2024; 11:161. [PMID: 38307894 PMCID: PMC10837431 DOI: 10.1038/s41597-024-03007-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/26/2024] [Indexed: 02/04/2024] Open
Abstract
Anisodus tanguticus is a medicinal herb that belongs to the Anisodus genus of the Solanaceae family. This endangered herb is mainly distributed in Qinghai-Tibet Plateau. In this study, we combined the Illumina short-read, Nanopore long-read and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to de novo assemble the A. tanguticus genome. A high-quality chromosomal-level genome assembly was obtained with a genome size of 1.26 Gb and a contig N50 of 25.07 Mb. Of the draft genome sequences, 97.47% were anchored to 24 pseudochromosomes with a scaffold N50 of 51.28 Mb. In addition, 842.14 Mb of transposable elements occupying 66.70% of the genome assembly were identified and 44,252 protein-coding genes were predicted. The genome assembly of A. tanguticus will provide genetic repertoire to understand the adaptation strategy of Anisodus species in the plateau, which will further promote the conservation of endangered A. tanguticus resources.
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Affiliation(s)
- Yongli Song
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jian-Ping Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yong-Jiang Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Sheng-Xiong Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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22
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Bowles AMC, Williamson CJ, Williams TA, Donoghue PCJ. Cryogenian Origins of Multicellularity in Archaeplastida. Genome Biol Evol 2024; 16:evae026. [PMID: 38333966 PMCID: PMC10883732 DOI: 10.1093/gbe/evae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
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23
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Malacrinò A, Böttner L, Nouere S, Huber M, Schäfer M, Xu S. Induced responses contribute to rapid adaptation of Spirodela polyrhiza to herbivory by Lymnaea stagnalis. Commun Biol 2024; 7:81. [PMID: 38200287 PMCID: PMC10781955 DOI: 10.1038/s42003-023-05706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolve populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail), testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We show that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggest that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.
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Affiliation(s)
- Antonino Malacrinò
- Department of Agriculture, Università degli Studi Mediterranea di Reggio Calabria, Reggio Calabria, Italy.
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
| | - Laura Böttner
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Sara Nouere
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Meret Huber
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Schäfer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany.
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24
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He J, Tian D, Li X, Wang X, Wang T, Wang Z, Zang H, He X, Zhang T, Yun Q, Zhang R, Jiang J, Jia S, Zhang Y. A chromosome-level genome assembly for Onobrychis viciifolia reveals gene copy number gain underlying enhanced proanthocyanidin biosynthesis. Commun Biol 2024; 7:19. [PMID: 38182881 PMCID: PMC10770414 DOI: 10.1038/s42003-023-05754-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024] Open
Abstract
Sainfoin (Onobrychis viciifolia), which belongs to subfamily Papilionoideae of Leguminosae, is a vital perennial forage known as "holy hay" due to its high contents of crude proteins and proanthocyanidins (PAs, also called condensed tannins) that have various pharmacological properties in animal feed, such as alleviating rumen tympanic disease in ruminants. In this study, we select an autotetraploid common sainfoin (2n = 4x = 28) and report its high-quality chromosome-level genome assembly with 28 pseudochromosomes and four haplotypes (~1950.14 Mb, contig N50 = 10.91 Mb). The copy numbers of genes involved in PA biosynthesis in sainfoin are significantly greater than those in four selected Fabales species, namely, autotetraploid Medicago sativa and three other diploid species, Lotus japonicus, Medicago truncatula, and Glycine max. Furthermore, gene expansion is confirmed to be the key contributor to the increased expression of these genes and subsequent PA enhancement in sainfoin. Transcriptomic analyses reveal that the expression of genes involved in the PA biosynthesis pathway is significantly increased in the lines with high PA content compared to the lines with medium and low PA content. The sainfoin genome assembly will improve our understanding of leguminous genome evolution and biosynthesis of secondary metabolites in sainfoin.
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Affiliation(s)
- Junyi He
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Danyang Tian
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xue Li
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xuemeng Wang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Tingting Wang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Ziyao Wang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Hui Zang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xiaofan He
- School of Grassland Science, Beijing Forestry University, 100083, Beijing, China
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, 100083, Beijing, China
| | - Quanzheng Yun
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, 261322, China
| | - Rengang Zhang
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, 261322, China
| | - Jishan Jiang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China.
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China.
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25
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Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell 2024; 187:130-148.e17. [PMID: 38128538 PMCID: PMC10783624 DOI: 10.1016/j.cell.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/29/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023]
Abstract
The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.
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Affiliation(s)
- Andre Kuhn
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Mark Roosjen
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Shiv Mani Dubey
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | | | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Aline Monzer
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jasper Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Joris Sprakel
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Jiří Friml
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands.
