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Russo A, Alessandrini M, El Baidouri M, Frei D, Galise TR, Gaidusch L, Oertel HF, Garcia Morales SE, Potente G, Tian Q, Smetanin D, Bertrand JAM, Onstein RE, Panaud O, Frey JE, Cozzolino S, Wicker T, Xu S, Grossniklaus U, Schlüter PM. Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation. Nat Commun 2024; 15:6308. [PMID: 39060266 PMCID: PMC11282089 DOI: 10.1038/s41467-024-50622-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Pollinator-driven evolution of floral traits is thought to be a major driver of angiosperm speciation and diversification. Ophrys orchids mimic female insects to lure male pollinators into pseudocopulation. This strategy, called sexual deception, is species-specific, thereby providing strong premating reproductive isolation. Identifying the genomic architecture underlying pollinator adaptation and speciation may shed light on the mechanisms of angiosperm diversification. Here, we report the 5.2 Gb chromosome-scale genome sequence of Ophrys sphegodes. We find evidence for transposable element expansion that preceded the radiation of the O. sphegodes group, and for gene duplication having contributed to the evolution of chemical mimicry. We report a highly differentiated genomic candidate region for pollinator-mediated evolution on chromosome 2. The Ophrys genome will prove useful for investigations into the repeated evolution of sexual deception, pollinator adaptation and the genomic architectures that facilitate evolutionary radiations.
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Affiliation(s)
- Alessia Russo
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
| | - Mattia Alessandrini
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Moaine El Baidouri
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Daniel Frei
- Department of Methods Development and Analytics, Agroscope, Wädenswil, Switzerland
| | | | - Lara Gaidusch
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Hannah F Oertel
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Sara E Garcia Morales
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Qin Tian
- Naturalis Biodiversity Centre, Leiden, The Netherlands
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Joris A M Bertrand
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Renske E Onstein
- Naturalis Biodiversity Centre, Leiden, The Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena - Leipzig, Leipzig, Germany
| | - Olivier Panaud
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Jürg E Frey
- Department of Methods Development and Analytics, Agroscope, Wädenswil, Switzerland
| | | | - Thomas Wicker
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Shuqing Xu
- Institute of Organismic and Molecular Evolution, University of Mainz, Mainz, Germany
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Philipp M Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
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Gastelbondo M, Nicholls U, Chen S, Chambers A, Wu X. First Gynogenesis of Vanilla planifolia for Haploid Production and Ploidy Verification Protocol. PLANTS (BASEL, SWITZERLAND) 2024; 13:1733. [PMID: 38999575 PMCID: PMC11243312 DOI: 10.3390/plants13131733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
Vanilla orchids are members of the Vanilloideae orchid subfamily, and they hold significant economic value as a spice crop in tropical regions. Despite the presence of 180 known species within this subfamily, commercial production focuses on only three species (Vanilla planifolia, V. odorata, and V. pompona) and one hybrid (V. × tahitensis), prized for their aromatic qualities and bioactive compounds. Limited modern breeding initiatives have been undertaken with vanilla orchids, although recent advancements in genomic research are shedding light on this crop's potential. The protracted breeding cycle of vanilla, coupled with increasing demand for germplasm, underscores the importance of research and breeding efforts in vanilla. This paper outlines a protocol for haploid production in V. planifolia using unfertilized ovaries in tissue culture conditions. Additionally, we present a methodology to confirm the haploid nature of putative haploid lines through stomatal size comparison, chromosome counting, and flow cytometry analysis, proving the successful development of haploid vanilla plants. These findings contribute to the advancement of breeding programs and genetic improvement strategies for the vanilla industry.
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Affiliation(s)
- Manuel Gastelbondo
- Plant Breeding Graduate Program, Tropical Research and Education Center, University of Florida, 18905 S.W. 280 Street, Homestead, FL 33031, USA; (M.G.); (S.C.)
| | - Ursula Nicholls
- Horticulture Department, Tropical Research and Education Center, University of Florida, 18905 S.W. 280 Street, Homestead, FL 33031, USA; (U.N.); (A.C.)
| | - Sisi Chen
- Plant Breeding Graduate Program, Tropical Research and Education Center, University of Florida, 18905 S.W. 280 Street, Homestead, FL 33031, USA; (M.G.); (S.C.)
| | - Alan Chambers
- Horticulture Department, Tropical Research and Education Center, University of Florida, 18905 S.W. 280 Street, Homestead, FL 33031, USA; (U.N.); (A.C.)
| | - Xingbo Wu
- Plant Breeding Graduate Program, Tropical Research and Education Center, University of Florida, 18905 S.W. 280 Street, Homestead, FL 33031, USA; (M.G.); (S.C.)
- Environmental Horticulture Department, Tropical Research and Education Center, University of Florida, 18905 S.W. 280 Street, Homestead, FL 33031, USA
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Gu F, Xu F, Wu G, Zhu H, Ji C, Wang Y, Zhao Q, Zhang Z. Annual Accumulation of CymMV May Lead to Loss in Production of Asymptomatic Vanilla Propagated by Cuttings. PLANTS (BASEL, SWITZERLAND) 2024; 13:1505. [PMID: 38891313 PMCID: PMC11174479 DOI: 10.3390/plants13111505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Vanilla (Vanilla planifolia Andrews) is a valuable orchid spice cultivated for its highly priced beans. Vanilla has been planted in Hainan province of China via cutting propagation for about 40 years. The yield has been decreasing annually for the past ten years due to pod numbers declining significantly even though it seems to grow normally without disease symptoms, while the reason is still unknown. In this study, we found that Cymbidium mosaic virus (CymMV), one of the most devastating viruses causing losses in the vanilla industry, massively presented within the pods and leaves of vanilla plants, so the virus infecting the vanilla seems to be a highly probable hypothesis of the main contributions to low yield via decreasing the number of pods. This represents the first speculation of CymMV possibly affecting the yield of vanilla in China, indicating the important role of virus elimination in restoring high yield in vanilla. This research can also serve as a warning to important economic crops that rely on cuttings for propagation, demonstrating that regular virus elimination is very important for these economically propagated crops through cuttings.
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Affiliation(s)
- Fenglin Gu
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; (F.G.); (C.J.); (Y.W.)
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (F.X.); (G.W.); (H.Z.)
| | - Fei Xu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (F.X.); (G.W.); (H.Z.)
| | - Guiping Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (F.X.); (G.W.); (H.Z.)
| | - Hongying Zhu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (F.X.); (G.W.); (H.Z.)
| | - Changmian Ji
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; (F.G.); (C.J.); (Y.W.)
| | - Yu Wang
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; (F.G.); (C.J.); (Y.W.)
| | - Qingyun Zhao
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; (F.G.); (C.J.); (Y.W.)