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26
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D'Ario M, Lane B, Fioratti Junod M, Leslie A, Mosca G, Smith RS. Hidden functional complexity in the flora of an early land ecosystem. New Phytol 2024; 241:937-949. [PMID: 37644727 PMCID: PMC10952896 DOI: 10.1111/nph.19228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023]
Abstract
The first land ecosystems were composed of organisms considered simple in nature, yet the morphological diversity of their flora was extraordinary. The biological significance of this diversity remains a mystery largely due to the absence of feasible study approaches. To study the functional biology of Early Devonian flora, we have reconstructed extinct plants from fossilised remains in silico. We explored the morphological diversity of sporangia in relation to their mechanical properties using finite element method. Our approach highlights the impact of sporangia morphology on spore dispersal and adaptation. We discovered previously unidentified innovations among early land plants, discussing how different species might have opted for different spore dispersal strategies. We present examples of convergent evolution for turgor pressure resistance, achieved by homogenisation of stress in spherical sporangia and by torquing force in Tortilicaulis-like specimens. In addition, we show a potential mechanism for stress-assisted sporangium rupture. Our study reveals the deceptive complexity of this seemingly simple group of organisms. We leveraged the quantitative nature of our approach and constructed a fitness landscape to understand the different ecological niches present in the Early Devonian Welsh Borderland flora. By connecting morphology to functional biology, these findings facilitate a deeper understanding of the diversity of early land plants and their place within their ecosystem.
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Affiliation(s)
| | | | | | | | - Gabriella Mosca
- Technical University of Munich80333MunichGermany
- Center for Plant Molecular Biology‐ZMBPUniversity of Tübingen72076TübingenGermany
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27
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Hu Y, Feng C, Wu B, Kang M. A chromosome-scale assembly of the early-flowering Prunus campanulata and comparative genomics of cherries. Sci Data 2023; 10:920. [PMID: 38129445 PMCID: PMC10739980 DOI: 10.1038/s41597-023-02843-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Prunus campanulata is an important flowering cherry germplasm of high ornamental value. Given its early-flowering phenotypes, P. campanulata could be used for molecular breeding of ornamental species and fruit crops belonging to the subgenus Cerasus. Here, we report a chromosome-scale assembly of P. campanulata with a genome size of 282.6 Mb and a contig N50 length of 12.04 Mb. The genome contained 24,861 protein-coding genes, of which 24,749 genes (99.5%) were functionally annotated, and 148.20 Mb (52.4%) of the assembled sequences are repetitive sequences. A combination of genomic and population genomic analyses revealed a number of genes under positive selection or accelerated molecular evolution in P. campanulata. Our study provides a reliable genome resource, and lays a solid foundation for genetic improvement of flowering cherry germplasm.
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Affiliation(s)
- Yuxi Hu
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Feng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Baohuan Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Ming Kang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
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28
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Mulvey H, Dolan L. RHO of plant signaling was established early in streptophyte evolution. Curr Biol 2023; 33:5515-5525.e4. [PMID: 38039969 DOI: 10.1016/j.cub.2023.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
The algal ancestors of land plants underwent a transition from a unicellular to a multicellular body plan.1 This transition likely took place early in streptophyte evolution, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage.2 How this transition was brought about is unknown; however, it was likely facilitated by the evolution of novel mechanisms to spatially regulate morphogenesis. In land plants, RHO of plant (ROP) signaling plays a conserved role in regulating polarized cell growth and cell division orientation to orchestrate morphogenesis.3,4,5,6,7,8 ROP constitutes a plant-specific subfamily of the RHO GTPases, which are more widely conserved throughout eukaryotes.9,10 Although the RHO family originated in early eukaryotes,11,12 how and when the ROP subfamily originated had remained elusive. Here, we demonstrate that ROP signaling was established early in the streptophyte lineage, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage. This period corresponds to when the unicellular-to-multicellular transition likely took place in the streptophytes. In addition to being critical for the complex morphogenesis of extant land plants, we speculate that ROP signaling contributed to morphological evolution in early streptophytes.
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Affiliation(s)
- Hugh Mulvey
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Liam Dolan
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria.
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Liu D, Tian X, Shao S, Ma Y, Zhang R. Haplotype-resolved chromosomal-level genome assembly of Buzhaye (Microcos paniculata). Sci Data 2023; 10:901. [PMID: 38102170 PMCID: PMC10724166 DOI: 10.1038/s41597-023-02821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Microcos paniculata is a shrub used traditionally as folk medicine and to make herbal teas. Previous research into this species has mainly focused on its chemical composition and medicinal value. However, the lack of a reference genome limits the study of the molecular mechanisms of active compounds in this species. Here, we assembled a haplotype-resolved chromosome-level genome of M. paniculata based on PacBio HiFi and Hi-C data. The assembly contains two haploid genomes with sizes 399.43 Mb and 393.10 Mb, with contig N50 lengths of 43.44 Mb and 30.17 Mb, respectively. About 99.93% of the assembled sequences could be anchored to 18 pseudo-chromosomes. Additionally, a total of 482 Mb repeat sequences were identified, accounting for 60.76% of the genome. A total of 49,439 protein-coding genes were identified, of which 48,979 (99%) were functionally annotated. This haplotype-resolved chromosome-level assembly and annotation of M. paniculata will serve as a valuable resource for investigating the biosynthesis and genetic basis of active compounds in this species, as well as advancing evolutionary phylogenomic studies in Malvales.
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Affiliation(s)
- Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaoling Tian
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China
| | - Shicheng Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- University of Chinese Academy of Sciences, Beijing, 101408, China.
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30
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Rey E, Maughan PJ, Maumus F, Lewis D, Wilson L, Fuller J, Schmöckel SM, Jellen EN, Tester M, Jarvis DE. A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes. Commun Biol 2023; 6:1263. [PMID: 38092895 PMCID: PMC10719370 DOI: 10.1038/s42003-023-05613-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for four accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we use in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean accession PI 614886 (QQ74). The final assembly spans 1.326 Gb, of which 90.5% is assembled into 18 chromosome-scale scaffolds. The genome is annotated with 54,499 protein-coding genes, 96.9% of which are located on the 18 largest scaffolds. We also report an updated genome assembly for the B-genome diploid C. suecicum and use it, together with the A-genome diploid C. pallidicaule, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.2%, 48.6%, and 57.9% of the quinoa, C. pallidicaule, and C. suecicum genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.