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (F.X.); (G.W.); (H.Z.)
| | - Zhiyuan Zhang
- Hainan Institute, Zhejiang University, Sanya 572025, China
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Chen JC, Lin HY, Novák O, Strnad M, Lee YI, Fang SC. Diverse geotropic responses in the orchid family. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38809156 DOI: 10.1111/pce.14975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/28/2024] [Accepted: 05/14/2024] [Indexed: 05/30/2024]
Abstract
In epiphytes, aerial roots are important to combat water-deficient, nutrient-poor, and high-irradiance microhabitats. However, whether aerial roots can respond to gravity and whether auxin plays a role in regulating aerial root development remain open-ended questions. Here, we investigated the gravitropic response of the epiphytic orchid Phalaenopsis aphrodite. Our data showed that aerial roots of P. aphrodite failed to respond to gravity, and this was correlated with a lack of starch granules/statolith sedimentation in the roots and the absence of the auxin efflux carrier PIN2 gene. Using an established auxin reporter, we discovered that auxin maximum was absent in the quiescent center of aerial roots of P. aphrodite. Also, gravity failed to trigger auxin redistribution in the root caps. Hence, loss of gravity sensing and gravity-dependent auxin redistribution may be the genetic factors contributing to aerial root development. Moreover, the architectural and functional innovations that achieve fast gravitropism in the flowering plants appear to be lost in both terrestrial and epiphytic orchids, but are present in the early diverged orchid subfamilies. Taken together, our findings provide physiological and molecular evidence to support the notion that epiphytic orchids lack gravitropism and suggest diverse geotropic responses in the orchid family.
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Affiliation(s)
- Jhun-Chen Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Science, Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Science, Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Yung-I Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Singh K, Huff M, Liu J, Park JW, Rickman T, Keremane M, Krueger RR, Kunta M, Roose ML, Dardick C, Staton M, Ramadugu C. Chromosome-Scale, De Novo, Phased Genome Assemblies of Three Australian Limes: Citrus australasica, C. inodora, and C. glauca. PLANTS (BASEL, SWITZERLAND) 2024; 13:1460. [PMID: 38891269 PMCID: PMC11174732 DOI: 10.3390/plants13111460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
Huanglongbing (HLB) is a severe citrus disease worldwide. Wild Australian limes like Citrus australasica, C. inodora, and C. glauca possess beneficial HLB resistance traits. Individual trees of the three taxa were extensively used in a breeding program for over a decade to introgress resistance traits into commercial-quality citrus germplasm. We generated high-quality, phased, de novo genome assemblies of the three Australian limes using PacBio long-read sequencing. The genome assembly sizes of the primary and alternate haplotypes were determined for C. australasica (337 Mb/335 Mb), C. inodora (304 Mb/299 Mb), and C. glauca (376 Mb/379 Mb). The nine chromosome-scale scaffolds included 86-91% of the genome sequences generated. The integrity and completeness of the assembled genomes were estimated to be at 97.2-98.8%. Gene annotation studies identified 25,461 genes in C. australasica, 27,665 in C. inodora, and 30,067 in C. glauca. Genes belonging to 118 orthogroups were specific to Australian lime genomes compared to other citrus genomes analyzed. Significantly fewer canonical resistance (R) genes were found in C. inodora and C. glauca (319 and 449, respectively) compared to C. australasica (576), C. clementina (579), and C. sinensis (651). Similar patterns were observed for other gene families associated with potential HLB resistance, including Phloem protein 2 (PP2) and Callose synthase (CalS) genes predicted in the Australian lime genomes. The genomic information on Australian limes developed in the present study will help understand the genetic basis of HLB resistance.
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Affiliation(s)
- Khushwant Singh
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
| | - Matthew Huff
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Jianyang Liu
- Innovative Fruit Production, Improvement, and Protection, Appalachian Fruit Research Station, USDA-ARS, Kearneysville, WV 25430, USA; (J.L.); (C.D.)
| | - Jong-Won Park
- Citrus Center, Texas A&M University-Kingsville, Weslaco, TX 78599, USA; (J.-W.P.); (M.K.)
| | - Tara Rickman
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Manjunath Keremane
- National Clonal Germplasm Repository for Citrus and Dates, USDA-ARS, Riverside, CA 92507, USA; (M.K.); (R.R.K.)
| | - Robert R. Krueger
- National Clonal Germplasm Repository for Citrus and Dates, USDA-ARS, Riverside, CA 92507, USA; (M.K.); (R.R.K.)
| | - Madhurababu Kunta
- Citrus Center, Texas A&M University-Kingsville, Weslaco, TX 78599, USA; (J.-W.P.); (M.K.)
| | - Mikeal L. Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
| | - Chris Dardick
- Innovative Fruit Production, Improvement, and Protection, Appalachian Fruit Research Station, USDA-ARS, Kearneysville, WV 25430, USA; (J.L.); (C.D.)
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
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Lu Y, Chen X, Yu H, Zhang C, Xue Y, Zhang Q, Wang H. Haplotype-resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:488-505. [PMID: 38173092 DOI: 10.1111/tpj.16620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Phanera championii is a medicinal liana plant that has successfully adapted to hostile karst habitats. Despite extensive research on its medicinal components and pharmacological effects, the molecular mechanisms underlying the biosynthesis of critical flavonoids and its adaptation to karst habitats remain elusive. In this study, we performed high-coverage PacBio and Hi-C sequencing of P. championii, which revealed its high heterozygosity and phased the genome into two haplotypes: Hap1 (384.60 Mb) and Hap2 (383.70 Mb), encompassing a total of 58 612 annotated genes. Comparative genomes analysis revealed that P. championii experienced two whole-genome duplications (WGDs), with approximately 59.59% of genes originating from WGD events, thereby providing a valuable genetic resource for P. championii. Moreover, we identified a total of 112 genes that were strongly positively selected. Additionally, about 81.60 Mb of structural variations between the two haplotypes. The allele-specific expression patterns suggested that the dominant effect of P. championii was the elimination of deleterious mutations and the promotion of beneficial mutations to enhance fitness. Moreover, our transcriptome and metabolome analysis revealed alleles in different tissues or different haplotypes collectively regulate the synthesis of flavonoid metabolites. In summary, our comprehensive study highlights the significance of genomic and morphological adaptation in the successful adaptation of P. championii to karst habitats. The high-quality phased genomes obtained in this study serve as invaluable genomic resources for various applications, including germplasm conservation, breeding, evolutionary studies, and elucidation of pathways governing key biological traits of P. championii.
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Affiliation(s)
- Yongbin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Xiao Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Chao Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Yajie Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
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Li R, Gao X, Wu Y, Wei C, Li MH, Liu DK, Liu ZJ. Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC. Int J Mol Sci 2024; 25:2055. [PMID: 38396732 PMCID: PMC10888551 DOI: 10.3390/ijms25042055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) gene family plays a crucial role in both plant growth and response to abiotic stress. Approximately half of the Orchidaceae species are estimated to perform CAM pathway, and the availability of sequenced orchid genomes makes them ideal subjects for investigating the PEPC gene family in CAM plants. In this study, a total of 33 PEPC genes were identified across 15 orchids. Specifically, one PEPC gene was found in Cymbidium goeringii and Platanthera guangdongensis; two in Apostasia shenzhenica, Dendrobium chrysotoxum, D. huoshanense, Gastrodia elata, G. menghaiensis, Phalaenopsis aphrodite, Ph. equestris, and Pl. zijinensis; three in C. ensifolium, C. sinense, D. catenatum, D. nobile, and Vanilla planifolia. These PEPC genes were categorized into four subgroups, namely PEPC-i, PEPC-ii, and PEPC-iii (PTPC), and PEPC-iv (BTPC), supported by the comprehensive analyses of their physicochemical properties, motif, and gene structures. Remarkably, PEPC-iv contained a heretofore unreported orchid PEPC gene, identified as VpPEPC4. Differences in the number of PEPC homolog genes among these species were attributed to segmental duplication, whole-genome duplication (WGD), or gene loss events. Cis-elements identified in promoter regions were predominantly associated with light responsiveness, and circadian-related elements were observed in each PEPC-i and PEPC-ii gene. The expression levels of recruited BTPC, VpPEPC4, exhibited a lower expression level than other VpPEPCs in the tested tissues. The expression analyses and RT-qPCR results revealed diverse expression patterns in orchid PEPC genes. Duplicated genes exhibited distinct expression patterns, suggesting functional divergence. This study offered a comprehensive analysis to unveil the evolution and function of PEPC genes in Orchidaceae.