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Affiliation(s)
- Elodie Rey
- 1King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Peter J Maughan
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Daniel Lewis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Leanne Wilson
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Juliana Fuller
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Sandra M Schmöckel
- University of Hohenheim, Institute of Crop Science, Department Physiology of Yield Stability, 70599, Stuttgart, Germany
| | - Eric N Jellen
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Mark Tester
- 1King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - David E Jarvis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA.
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31
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Bidhendi AJ, Lampron O, Gosselin FP, Geitmann A. Cell geometry regulates tissue fracture. Nat Commun 2023; 14:8275. [PMID: 38092784 PMCID: PMC10719271 DOI: 10.1038/s41467-023-44075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
In vascular plants, the epidermal surfaces of leaves and flower petals often display cells with wavy geometries forming intricate jigsaw puzzle patterns. The prevalence and diversity of these complex epidermal patterns, originating from simple polyhedral progenitor cells, suggest adaptive significance. However, despite multiple efforts to explain the evolutionary drivers behind these geometrical features, compelling validation remains elusive. Employing a multidisciplinary approach that integrates microscopic and macroscopic fracture experiments with computational fracture mechanics, we demonstrate that wavy epidermal cells toughen the plants' protective skin. Through a multi-scale framework, we demonstrate that this energy-efficient patterning mechanism is universally applicable for toughening biological and synthetic materials. Our findings reveal a tunable structural-mechanical strategy employed in the microscale design of plants to protect them from deleterious surface fissures while facilitating and strategically directing beneficial ones. These findings hold implications for targeted plant breeding aimed at enhancing resilience in fluctuating environmental conditions. From an engineering perspective, our work highlights the sophisticated design principles the plant kingdom offers to inspire metamaterials.
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Affiliation(s)
- Amir J Bidhendi
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore, Ste-Anne-de-Bellevue, Québec, H9X 3V9, Canada.
- EERS Global Technologies, Montreal, Canada.
| | - Olivier Lampron
- Laboratoire de Mécanique Multi-échelles, Département de génie mécanique, École Polytechnique de Montréal, Montreal, Québec, H3C 3A7, Canada
| | - Frédérick P Gosselin
- Laboratoire de Mécanique Multi-échelles, Département de génie mécanique, École Polytechnique de Montréal, Montreal, Québec, H3C 3A7, Canada
| | - Anja Geitmann
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore, Ste-Anne-de-Bellevue, Québec, H9X 3V9, Canada.
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32
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Ji Z, Belfield EJ, Zhang S, Bouvier J, Li S, Schnell J, Fu X, Harberd NP. Evolution of a plant growth-regulatory protein interaction specificity. Nat Plants 2023; 9:2059-2070. [PMID: 37903985 PMCID: PMC10724065 DOI: 10.1038/s41477-023-01556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023]
Abstract
Specific protein-protein interactions (PPIs) enable biological regulation. However, the evolution of PPI specificity is little understood. Here we trace the evolution of the land-plant growth-regulatory DELLA-SLY1/GID2 PPI, revealing progressive increase in specificity of affinity of SLY1/GID2 for a particular DELLA form. While early-diverging SLY1s display relatively broad-range DELLA affinity, later-diverging SLY1s tend towards increasingly stringent affinity for a specific DELLA A' form generated by the growth-promoting phytohormone gibberellin (GA). Our novel mutational strategy reveals amino acid substitutions contributing to the evolution of Arabidopsis thaliana SLY1 A' specificity, also showing that routes permitting reversion to broader affinity became increasingly constrained over evolutionary time. We suggest that progressive affinity narrowing may be an important evolutionary driver of PPI specificity and that increase in SLY1/GID2-DELLA specificity enabled the enhanced flexibility of plant physiological environmental adaptation conferred by the GA-DELLA growth-regulatory mechanism.
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Affiliation(s)
- Zhe Ji
- Department of Biology, University of Oxford, Oxford, UK
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
| | | | - Siyu Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, PR China
| | | | - Shan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, PR China
| | - Jason Schnell
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P. R. China
- New Cornerstone Science Laboratory, Beijing, P. R. China
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Chen T, Xu J, Wang L, Wang H, You E, Deng C, Bian H, Shen Y. Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau. Heredity (Edinb) 2023; 131:316-326. [PMID: 37935814 PMCID: PMC10673939 DOI: 10.1038/s41437-023-00647-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 11/09/2023] Open
Abstract
Understanding the local adaptation of crops has long been a concern of evolutionary biologists and molecular ecologists. Identifying the adaptive genetic variability in the genome is crucial not only to provide insights into the genetic mechanism of local adaptation but also to explore the adaptation potential of crops. This study aimed to identify the climatic drivers of naked barley landraces and putative adaptive loci driving local adaptation on the Qinghai-Tibetan Plateau (QTP). To this end, a total of 157 diverse naked barley accessions were genotyped using the genotyping-by-sequencing approach, which yielded 3123 high-quality SNPs for population structure analysis and partial redundancy analysis, and 37,636 SNPs for outlier analysis. The population structure analysis indicated that naked barley landraces could be divided into four groups. We found that the genomic diversity of naked barley landraces could be partly traced back to the geographical and environmental diversity of the landscape. In total, 136 signatures associated with temperature, precipitation, and ultraviolet radiation were identified, of which 13 had pleiotropic effects. We mapped 447 genes, including a known gene HvSs1. Some genes involved in cold stress and regulation of flowering time were detected near eight signatures. Taken together, these results highlight the existence of putative adaptive loci in naked barley on QTP and thus improve our current understanding of the genetic basis of local adaptation.