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Affiliation(s)
- Ruyi Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Xuyong Gao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Yuwei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Chunyi Wei
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Gilman IS, Smith JAC, Holtum JAM, Sage RF, Silvera K, Winter K, Edwards EJ. The CAM lineages of planet Earth. ANNALS OF BOTANY 2023; 132:627-654. [PMID: 37698538 PMCID: PMC10799995 DOI: 10.1093/aob/mcad135] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/09/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND AND SCOPE The growth of experimental studies of crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances in molecular systematics, presents an opportunity to re-assess the phylogenetic distribution and diversity of species capable of CAM. It has been more than two decades since the last comprehensive lists of CAM taxa were published, and an updated survey of the occurrence and distribution of CAM taxa is needed to facilitate and guide future CAM research. We aimed to survey the phylogenetic distribution of these taxa, their diverse morphology, physiology and ecology, and the likely number of evolutionary origins of CAM based on currently known lineages. RESULTS AND CONCLUSIONS We found direct evidence (in the form of experimental or field observations of gas exchange, day-night fluctuations in organic acids, carbon isotope ratios and enzymatic activity) for CAM in 370 genera of vascular plants, representing 38 families. Further assumptions about the frequency of CAM species in CAM clades and the distribution of CAM in the Cactaceae and Crassulaceae bring the currently estimated number of CAM-capable species to nearly 7 % of all vascular plants. The phylogenetic distribution of these taxa suggests a minimum of 66 independent origins of CAM in vascular plants, possibly with dozens more. To achieve further insight into CAM origins, there is a need for more extensive and systematic surveys of previously unstudied lineages, particularly in living material to identify low-level CAM activity, and for denser sampling to increase phylogenetic resolution in CAM-evolving clades. This should allow further progress in understanding the functional significance of this pathway by integration with studies on the evolution and genomics of CAM in its many forms.
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Affiliation(s)
- Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - Joseph A M Holtum
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Katia Silvera
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Botany & Plant Sciences, University of California, Riverside, CA, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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9
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Favre F, Jourda C, Grisoni M, Chiroleu F, Dijoux JB, Jade K, Rivallan R, Besse P, Charron C. First Vanilla planifolia High-Density Genetic Linkage Map Provides Quantitative Trait Loci for Resistance to Fusarium oxysporum. PLANT DISEASE 2023; 107:2997-3006. [PMID: 36856646 DOI: 10.1094/pdis-10-22-2386-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium oxysporum f. sp. radicis-vanillae (Forv), the causal agent of root and stem rot disease, is the main pathogen affecting vanilla production. Sources of resistance have been reported in Vanilla planifolia G. Jackson ex Andrews, the main cultivated vanilla species. In this study, we developed the first high-density genetic map in this species with 1,804 genotyping-by-sequencing (GBS)-generated single nucleotide polymorphism (SNP) markers using 125 selfed progenies of the CR0040 traditional vanilla cultivar. Sixteen linkage groups (LG) were successfully constructed, with a mean of 113 SNPs and an average length of 207 cM per LG. The map had a high density with an average of 5.45 SNP every 10 cM and an average distance of 1.85 cM between adjacent markers. The first three LG were aligned against the first assembled chromosome of CR0040, and the other 13 LG were correctly associated with the other 13 assembled chromosomes. The population was challenged with the highly pathogenic Forv strain Fo072 using the root-dip inoculation method. Five traits were mapped, and 20 QTLs were associated with resistance to Fo072. Among the genes retrieved in the CR0040 physical regions associated with QTLs, genes potentially involved in biotic resistance mechanisms, coding for kinases, E3 ubiquitin ligases, pentatricopeptide repeat-containing proteins, and one leucine-rich repeat receptor underlying the qFo72_08.1 QTL have been highlighted. This study should provide useful resources for marker-assisted selection in V. planifolia.
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Affiliation(s)
- Félicien Favre
- University of Reunion Island, UMR PVBMT, F-97410 St. Pierre, Reunion Island, France
| | - Cyril Jourda
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| | | | | | | | - Katia Jade
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pascale Besse
- University of Reunion Island, UMR PVBMT, F-97410 St. Pierre, Reunion Island, France
| | - Carine Charron
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
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10
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Li Y, Zhao X, Zhang MM, He X, Huang Y, Ahmad S, Liu ZJ, Lan S. Genome-based identification of the CYP75 gene family in Orchidaceae and its expression patterns in Cymbidium goeringii. FRONTIERS IN PLANT SCIENCE 2023; 14:1243828. [PMID: 37828920 PMCID: PMC10564990 DOI: 10.3389/fpls.2023.1243828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
With a great diversity of species, Orchidaceae stands out as an essential component of plant biodiversity, making it a primary resource for studying angiosperms evolution and genomics. This study focuses on 13 published orchid genomes to identify and analyze the CYP75 gene family belonging to the cytochrome P450 superfamily, which is closely related to flavonoid biosynthetic enzymes and pigment regulation. We found 72 CYP75s in the 13 orchid genomes and further classified them into two classes: CYP75A and CYP75B subfamily, the former synthesizes blue anthocyanins, while the latter is involved in the production of red anthocyanins. Furthermore, the amount of CYP75Bs (53/72) greatly exceeds the amount of CYP75As (19/72) in orchids. Our findings suggest that CYP75B genes have a more important evolutionary role, as red plants are more common in nature than blue plants. We also discovered unique conserved motifs in each subfamily that serve as specific recognition features (motif 19 belong to CYP75A; motif 17 belong to CYP75B). Two diverse-colored varieties of C. goeringii were selected for qRT-PCR experiments. The expression of CgCYP75B1 was significantly higher in the purple-red variant compared to the yellow-green variant, while CgCYP75A1 showed no significant difference. Based on transcriptomic expression analysis, CYP75Bs are more highly expressed than CYP75As in floral organs, especially in colorful petals and lips. These results provide valuable information for future studies on CYP75s in orchids and other angiosperms.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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11