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Affiliation(s)
- Tongrui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinqing Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - Handong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - En You
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Deng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Bian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhu Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China.
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Tamaki I, Mizuno M, Ohtsuki T, Shutoh K, Tabata R, Tsunamoto Y, Suyama Y, Nakajima Y, Kubo N, Ito T, Noma N, Harada E. Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced. Sci Rep 2023; 13:20746. [PMID: 38007576 PMCID: PMC10676423 DOI: 10.1038/s41598-023-48079-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023] Open
Abstract
Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300-400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native.
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Affiliation(s)
- Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan
- Gifu Prefectural Research Institute for Forests, 1128-1 Sodai, Mino, Gifu, 501-3714, Japan
| | - Mizuo Mizuno
- Gifu Pharmaceutical University, 5-6-1 Mitahora-Higashi, Gifu, 502-8585, Japan
| | - Tatsuo Ohtsuki
- Lake Biwa Museum, 1091 Oroshimo, Kusatsu, Shiga, 525-0001, Japan
| | - Kohtaroh Shutoh
- The Hokkaido University Museum, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Ryoichi Tabata
- Lake Biwa Museum, 1091 Oroshimo, Kusatsu, Shiga, 525-0001, Japan
| | - Yoshihiro Tsunamoto
- Research Institute of Energy, Environment and Geology, Hokkaido Research Organization, Kita 19 Nishi 12, Kita-ku, Sapporo, Hokkaido, 060-0819, Japan
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yusuke Nakajima
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan
| | - Naoki Kubo
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan
| | - Takeru Ito
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan
| | - Naohiko Noma
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan
| | - Emiko Harada
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan.
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35
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Li Z, Zhang Y, Ding CH, Chen Y, Wang H, Zhang J, Ying S, Wang M, Zhang R, Liu J, Xie Y, Tang T, Diao H, Ye L, Zhuang Y, Teng W, Zhang B, Huang L, Tong Y, Zhang W, Li G, Benhamed M, Dong Z, Gou JY, Zhang Y. LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat. Nat Commun 2023; 14:7538. [PMID: 37985755 PMCID: PMC10661560 DOI: 10.1038/s41467-023-43178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
Polyploidization is a major driver of genome diversification and environmental adaptation. However, the merger of different genomes may result in genomic conflicts, raising a major question regarding how genetic diversity is interpreted and regulated to enable environmental plasticity. By analyzing the genome-wide binding of 191 trans-factors in allopolyploid wheat, we identified like heterochromatin protein 1 (LHP1) as a master regulator of subgenome-diversified genes. Transcriptomic and epigenomic analyses of LHP1 mutants reveal its role in buffering the expression of subgenome-diversified defense genes by controlling H3K27me3 homeostasis. Stripe rust infection releases latent subgenomic variations by eliminating H3K27me3-related repression. The simultaneous inactivation of LHP1 homoeologs by CRISPR-Cas9 confers robust stripe rust resistance in wheat seedlings. The conditional repression of subgenome-diversified defenses ensures developmental plasticity to external changes, while also promoting neutral-to-non-neutral selection transitions and adaptive evolution. These findings establish an LHP1-mediated buffering system at the intersection of genotypes, environments, and phenotypes in polyploid wheat. Manipulating the epigenetic buffering capacity offers a tool to harness cryptic subgenomic variations for crop improvement.
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Affiliation(s)
- Zijuan Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuyun Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ci-Hang Ding
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China
| | - Haoyu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- Henan University, School of Life Science, 457000, Kaifeng, Henan, China
| | - Jinyu Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Songbei Ying
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Meiyue Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Rongzhi Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Jinan, China
- National Engineering Research Center for Wheat and Maize, Jinan, Shandong, China
| | - Jinyi Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yilin Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Tengfei Tang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- Henan University, School of Life Science, 457000, Kaifeng, Henan, China
| | - Huishan Diao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bo Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Wenjiang, Chengdu, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, 210095, Nanjing, Jiangsu, China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Jinan, China
- National Engineering Research Center for Wheat and Maize, Jinan, Shandong, China
| | - Moussa Benhamed
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006, Paris, France.
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China.
| | - Jin-Ying Gou
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China.
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.
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You S, Zhao Z, Yu X, Zhu S, Wang J, Lei D, Zhou J, Li J, Chen H, Xiao Y, Chen W, Wang Q, Lu J, Chen K, Zhou C, Zhang X, Cheng Z, Guo X, Ren Y, Zheng X, Liu S, Liu X, Tian Y, Jiang L, Tao D, Wu C, Wan J. A toxin-antidote system contributes to interspecific reproductive isolation in rice. Nat Commun 2023; 14:7528. [PMID: 37980335 PMCID: PMC10657391 DOI: 10.1038/s41467-023-43015-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/18/2023] [Indexed: 11/20/2023] Open
Abstract
Breakdown of reproductive isolation facilitates flow of useful trait genes into crop plants from their wild relatives. Hybrid sterility, a major form of reproductive isolation exists between cultivated rice (Oryza sativa) and wild rice (O. meridionalis, Mer). Here, we report the cloning of qHMS1, a quantitative trait locus controlling hybrid male sterility between these two species. Like qHMS7, another locus we cloned previously, qHMS1 encodes a toxin-antidote system, but differs in the encoded proteins, their evolutionary origin, and action time point during pollen development. In plants heterozygous at qHMS1, ~ 50% of pollens carrying qHMS1-D (an allele from cultivated rice) are selectively killed. In plants heterozygous at both qHMS1 and qHMS7, ~ 75% pollens without co-presence of qHMS1-Mer and qHMS7-D are selectively killed, indicating that the antidotes function in a toxin-dependent manner. Our results indicate that different toxin-antidote systems provide stacked reproductive isolation for maintaining species identity and shed light on breakdown of hybrid male sterility.
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Affiliation(s)
- Shimin You
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Zhigang Zhao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Xiaowen Yu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Shanshan Zhu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Dekun Lei
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Jiawu Zhou
- Yunnan Seed Laboratory/Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, P. R. China
| | - Jing Li
- Yunnan Seed Laboratory/Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, P. R. China
| | - Haiyuan Chen
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Yanjia Xiao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Weiwei Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Qiming Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Jiayu Lu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Keyi Chen
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Xin Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiuping Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiaoming Zheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Dayun Tao
- Yunnan Seed Laboratory/Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, P. R. China.
| | - Chuanyin Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China.
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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37
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Miyagishima SY. Taming the perils of photosynthesis by eukaryotes: constraints on endosymbiotic evolution in aquatic ecosystems. Commun Biol 2023; 6:1150. [PMID: 37952050 PMCID: PMC10640588 DOI: 10.1038/s42003-023-05544-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
An ancestral eukaryote acquired photosynthesis by genetically integrating a cyanobacterial endosymbiont as the chloroplast. The chloroplast was then further integrated into many other eukaryotic lineages through secondary endosymbiotic events of unicellular eukaryotic algae. While photosynthesis enables autotrophy, it also generates reactive oxygen species that can cause oxidative stress. To mitigate the stress, photosynthetic eukaryotes employ various mechanisms, including regulating chloroplast light absorption and repairing or removing damaged chloroplasts by sensing light and photosynthetic status. Recent studies have shown that, besides algae and plants with innate chloroplasts, several lineages of numerous unicellular eukaryotes engage in acquired phototrophy by hosting algal endosymbionts or by transiently utilizing chloroplasts sequestrated from algal prey in aquatic ecosystems. In addition, it has become evident that unicellular organisms engaged in acquired phototrophy, as well as those that feed on algae, have also developed mechanisms to cope with photosynthetic oxidative stress. These mechanisms are limited but similar to those employed by algae and plants. Thus, there appear to be constraints on the evolution of those mechanisms, which likely began by incorporating photosynthetic cells before the establishment of chloroplasts by extending preexisting mechanisms to cope with oxidative stress originating from mitochondrial respiration and acquiring new mechanisms.
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Affiliation(s)
- Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
- The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
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38
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Polturak G, Misra RC, El-Demerdash A, Owen C, Steed A, McDonald HP, Wang J, Saalbach G, Martins C, Chartrain L, Wilkinson B, Nicholson P, Osbourn A. Discovery of isoflavone phytoalexins in wheat reveals an alternative route to isoflavonoid biosynthesis. Nat Commun 2023; 14:6977. [PMID: 37914713 PMCID: PMC10620232 DOI: 10.1038/s41467-023-42464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
Isoflavones are a group of phenolic compounds mostly restricted to plants of the legume family, where they mediate important interactions with plant-associated microbes, including in defense from pathogens and in nodulation. Their well-studied health promoting attributes have made them a prime target for metabolic engineering, both for bioproduction of isoflavones as high-value molecules, and in biofortification of food crops. A key gene in their biosynthesis, isoflavone synthase, was identified in legumes over two decades ago, but little is known about formation of isoflavones outside of this family. Here we identify a specialized wheat-specific isoflavone synthase, TaCYP71F53, which catalyzes a different reaction from the leguminous isoflavone synthases, thus revealing an alternative path to isoflavonoid biosynthesis and providing a non-transgenic route for engineering isoflavone production in wheat. TaCYP71F53 forms part of a biosynthetic gene cluster that produces a naringenin-derived O-methylated isoflavone, 5-hydroxy-2',4',7-trimethoxyisoflavone, triticein. Pathogen-induced production and in vitro antimicrobial activity of triticein suggest a defense-related role for this molecule in wheat. Genomic and metabolic analyses of wheat ancestral grasses further show that the triticein gene cluster was introduced into domesticated emmer wheat through natural hybridization ~9000 years ago, and encodes a pathogen-responsive metabolic pathway that is conserved in modern bread wheat varieties.
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Affiliation(s)
- Guy Polturak
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK.
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | | | - Amr El-Demerdash
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
- Division of Organic Chemistry, Department of Chemistry, School of Sciences, Mansoura University, Mansoura, 35516, Egypt
| | - Charlotte Owen
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Andrew Steed
- Crop Genetics Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Hannah P McDonald
- Molecular Microbiology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - JiaoJiao Wang
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
- Tsinghua-Peking Joint Center for Life Sciences, and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | | | - Carlo Martins
- Proteomics Facility, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Barrie Wilkinson
- Molecular Microbiology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Paul Nicholson
- Crop Genetics Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Anne Osbourn
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK.