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Fan W, He ZS, Zhe M, Feng JQ, Zhang L, Huang Y, Liu F, Huang JL, Ya JD, Zhang SB, Yang JB, Zhu A, Li DZ. High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes. PLANT COMMUNICATIONS 2023; 4:100564. [PMID: 36809882 PMCID: PMC10504564 DOI: 10.1016/j.xplc.2023.100564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Epiphytes with crassulacean acid metabolism (CAM) photosynthesis are widespread among vascular plants, and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation. However, we lack a complete understanding of the molecular regulation of CAM photosynthesis in epiphytes. Here, we report a high-quality chromosome-level genome assembly of a CAM epiphyte, Cymbidium mannii (Orchidaceae). The 2.88-Gb orchid genome with a contig N50 of 22.7 Mb and 27 192 annotated genes was organized into 20 pseudochromosomes, 82.8% of which consisted of repetitive elements. Recent expansions of long terminal repeat retrotransposon families have made a major contribution to the evolution of genome size in Cymbidium orchids. We reveal a holistic scenario of molecular regulation of metabolic physiology using high-resolution transcriptomics, proteomics, and metabolomics data collected across a CAM diel cycle. Patterns of rhythmically oscillating metabolites, especially CAM-related products, reveal circadian rhythmicity in metabolite accumulation in epiphytes. Genome-wide analysis of transcript and protein level regulation revealed phase shifts during the multifaceted regulation of circadian metabolism. Notably, we observed diurnal expression of several core CAM genes (especially βCA and PPC) that may be involved in temporal fixation of carbon sources. Our study provides a valuable resource for investigating post-transcription and translation scenarios in C. mannii, an Orchidaceae model for understanding the evolution of innovative traits in epiphytes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zheng-Shan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Mengqing Zhe
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Qiu Feng
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yiwei Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | | | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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12
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Bai MZ, Guo YY. Bioinformatics Analysis of MSH1 Genes of Green Plants: Multiple Parallel Length Expansions, Intron Gains and Losses, Partial Gene Duplications, and Alternative Splicing. Int J Mol Sci 2023; 24:13620. [PMID: 37686425 PMCID: PMC10487979 DOI: 10.3390/ijms241713620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
MutS homolog 1 (MSH1) is involved in the recombining and repairing of organelle genomes and is essential for maintaining their stability. Previous studies indicated that the length of the gene varied greatly among species and detected species-specific partial gene duplications in Physcomitrella patens. However, there are critical gaps in the understanding of the gene size expansion, and the extent of the partial gene duplication of MSH1 remains unclear. Here, we screened MSH1 genes in 85 selected species with genome sequences representing the main clades of green plants (Viridiplantae). We identified the MSH1 gene in all lineages of green plants, except for nine incomplete species, for bioinformatics analysis. The gene is a singleton gene in most of the selected species with conserved amino acids and protein domains. Gene length varies greatly among the species, ranging from 3234 bp in Ostreococcus tauri to 805,861 bp in Cycas panzhihuaensis. The expansion of MSH1 repeatedly occurred in multiple clades, especially in Gymnosperms, Orchidaceae, and Chloranthus spicatus. MSH1 has exceptionally long introns in certain species due to the gene length expansion, and the longest intron even reaches 101,025 bp. And the gene length is positively correlated with the proportion of the transposable elements (TEs) in the introns. In addition, gene structure analysis indicated that the MSH1 of green plants had undergone parallel intron gains and losses in all major lineages. However, the intron number of seed plants (gymnosperm and angiosperm) is relatively stable. All the selected gymnosperms contain 22 introns except for Gnetum montanum and Welwitschia mirabilis, while all the selected angiosperm species preserve 21 introns except for the ANA grade. Notably, the coding region of MSH1 in algae presents an exceptionally high GC content (47.7% to 75.5%). Moreover, over one-third of the selected species contain species-specific partial gene duplications of MSH1, except for the conserved mosses-specific partial gene duplication. Additionally, we found conserved alternatively spliced MSH1 transcripts in five species. The study of MSH1 sheds light on the evolution of the long genes of green plants.
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Affiliation(s)
| | - Yan-Yan Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
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13
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Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D. A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Curr Res Food Sci 2023; 7:100579. [PMID: 37701635 PMCID: PMC10494321 DOI: 10.1016/j.crfs.2023.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
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Affiliation(s)
- Parinita Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankita Negi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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14
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Kong W, Wang Y, Zhang S, Yu J, Zhang X. Recent Advances in Assembly of Complex Plant Genomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:427-439. [PMID: 37100237 PMCID: PMC10787022 DOI: 10.1016/j.gpb.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 03/18/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023]
Abstract
Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.
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Affiliation(s)
- Weilong Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yibin Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shengcheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiaxin Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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15
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Zhang G, Hu Y, Huang MZ, Huang WC, Liu DK, Zhang D, Hu H, Downing JL, Liu ZJ, Ma H. Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1204-1225. [PMID: 36738233 DOI: 10.1111/jipb.13462] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/03/2023] [Indexed: 05/13/2023]
Abstract
Orchidaceae (with >28,000 orchid species) are one of the two largest plant families, with economically and ecologically important species, and occupy global and diverse niches with primary distribution in rainforests. Among orchids, 70% grow on other plants as epiphytes; epiphytes contribute up to ~50% of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes, thereby contributing to the health of these ecosystems. Orchids account for over two-thirds of vascular epiphytes and provide an excellent model for studying evolution of epiphytism. Extensive phylogenetic studies of Orchidaceae and subgroups have ;been crucial for understanding relationships among many orchid lineages, although some uncertainties remain. For example, in the largest subfamily Epidendroideae with nearly all epiphytic orchids, relationships among some tribes and many subtribes are still controversial, hampering evolutionary analyses of epiphytism. Here we obtained 1,450 low-copy nuclear genes from 610 orchid species, including 431 with newly generated transcriptomes, and used them for the reconstruction of robust Orchidaceae phylogenetic trees with highly supported placements of tribes and subtribes. We also provide generally well-supported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic studies. Molecular clock analyses estimated the Orchidaceae origin at ~132 million years ago (Ma) and divergences of most subtribes from 52 to 29 Ma. Character reconstruction supports at least 14 parallel origins of epiphytism; one such origin was placed at the most recent common ancestor of ~95% of epiphytic orchids and linked to modern rainforests. Ten occurrences of rapid increase in the diversification rate were detected within Epidendroideae near and after the K-Pg boundary, contributing to ~80% of the Orchidaceae diversity. This study provides a robust and the largest family-wide Orchidaceae nuclear phylogenetic tree thus far and new insights into the evolution of epiphytism in vascular plants.