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39
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Zhao H, Wang W, Yang Y, Wang Z, Sun J, Yuan K, Rabbi SMHA, Khanam M, Kabir MS, Seraj ZI, Rahman MS, Zhang Z. A high-quality chromosome-level wild rice genome of Oryza coarctata. Sci Data 2023; 10:701. [PMID: 37838726 PMCID: PMC10576809 DOI: 10.1038/s41597-023-02594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
Oryza coarctata (2n = 4X = 48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of O. coarctata. PacBio high-quality HiFi reads generated 460 contigs with a total length of 573.4 Mb and an N50 of 23.1 Mb, which were assembled into scaffolds with Hi-C data, anchoring 96.99% of the assembly onto 24 chromosomes. The genome assembly comprises 45,571 genes, and repetitive content contributes 25.5% of the genome. This study provides the novel identification of the KK and LL genome types of the genus Oryza, leading to valuable insights into rice genome evolution. The chromosome-level genome assembly of O. coarctata is a valuable resource for rice research and molecular breeding.
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Affiliation(s)
- Hang Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Wenzheng Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yirong Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiwei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaijun Yuan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Duke university, Durham, USA
| | | | - Munnujan Khanam
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | | | - Zeba I Seraj
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | | | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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40
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Kang M, Wu H, Liu H, Liu W, Zhu M, Han Y, Liu W, Chen C, Song Y, Tan L, Yin K, Zhao Y, Yan Z, Lou S, Zan Y, Liu J. The pan-genome and local adaptation of Arabidopsis thaliana. Nat Commun 2023; 14:6259. [PMID: 37802986 PMCID: PMC10558531 DOI: 10.1038/s41467-023-42029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 09/27/2023] [Indexed: 10/08/2023] Open
Abstract
Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.
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Affiliation(s)
- Minghui Kang
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Haolin Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huanhuan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wenyu Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yu Han
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wei Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chunlin Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yan Song
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Luna Tan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Kangqun Yin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yusen Zhao
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhen Yan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Shangling Lou
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Yanjun Zan
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266000, China.
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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41
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Man J, Harrington TA, Lally K, Bartlett ME. Asymmetric Evolution of Protein Domains in the Leucine-Rich Repeat Receptor-Like Kinase Family of Plant Signaling Proteins. Mol Biol Evol 2023; 40:msad220. [PMID: 37787619 PMCID: PMC10588794 DOI: 10.1093/molbev/msad220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/29/2023] [Accepted: 09/26/2023] [Indexed: 10/04/2023] Open
Abstract
The coding sequences of developmental genes are expected to be deeply conserved, with cis-regulatory change driving the modulation of gene function. In contrast, proteins with roles in defense are expected to evolve rapidly, in molecular arms races with pathogens. However, some gene families include both developmental and defense genes. In these families, does the tempo and mode of evolution differ between genes with divergent functions, despite shared ancestry and structure? The leucine-rich repeat receptor-like kinase (LRR-RLKs) protein family includes members with roles in plant development and defense, thus providing an ideal system for answering this question. LRR-RLKs are receptors that traverse plasma membranes. LRR domains bind extracellular ligands; RLK domains initiate intracellular signaling cascades in response to ligand binding. In LRR-RLKs with roles in defense, LRR domains evolve faster than RLK domains. To determine whether this asymmetry extends to LRR-RLKs that function primarily in development, we assessed evolutionary rates and tested for selection acting on 11 subfamilies of LRR-RLKs, using deeply sampled protein trees. To assess functional evolution, we performed heterologous complementation assays in Arabidopsis thaliana (Arabidopsis). We found that the LRR domains of all tested LRR-RLK proteins evolved faster than their cognate RLK domains. All tested subfamilies of LRR-RLKs had strikingly similar patterns of molecular evolution, despite divergent functions. Heterologous transformation experiments revealed that multiple mechanisms likely contribute to the evolution of LRR-RLK function, including escape from adaptive conflict. Our results indicate specific and distinct evolutionary pressures acting on LRR versus RLK domains, despite diverse organismal roles for LRR-RLK proteins.
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Affiliation(s)
- Jarrett Man
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01002, USA
| | - T A Harrington
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01002, USA
| | - Kyra Lally
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01002, USA
| | - Madelaine E Bartlett
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01002, USA
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42
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Resco de Dios V. Interpreting shoot flammability experiments: from fire behaviour to plant evolution. New Phytol 2023; 240:5-6. [PMID: 37488706 DOI: 10.1111/nph.19152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
This article is a Commentary on Cui et al. (2023), 240: 105–113.
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Affiliation(s)
- Víctor Resco de Dios
- Department of Forest and Agricultural Sciences, Universitat de Lleida, 25198, Lérida, Spain
- Joint Research Unit CTFC-AGROTECNIO-CERCA Center, 25198, Lérida, Spain
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43
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Clark JW, Hetherington AJ, Morris JL, Pressel S, Duckett JG, Puttick MN, Schneider H, Kenrick P, Wellman CH, Donoghue PCJ. Evolution of phenotypic disparity in the plant kingdom. Nat Plants 2023; 9:1618-1626. [PMID: 37666963 PMCID: PMC10581900 DOI: 10.1038/s41477-023-01513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/07/2023] [Indexed: 09/06/2023]
Abstract
The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with disparity but with ploidy history, reflecting the role of genome duplication in plant macroevolution. Overall, the plant kingdom exhibits a pattern of episodically increasing disparity throughout its evolutionary history that mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern also parallels that seen in the animal and fungal kingdoms, suggesting a general pattern for the evolution of multicellular bodyplans.