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Affiliation(s)
- Guojin Zhang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ming-Zhong Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei-Chang Huang
- Shanghai Chenshan Botanical Garden, Songjiang, Shanghai, 201602, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haihua Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jason L Downing
- Fairchild Tropical Botanic Garden, Coral Gables, Florida, 33156, USA
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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16
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Zhang L, Kang L, Xu Y. Phenotypic, Genomic, and Transcriptomic Comparison of Industrial Aspergillus oryzae Used in Chinese and Japanese Soy Sauce: Analysis of Key Proteolytic Enzymes Produced by Koji Molds. Microbiol Spectr 2023; 11:e0083622. [PMID: 36744888 PMCID: PMC10100866 DOI: 10.1128/spectrum.00836-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 01/11/2023] [Indexed: 02/07/2023] Open
Abstract
Aspergillus oryzae, which generates numerous enzymes for the breakdown of raw materials, is an essential koji mold in soy sauce production. For better soy sauce productivity and flavor quality, China and Japan have developed their own industrial A. oryzae strains at distinct evolutionary branches for use in soy sauce production for decades. However, systematic comparison between the two national industrial strains has been poorly conducted, and thus we have not been able to generate adequate knowledge, especially regarding what are the key hydrolytic enzymes produced by A. oryzae during koji production. This study sequenced and assembled three high-quality genome sequences of industrial A. oryzae originating from China and Japan. Based on the genome sequences, a phylogenetic tree analysis was performed and revealed the evolutional distances between the two national industrial koji molds. Meanwhile, a comparative phenotypic analysis revealed that the two national industrial strains differed in growth and catalytic characteristics, particularly in proteolytic enzyme activities. To investigate the molecular mechanism underlying the phenotypic difference, we conducted systematic comparative genome and transcriptome investigations. We found minor differences in the quantity and diversity of proteolytic enzyme genes between Chinese and Japanese koji molds, while the protease secretion ratio and transcriptional level were dissimilar. We identified 58 potential important enzymes associated with high protein breakdown efficiency during industrial koji fermentation by combining comparative phenotypic and transcriptome data. More research is required to confirm the function of these putative key hydrolytic enzymes. IMPORTANCE Aspergillus oryzae is widely used as an industrial koji mold for soy sauce brewing due to its powerful raw material decomposition capability. Although various proteases in A. oryzae have been identified, it remains a challenge to find essential enzymes involved in soy sauce production. Generally, the industrial A. oryzae used in soy sauce brewing has excellent proteolytic activity. Based on this, we analyzed key proteolytic enzymes according to a comparison of the genome and transcriptome between three industrial strains. This study found little difference in gene numbers and mutations of proteolytic enzymes between three industrial A. oryzae strains. However, variations in protease secretion ratio and transcriptome were discovered between industrial strains. Based on that, we generated 58 candidate key proteolytic enzymes. This work comprehensively analyzed three industrial koji molds, revealing genome development under separate artificial domestication and helping in the study of key proteolytic enzymes during soy sauce production.
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Affiliation(s)
- Lijie Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Le Kang
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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17
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Diagnostic KASP markers differentiate Vanilla planifolia, V. odorata, V. pompona, and their hybrids using leaf or cured pod tissues. Mol Biol Rep 2023; 50:707-717. [PMID: 36370295 DOI: 10.1007/s11033-022-08085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Vanilla is a globally important spice crop used in a variety of food, cosmetic, and pharmaceutical products. V. planifolia is the primary commercial species with V. x tahitensis also permissible for food use. Other aromatic species, including V. pompona, are used for food throughout Central and South America. Supply chain complexity hinders the vanilla bean industry and can lead to false claims of genetic and geographical origins to obtain higher prices. Beans of some species can be differentiated by experienced buyers, but hybrids and morphological differences caused by environmental variability or disease would best be resolved by diagnostic tests. METHODS AND RESULTS: Kompetitive Allele Specific Polymerase Chain Reaction is a widely used molecular marker that can genotype single nucleotide polymorphisms efficiently and inexpensively. Assays were designed to differentiate V. planifolia, V. x tahitensis, and V. pompona using publicly available vanilla genomics data. Ten KASP assays on chromosomes 1 through 7, the ITS region, and plastid-encoded rbcL gene successfully differentiated V. planifolia, V. odorata, and V. x tahitensis. Additional KASP assays on chromosomes 1 through 4, the ITS region, and rbcL gene successfully differentiated V. planifolia and V. pompona. Further, a method for extracting KASP-quality DNA from cured vanilla bean seeds was developed and successfully differentiated V. planifolia, V. odorata, V. x tahitensis, V. pompona, and their hybrids. CONCLUSION The methods and results from this study can be used to identify interspecific hybrids, ensure the authenticity of cured vanilla beans, and reduce abuse within the vanilla supply chain.
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18
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Chen YY, Li C, Hsiao YY, Ho SY, Zhang ZB, Liao CC, Lee BR, Lin ST, Wu WL, Wang JS, Zhang D, Liu KW, Liu DK, Zhao XW, Li YY, Ke SJ, Zhou Z, Huang MZ, Wu YS, Peng DH, Lan SR, Chen HH, Liu ZJ, Wu WS, Tsai WC. OrchidBase 5.0: updates of the orchid genome knowledgebase. BMC PLANT BIOLOGY 2022; 22:557. [PMID: 36456919 PMCID: PMC9717476 DOI: 10.1186/s12870-022-03955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study.In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization.OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/.
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Affiliation(s)
- You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Chung‐I Li
- Department of Statistics, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
| | - Sau-Yee Ho
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Zhe-Bin Zhang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Chien-Chi Liao
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Bing-Ru Lee
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shao-Ting Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Jeen-Shing Wang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Diyang Zhang
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055 China
| | - Ding-Kun Liu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Xue-Wei Zhao
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yuan-Yuan Li
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Shi-Jie Ke
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Zhuang Zhou
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005 China
| | - Ming-Zhong Huang
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yong-Shu Wu
- Education Botanical Garden of Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Dong-Hui Peng
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Si-Ren Lan
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Hong-Hwa Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Zhong-Jian Liu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005 China
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100 China
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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19
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Malik US, Duan Q, Niazi MBK, Jahan Z, Liaqat U, Sher F, Gan Y, Hou H. Vanillin cross-linked hydrogel membranes interfacial reinforced by carbon nitride nanosheets for enhanced antibacterial activity and mechanical properties. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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de Oliveira RT, da Silva Oliveira JP, Macedo AF. Vanilla beyond Vanilla planifolia and Vanilla × tahitensis: Taxonomy and Historical Notes, Reproductive Biology, and Metabolites. PLANTS (BASEL, SWITZERLAND) 2022; 11:3311. [PMID: 36501350 PMCID: PMC9739750 DOI: 10.3390/plants11233311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Vanilla is a worldwide cherished condiment, and its volatile market is associated with the so-called "vanilla crisis". Even though only two species (Vanilla planifolia and V. × tahitensis) are cultivated on a large scale for commercial purposes, the Vanilla genus is comprised of 140 species. The present review article discusses the facets of this crisis, and vanilla crop wild relatives (WRs) are showcased as alternatives to overcome them. Historical, taxonomic, and reproductive biology aspects of the group were covered. Emphasis was given to the metabolic characterization of the vanilla crop WRs, highlighting their main chemical classes and the potential flavor descriptors. Many of these species can produce important flavor compounds such as vanillin, vanillic acid, and acetovanillone, among others. Overall, this review compiles valuable information that can help unravel new chapters of the history of this treasured product by evidencing the biotechnological potential of vanilla crop WRs.