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Affiliation(s)
- James W Clark
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK.
| | - Alexander J Hetherington
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - Jennifer L Morris
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | | | - Mark N Puttick
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Harald Schneider
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
- The Natural History Museum, London, UK
- Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | | | | | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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Gasser M, Keller J, Fournier P, Pujic P, Normand P, Boubakri H. Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24. Sci Rep 2023; 13:16020. [PMID: 37749152 PMCID: PMC10520049 DOI: 10.1038/s41598-023-41117-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023] Open
Abstract
Non-specific lipid transfer proteins (nsLTPs) are antimicrobial peptides, involved in several plant biological processes including root nodule nitrogen fixation (RNF). Nodulating plants belonging to the RNF clade establish symbiosis with the nitrogen-fixing bacteria rhizobia (legumes symbiosis model) and Frankia (actinorhizal symbiosis model) leading to root nodule formation. nsLTPs are involved in processes active in early step of symbiosis and functional nodule in both models. In legumes, nsLTPs have been shown to regulate symbiont entry, promote root cortex infection, membrane biosynthesis, and improve symbiosis efficiency. More recently, a nsLTP, AgLTP24 has been described in the context of actinorhizal symbiosis between Alnus glutinosa and Frankia alni ACN14a. AgLTP24 is secreted at an early step of symbiosis on the deformed root hairs and targets the symbiont in the nitrogen-fixing vesicles in functional nodules. nsLTPs are involved in RNF, but their functions and evolutionary history are still largely unknown. Numerous putative nsLTPs were found up-regulated in functional nodules compared to non-infected roots in different lineages within the RNF clade. Here, results highlight that nodulating plants that are co-evolving with their nitrogen-fixing symbionts appear to have independently specialized nsLTPs for this interaction, suggesting a possible convergence of function, which opens perspectives to investigate nsLTPs functions in RNF.
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Affiliation(s)
- Mélanie Gasser
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Pascale Fournier
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Petar Pujic
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Philippe Normand
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Hasna Boubakri
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France.
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Chen R, Xiao N, Lu Y, Tao T, Huang Q, Wang S, Wang Z, Chuan M, Bu Q, Lu Z, Wang H, Su Y, Ji Y, Ding J, Gharib A, Liu H, Zhou Y, Tang S, Liang G, Zhang H, Yi C, Zheng X, Cheng Z, Xu Y, Li P, Xu C, Huang J, Li A, Yang Z. A de novo evolved gene contributes to rice grain shape difference between indica and japonica. Nat Commun 2023; 14:5906. [PMID: 37737275 PMCID: PMC10516980 DOI: 10.1038/s41467-023-41669-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes to grain shape difference between indica/xian and japonica/geng varieties. GSE9 evolves from a previous non-coding region of wild rice Oryza rufipogon through the acquisition of start codon. This gene is inherited by most japonica varieties, while the original sequence (absence of start codon, gse9) is present in majority of indica varieties. Knockout of GSE9 in japonica varieties leads to slender grains, whereas introgression to indica background results in round grains. Population evolutionary analyses reveal that gse9 and GSE9 are derived from wild rice Or-I and Or-III groups, respectively. Our findings uncover that the de novo GSE9 gene contributes to the genetic and morphological divergence between indica and japonica subspecies, and provide a target for precise manipulation of rice grain shape.
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Affiliation(s)
- Rujia Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009, China
| | - Yue Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Tianyun Tao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Qianfeng Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Shuting Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Mingli Chuan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Qing Bu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Zhou Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Hanyao Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Yanze Su
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Yi Ji
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Jianheng Ding
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
| | - Ahmed Gharib
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Rice Department, Field Crops Research Institute, ARC, Sakha, Kafr El-Sheikh, 33717, Egypt
| | - Huixin Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Honggen Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Chuandeng Yi
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhukuan Cheng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Aihong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009, China.
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agriculture College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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San MH, Kawamura Y, Kimura K, Witharana EP, Shimogiri T, Aye SS, Min TT, Aung C, Khaing MM, Nagano Y. Characterization and organelle genome sequencing of Pyropia species from Myanmar. Sci Rep 2023; 13:15677. [PMID: 37735516 PMCID: PMC10514050 DOI: 10.1038/s41598-023-42262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Pyropia is a genus comprising red algae of the Bangiaceae family that is commonly found in intertidal zones worldwide. However, understanding of Pyropia species that are prone to tropical regions remains limited despite recent breakthroughs in genomic research. Within the realm of Pyropia species thriving in tropical regions, P. vietnamensis stands out as a widely recognized species. In this study, we aimed to investigate Pyropia species in the southwest coast of Myanmar using physiological and molecular approaches, culture-based analyses, chloroplast rbcL and nuclear SSU gene sequencing, and whole chloroplast and mitochondrial genome sequencing. Physiological analysis showed that the Myanmar samples were more heat-tolerant than their Japanese counterparts, including those of subtropical origin. Additionally, molecular characterization revealed that the Myanmar samples were closely related to P. vietnamensis from India. This study is the first to sequence the chloroplast and mitochondrial genomes of Pyropia species from tropical regions. A unique deletion event was observed within a ribosomal RNA gene cluster in the chloroplast genome of the studied Pyropia species, which is a deviation from the usual characteristics of most Pyropia species. This study improves current understanding of the physiological and molecular characteristics of this comparatively understudied Pyropia species that grows in tropical regions.