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21
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Wang J, Li J, Lin W, Deng B, Lin L, Lv X, Hu Q, Liu K, Fatima M, He B, Qiu D, Ma X. Genome-wide identification and adaptive evolution of CesA/Csl superfamily among species with different life forms in Orchidaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:994679. [PMID: 36247544 PMCID: PMC9559377 DOI: 10.3389/fpls.2022.994679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Orchidaceae, with more than 25,000 species, is one of the largest flowering plant families that can successfully colonize wide ecological niches, such as land, trees, or rocks, and its members are divided into epiphytic, terrestrial, and saprophytic types according to their life forms. Cellulose synthase (CesA) and cellulose synthase-like (Csl) genes are key regulators in the synthesis of plant cell wall polysaccharides, which play an important role in the adaptation of orchids to resist abiotic stresses, such as drought and cold. In this study, nine whole-genome sequenced orchid species with three types of life forms were selected; the CesA/Csl gene family was identified; the evolutionary roles and expression patterns of CesA/Csl genes adapted to different life forms and abiotic stresses were investigated. The CesA/Csl genes of nine orchid species were divided into eight subfamilies: CesA and CslA/B/C/D/E/G/H, among which the CslD subfamily had the highest number of genes, followed by CesA, whereas CslB subfamily had the least number of genes. Expansion of the CesA/Csl gene family in orchids mainly occurred in the CslD and CslF subfamilies. Conserved domain analysis revealed that eight subfamilies were conserved with variations in orchids. In total, 17 pairs of CesA/Csl homologous genes underwent positive selection, of which 86%, 14%, and none belonged to the epiphytic, terrestrial, and saprophytic orchids, respectively. The inter-species collinearity analysis showed that the CslD genes expanded in epiphytic orchids. Compared with terrestrial and saprophytic orchids, epiphytic orchids experienced greater strength of positive selection, with expansion events mostly related to the CslD subfamily, which might have resulted in strong adaptability to stress in epiphytes. Experiments on stem expression changes under abiotic stress showed that the CslA might be a key subfamily in response to drought stress for orchids with different life forms, whereas the CslD might be a key subfamily in epiphytic and saprophytic orchids to adapt to freezing stress. This study provides the basic knowledge for the further systematic study of the adaptive evolution of the CesA/Csl superfamily in angiosperms with different life forms, and research on orchid-specific functional genes related to life-history trait evolution.
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Affiliation(s)
- Jingjing Wang
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Li
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ban Deng
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lixian Lin
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuanrui Lv
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qilin Hu
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kunpeng Liu
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mahpara Fatima
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bizhu He
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongliang Qiu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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22
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Michael TP. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. PLANT PHYSIOLOGY 2022; 190:1037-1056. [PMID: 35674369 PMCID: PMC9516744 DOI: 10.1093/plphys/kiac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.
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Affiliation(s)
- Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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23
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Zhang D, Zhao XW, Li YY, Ke SJ, Yin WL, Lan S, Liu ZJ. Advances and prospects of orchid research and industrialization. HORTICULTURE RESEARCH 2022; 9:uhac220. [PMID: 36479582 PMCID: PMC9720451 DOI: 10.1093/hr/uhac220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shi-Jie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Lun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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24
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Lim AH, Low ZJ, Shingate PN, Hong JH, Chong SC, Ng CCY, Liu W, Vaser R, Šikić M, Sung WKK, Nagarajan N, Tan P, Teh BT. Genome assembly and chemogenomic profiling of National Flower of Singapore Papilionanthe Miss Joaquim 'Agnes' reveals metabolic pathways regulating floral traits. Commun Biol 2022; 5:967. [PMID: 36109650 PMCID: PMC9477820 DOI: 10.1038/s42003-022-03940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/02/2022] [Indexed: 11/22/2022] Open
Abstract
Singapore's National Flower, Papilionanthe (Ple.) Miss Joaquim 'Agnes' (PMJ) is highly prized as a horticultural flower from the Orchidaceae family. A combination of short-read sequencing, single-molecule long-read sequencing and chromatin contact mapping was used to assemble the PMJ genome, spanning 2.5 Gb and 19 pseudo-chromosomal scaffolds. Genomic resources and chemical profiling provided insights towards identifying, understanding and elucidating various classes of secondary metabolite compounds synthesized by the flower. For example, presence of the anthocyanin pigments detected by chemical profiling coincides with the expression of ANTHOCYANIN SYNTHASE (ANS), an enzyme responsible for the synthesis of the former. Similarly, the presence of vandaterosides (a unique class of glycosylated organic acids with the potential to slow skin aging) discovered using chemical profiling revealed the involvement of glycosyltransferase family enzymes candidates in vandateroside biosynthesis. Interestingly, despite the unnoticeable scent of the flower, genes involved in the biosynthesis of volatile compounds and chemical profiling revealed the combination of oxygenated hydrocarbons, including traces of linalool, beta-ionone and vanillin, forming the scent profile of PMJ. In summary, by combining genomics and biochemistry, the findings expands the known biodiversity repertoire of the Orchidaceae family and insights into the genome and secondary metabolite processes of PMJ.
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Affiliation(s)
- Abner Herbert Lim
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
| | - Zhen Jie Low
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
| | | | - Jing Han Hong
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Shu Chen Chong
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
| | | | - Wei Liu
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
| | - Robert Vaser
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Mile Šikić
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Wing-Kin Ken Sung
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, Singapore, Singapore.
| | - Bin Tean Teh
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore.
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Singapore, Singapore.
- National Cancer Center Singapore, Singapore, Singapore.
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25
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Piet Q, Droc G, Marande W, Sarah G, Bocs S, Klopp C, Bourge M, Siljak-Yakovlev S, Bouchez O, Lopez-Roques C, Lepers-Andrzejewski S, Bourgois L, Zucca J, Dron M, Besse P, Grisoni M, Jourda C, Charron C. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly. PLANT COMMUNICATIONS 2022; 3:100330. [PMID: 35617961 PMCID: PMC9482989 DOI: 10.1016/j.xplc.2022.100330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 04/10/2022] [Accepted: 04/27/2022] [Indexed: 06/02/2023]
Abstract
Vanilla planifolia, the species cultivated to produce one of the world's most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.
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Affiliation(s)
- Quentin Piet
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France
| | - Gaetan Droc
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France.
| | | | - Gautier Sarah
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France; AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Mickael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sonja Siljak-Yakovlev
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution (ESE), 91190 Gif-sur-Yvette, France
| | | | | | | | | | - Joseph Zucca
- Département Biotechnologie, V. Mane Fils, 06620 Le Bar Sur Loup, France
| | - Michel Dron
- Université Paris-Saclay, CNRS, INRAE, Univ. Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
| | - Pascale Besse
- Université de la Réunion, UMR PVBMT, Saint-Pierre, La Réunion, France
| | | | - Cyril Jourda
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France.
| | - Carine Charron
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France
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26
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Jiang L, Lin M, Wang H, Song H, Zhang L, Huang Q, Chen R, Song C, Li G, Cao Y. Haplotype-resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1340-1353. [PMID: 35785503 DOI: 10.1111/tpj.15892] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Bletilla striata, commonly known as baiji, is a species used in traditional Chinese medicine; it is highly regarded for its medicinal applications and therefore has high economic value. Here, we report a high-quality haplotype-resolved genome of B. striata, haplotype A (2.37 Gb, with a scaffold N50 of 146.39 Mb and a contig N50 of 1.65 Mb) and haplotype B (2.43 Gb, with a scaffold N50 of 150.22 Mb and a contig N50 of 1.66 Mb), assembled from high-fidelity (HiFi) reads and chromosome conformation capture (Hi-C) reads. We find evidence that B. striata has undergone two whole-genome duplication (WGD) events: an ancient WGD event shared by most monocots and a recent WGD event unique to all orchids. We also reconstructed the ancestral orchid karyotype (AOK) of 18 ancient chromosomes and the evolutionary trajectories of 16 modern B. striata chromosomes. Comparative genomic analysis suggests that the expanded gene families of B. striata might play important roles in secondary metabolite biosynthesis and environmental adaptation. By combining genomic and transcriptomic data, we identified the 10 core members from nine gene families that were probably involved in B. striata polysaccharide (BSP) biosynthesis. Based on virus-induced gene silencing (VIGS) and yeast two-hybrid experiments, we present an MYB transcription factor (TF), BsMYB2, that can regulate BSP biosynthesis by directly interacting with eight key BSP-related genes: sacA1, HK1, scrK1, scrK2, GPI1, manA1, GMPP1 and UGP2_1. Our study will enhance the understanding of orchid evolution and accelerate the molecular-assisted breeding of B. striata for improving traits of medicinal value.
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Affiliation(s)
- Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, 241000, China
| | - Mengfei Lin
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330224, Jiangxi, China
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hui Song
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Zhang
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Qingyu Huang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Renrui Chen
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Guohui Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
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Hu Y, Šmarda P, Liu G, Wang B, Gao X, Guo Q. High-Depth Transcriptome Reveals Differences in Natural Haploid Ginkgo biloba L. Due to the Effect of Reduced Gene Dosage. Int J Mol Sci 2022; 23:8958. [PMID: 36012222 PMCID: PMC9409250 DOI: 10.3390/ijms23168958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/31/2022] [Accepted: 08/10/2022] [Indexed: 12/13/2022] Open
Abstract
As a representative of gymnosperms, the discovery of natural haploids of Ginkgo biloba L. has opened a new door for its research. Haploid germplasm has always been a research material of interest to researchers because of its special characteristics. However, we do not yet know the special features and mechanisms of haploid ginkgo following this significant discovery. In this study, we conducted a homogenous garden experiment on haploid and diploid ginkgo to explore the differences in growth, physiology and biochemistry between the two. Additionally, a high-depth transcriptome database of both was established to reveal their transcriptional differences. The results showed that haploid ginkgo exhibited weaker growth potential, lower photosynthesis and flavonoid accumulation capacity. Although the up-regulated expression of DEGs in haploid ginkgo reached 46.7% of the total DEGs in the whole transcriptome data, the gene sets of photosynthesis metabolic, glycolysis/gluconeogenesis and flavonoid biosynthesis pathways, which were significantly related to these differences, were found to show a significant down-regulated expression trend by gene set enrichment analysis (GSEA). We further found that the major metabolic pathways in the haploid ginkgo transcriptional database were down-regulated in expression compared to the diploid. This study reveals for the first time the phenotypic, growth and physiological differences in haploid ginkgos, and demonstrates their transcriptional patterns based on high-depth transcriptomic data, laying the foundation for subsequent in-depth studies of haploid ginkgos.
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Affiliation(s)
- Yaping Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Department of Botany and Zoology, Masaryk University, Koltlářská 2, 61137 Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Koltlářská 2, 61137 Brno, Czech Republic
| | - Ganping Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Beibei Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoge Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qirong Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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28
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Ellestad P, Pérez-Farrera MA, Buerki S. Genomic Insights into Cultivated Mexican Vanilla planifolia Reveal High Levels of Heterozygosity Stemming from Hybridization. PLANTS (BASEL, SWITZERLAND) 2022; 11:2090. [PMID: 36015395 PMCID: PMC9412680 DOI: 10.3390/plants11162090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/02/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
Abstract
Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species, Vanilla planifolia, within its cultivated origin, Mexico. High genomic heterozygosity levels within the globally cultivated 'Daphna' genome have raised questions on the possibility of a hybrid origin and analogous genomic signatures of vanilla cultivated within its origin. This study investigated these questions by assessing whether the genomic structure of Mexican V. planifolia reflected domestication events. Whole genome re-sequencing was used to compare genome complexity between 15 cultivated accessions from different regions and gene pools. Results showed high levels of heterozygosity, ranging from 2.48% to 2.85%, in all but one accession, which exhibited a low level (0.403%). Chromosome-level comparative analyses revealed genomic variability among samples, but no signals of chromosome rearrangements. These findings support the hypotheses that cultivated vanilla resulted from hybridization and that multiple domestication events have shaped cultivated vanilla leading to the formation of landraces. High cultural diversity within this region further supports the occurrence of multiple domestication processes. These results may help to improve breeding and conservation efforts aiming to preserve the genetic diversity of this beloved spice threatened by climate change.
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Affiliation(s)
- Paige Ellestad
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725, USA
| | - Miguel Angel Pérez-Farrera
- Herbario Eizi Matuda, Laboratory of Evolutionary Ecology, Institute of Biological Sciences, Universidad de Ciencias y Artes deChiapas, Libramiento Norte Poniente 1151, Col. Lajas Maciel, Tuxtla Gutiérrez 29039, Mexico
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725, USA
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29
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Wei YL, Jin JP, Liang D, Gao J, Li J, Xie Q, Lu CQ, Yang FX, Zhu GF. Genome-wide identification of Cymbidium sinense WRKY gene family and the importance of its Group III members in response to abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:969010. [PMID: 35968117 PMCID: PMC9365948 DOI: 10.3389/fpls.2022.969010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 05/13/2023]
Abstract
Transcription factors (TFs) of the WRKY family play pivotal roles in defense responses and secondary metabolism of plants. Although WRKY TFs are well documented in numerous plant species, no study has performed a genome-wide investigation of the WRKY gene family in Cymbidium sinense. In the present work, we found 64 C. sinense WRKY (CsWRKY) TFs, and they were further divided into eight subgroups. Chromosomal distribution of CsWRKYs revealed that the majority of these genes were localized on 16 chromosomes, especially on Chromosome 2. Syntenic analysis implied that 13 (20.31%) genes were derived from segmental duplication events, and 17 orthologous gene pairs were identified between Arabidopsis thaliana WRKY (AtWRKY) and CsWRKY genes. Moreover, 55 of the 64 CsWRKYs were detectable in different plant tissues in response to exposure to plant hormones. Among them, Group III members were strongly induced in response to various hormone treatments, indicating their potential essential roles in hormone signaling. We subsequently analyzed the function of CsWRKY18 in Group III. The CsWRKY18 was localized in the nucleus. The constitutive expression of CsWRKY18 in Arabidopsis led to enhanced sensitivity to ABA-mediated seed germination and root growth and elevated plant tolerance to abiotic stress within the ABA-dependent pathway. Overall, our study represented the first genome-wide characterization and functional analysis of WRKY TFs in C. sinense, which could provide useful clues about the evolution and functional description of CsWRKY genes.
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Affiliation(s)
| | | | | | | | | | | | | | - Feng-Xi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gen-Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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30
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Ellestad P, Farrera MAP, Forest F, Buerki S. Uncovering haplotype diversity in cultivated Mexican vanilla species. AMERICAN JOURNAL OF BOTANY 2022; 109:1120-1138. [PMID: 35709340 DOI: 10.1002/ajb2.16024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Although vanilla is one of the best-known spices, there is only a limited understanding of its biology and genetics within Mexico, where its cultivation originated and where phenotypic variability is high. This study aims to augment our understanding of vanilla's genetic resources by assessing species delimitation and genetic, geographic, and climatic variability within Mexican cultivated vanilla. METHODS Using nuclear and plastid DNA sequence data from 58 Mexican samples collected from three regions and 133 ex situ accessions, we assessed species monophyly using phylogenetic analyses and genetic distances. Intraspecific genetic variation was summarized through the identification of haplotypes. Within the primarily cultivated species, Vanilla planifolia, haplotype relationships were further verified using plastome and rRNA gene sequences. Climatic niche and haplotype composition were assessed across the landscape. RESULTS Three species (Vanilla planifolia, V. pompona, and V. insignis) and 13 haplotypes were identified among Mexican vanilla. Within V. planifolia haplotypes, hard phylogenetic incongruences between plastid and nuclear sequences suggest past hybridization events. Eight haplotypes consisted exclusively of Mexican samples. The dominant V. planifolia haplotype occurred throughout all three regions as well as outside of its country of origin. Haplotype richness was found to be highest in regions around Papantla and Chinantla. CONCLUSIONS Long histories of regional cultivation support the consideration of endemic haplotypes as landraces shaped by adaptation to local conditions and/or hybridization. Results may aid further genomic investigations of vanilla's genetic resources and ultimately support the preservation of genetic diversity within the economically important crop.