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Affiliation(s)
- Myat Htoo San
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
| | | | - Kei Kimura
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
| | | | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | | | - Thu Thu Min
- Marine Science Department, Pathein University, Pathein, Myanmar
| | - Cherry Aung
- Marine Science Department, Myeik University, Myeik, Myanmar
| | | | - Yukio Nagano
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
- Graduate School of Advanced Health Science, Saga University, Saga, Japan.
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Tian Y, Liu X, Xu Y, Yu B, Wang L, Qu X. Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots. Sci Rep 2023; 13:15622. [PMID: 37730791 PMCID: PMC10511529 DOI: 10.1038/s41598-023-42945-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023] Open
Abstract
Tiandong is a vital traditional Chinese herbal medicine. It is derived from the tuber root of the Asparagus cochinchinensis according to the Pharmacopoeia of the people's republic of China (2020 Edition). On account of the similar morphology, Asparagus meioclados and Asparagus munitus were used as Tian-Dong in southwest China. Chloroplast (cp) genomes are highly active genetic components of plants and play an extremely important role in improving the efficiency of the identification of plant species. To differentiate the medicinal plants belonging to the genus Asparagus, we sequenced and analyzed the complete plastomes (plastid genomes) of A. meioclados and A. munitus and obtained two plastomes whose length changed to 156,515 bp and 156,381 bp, respectively. A total of 111 unique genes have been detected in plastome, which included 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In plastomes of A. meioclados and A. munitus, 14,685 and 14,987 codons were detected, among which 9942 and 10,207 had the relative synonymous codon usage (RSCU) values higher than 1, respectively. A. meioclados and A. munitus have 26 SSRs patterns, among which A. meioclados was 25 and A. munitus 21. The average Ka/Ks value was 0.36, and positive selection was detected in genes of the photosynthetic system (ndhF and rbcL) in Asparagus species. To perform the comparative analysis of plastomes, the two newly sequenced plastomes of the A. meioclados and A. munitus species were compared with that of A. cochinchinensis, and 12 hotspots, including 5 coding regions and 7 inter-genomic regions, were identified. Based on the whole plastome of Asparagus, 2 divergent hotspots (accD and rpl32-trnL-UAG) and 1 international barcode fragment (rbcL) were screened, which may be used as particular molecular markers for the identification of Asparagus species. In addition, we determined the phylogenetic relationship between A. meioclados and A. munitus in the genus Asparagus. This study enriches our knowledge of the molecular evolutionary relationships of the Asparagus genus and provides treasured data records for species identification, molecular breeding, and evolutionary analysis of this genus.
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Affiliation(s)
- Yulu Tian
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, No. 1166 Liutai Avenue, Wenjiang District, Chengdu, 611137, China
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Xue Liu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
| | - Yuanjiang Xu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Benxia Yu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Le Wang
- College of Life Science and Food Engineering, Chongqing Three Gorges University, 666 Tianxing Road, Wanzhou District, Chongqing, 404100, China
| | - Xianyou Qu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
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Yang Z, Ma X, Wang Q, Tian X, Sun J, Zhang Z, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae. Nat Commun 2023; 14:5542. [PMID: 37696791 PMCID: PMC10495350 DOI: 10.1038/s41467-023-41137-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
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Affiliation(s)
- Zhiping Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolin Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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Wang Y, Yang T, Wang D, Gou R, Jiang Y, Zhang G, Zheng Y, Gao D, Chen L, Zhang X, Wei Z. Chromosome level genome assembly of colored calla lily (Zantedeschia elliottiana). Sci Data 2023; 10:605. [PMID: 37689767 PMCID: PMC10492805 DOI: 10.1038/s41597-023-02516-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/22/2023] [Indexed: 09/11/2023] Open
Abstract
The colored calla lily is an ornamental floral plant native to southern Africa, belonging to the Zantedeschia genus of the Araceae family. We generated a high-quality chromosome-level genome of the colored calla lily, with a size of 1,154 Mb and a contig N50 of 42 Mb. We anchored 98.5% of the contigs (1,137 Mb) into 16 pseudo-chromosomes, and identified 60.18% of the sequences (694 Mb) as repetitive sequences. Functional annotations were assigned to 95.1% of the predicted protein-coding genes (36,165). Additionally, we annotated 469 miRNAs, 1,652 tRNAs, 10,033 rRNAs, and 1,677 snRNAs. Furthermore, Gypsy-type LTR retrotransposons insertions in the genome are the primary factor causing significant genome size variation in Araceae species. This high-quality genome assembly provides valuable resources for understanding genome size differences within the Araceae family and advancing genomic research on colored calla lily.
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Affiliation(s)
- Yi Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Tuo Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Di Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Horticultural Science & Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization/Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao, 66004, China
| | - Rongxin Gou
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Horticultural Science & Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization/Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao, 66004, China
| | - Yin Jiang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Horticultural Science & Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization/Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao, 66004, China
| | - Guojun Zhang
- College of Horticultural Science & Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization/Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao, 66004, China
| | - Yuhong Zheng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, 210014, China
| | - Dan Gao
- Smartgenomics Technology Institute, Tianjin, 301700, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, 301700, China
| | - Xiuhai Zhang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Zunzheng Wei
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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