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Affiliation(s)
- Paige Ellestad
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, USA
| | - Miguel Angel Perez Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes, Chiapas, Mexico, Libramiento Norte Poniente 1151, Col. Lajas Maciel, Tuxtla Gutiérrez, Chiapas, CP, 29039, Mexico
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, USA
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31
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Qiao X, Zhang S, Paterson AH. Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions. Comput Struct Biotechnol J 2022; 20:3248-3256. [PMID: 35782740 PMCID: PMC9237934 DOI: 10.1016/j.csbj.2022.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 01/09/2023] Open
Abstract
Whole-genome duplication (WGD) has occurred repeatedly during plant evolution and diversification, providing genetic layers for evolving new functions and phenotypes. Advances in long-read sequencing technologies have enabled sequencing and assembly of over 1000 plant genomes spanning nearly 800 species, in which a large set of ancient WGDs has been uncovered. Here, we review the recently reported WGDs that occurred in major plant lineages and key evolutionary positions, and highlight their contributions to morphological innovation and adaptive evolution. Current gaps and challenges in integrating enormous volumes of sequenced plant genomes, accurately inferring WGDs, and developing web-based analysis tools are emphasized. Looking to the future, ambitious genome sequencing projects and global efforts may substantially recapitulate the plant tree of life based on broader sampling of phylogenetic diversity, reveal much of the timetable of ancient WGDs, and address the biological significance of WGDs in plant adaptation and radiation.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA
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32
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Guk J, Jang M, Choi J, Lee YM, Kim S. De novo phasing resolves haplotype sequences in complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1031-1041. [PMID: 35332665 PMCID: PMC9129073 DOI: 10.1111/pbi.13815] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/07/2022] [Accepted: 03/20/2022] [Indexed: 05/12/2023]
Abstract
Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Because differences between haplotypes are ignored in most published de novo genomes, assemblies are available as consensus genomes consisting of haplotype mixtures, thus increasing the need for genome phasing. Here, we review the operating principles and characteristics of several freely available and widely used phasing tools (TrioCanu, FALCON-Phase, and ALLHiC). An examination of downstream analyses using haplotype-resolved genome assemblies in plants indicated significant differences among haplotypes regarding chromosomal rearrangements, sequence insertions, and expression of specific alleles that contribute to the acquisition of the biological characteristics of plant species. Finally, we suggest directions to solve addressing limitations of current genome-phasing methods. This review provides insights into the current progress, limitations, and future directions of de novo genome phasing, which will enable researchers to easily access and utilize genome-phasing in studies involving highly heterozygous complex plant genomes.
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Affiliation(s)
- Ji‐Yoon Guk
- Department of Environmental HorticultureUniversity of SeoulSeoulKorea
| | - Min‐Jeong Jang
- Department of Environmental HorticultureUniversity of SeoulSeoulKorea
| | - Jin‐Wook Choi
- Department of Environmental HorticultureUniversity of SeoulSeoulKorea
| | - Yeon Mi Lee
- Department of Environmental HorticultureUniversity of SeoulSeoulKorea
| | - Seungill Kim
- Department of Environmental HorticultureUniversity of SeoulSeoulKorea
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33
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Cheng H, Xie X, Ren M, Yang S, Zhao X, Mahna N, Liu Y, Xu Y, Xiang Y, Chai H, Zheng L, Ge H, Jia R. Characterization of Three SEPALLATA-Like MADS-Box Genes Associated With Floral Development in Paphiopedilum henryanum (Orchidaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:916081. [PMID: 35693163 PMCID: PMC9178235 DOI: 10.3389/fpls.2022.916081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Paphiopedilum (Orchidaceae) is one of the world's most popular orchids that is found in tropical and subtropical forests and has an enormous ornamental value. SEPALLATA-like (SEP-like) MADS-box genes are responsible for floral organ specification. In this study, three SEP-like MADS-box genes, PhSEP1, PhSEP2, and PhSEP3, were identified in Paphiopedilum henryanum. These genes were 732-916 bp, with conserved SEPI and SEPII motifs. Phylogenetic analysis revealed that PhSEP genes were evolutionarily closer to the core eudicot SEP3 lineage, whereas none of them belonged to core eudicot SEP1/2/4 clades. PhSEP genes displayed non-ubiquitous expression, which was detectable across all floral organs at all developmental stages of the flower buds. Furthermore, subcellular localization experiments revealed the localization of PhSEP proteins in the nucleus. Yeast two-hybrid assays revealed no self-activation of PhSEPs. The protein-protein interactions revealed that PhSEPs possibly interact with B-class DEFICIENS-like and E-class MADS-box proteins. Our study suggests that the three SEP-like genes may play key roles in flower development in P. henryanum, which will improve our understanding of the roles of the SEP-like MADS-box gene family and provide crucial insights into the mechanisms underlying floral development in orchids.
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Affiliation(s)
- Hao Cheng
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Xiulan Xie
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Maozhi Ren
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Shuhua Yang
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Zhao
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nasser Mahna
- Department of Horticultural Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Yi Liu
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Yufeng Xu
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yukai Xiang
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Hua Chai
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Liang Zheng
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Hong Ge
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruidong Jia
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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34
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Russo A, Mayjonade B, Frei D, Potente G, Kellenberger RT, Frachon L, Copetti D, Studer B, Frey JE, Grossniklaus U, Schlüter PM. Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families. FRONTIERS IN PLANT SCIENCE 2022; 13:883897. [PMID: 35665166 PMCID: PMC9161206 DOI: 10.3389/fpls.2022.883897] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/21/2022] [Indexed: 05/16/2023]
Abstract
Long-read DNA sequencing technologies require high molecular weight (HMW) DNA of adequate purity and integrity, which can be difficult to isolate from plant material. Plant leaves usually contain high levels of carbohydrates and secondary metabolites that can impact DNA purity, affecting downstream applications. Several protocols and kits are available for HMW DNA extraction, but they usually require a high amount of input material and often lead to substantial DNA fragmentation, making sequencing suboptimal in terms of read length and data yield. We here describe a protocol for plant HMW DNA extraction from low input material (0.1 g) which is easy to follow and quick (2.5 h). This method successfully enabled us to extract HMW from four species from different families (Orchidaceae, Poaceae, Brassicaceae, Asteraceae). In the case of recalcitrant species, we show that an additional purification step is sufficient to deliver a clean DNA sample. We demonstrate the suitability of our protocol for long-read sequencing on the Oxford Nanopore Technologies PromethION® platform, with and without the use of a short fragment depletion kit.
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Affiliation(s)
- Alessia Russo
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
- Department of Systematic and Evolutionary Botany and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), INRAE, Toulouse, France
| | - Daniel Frei
- Department of Method Development and Analytics, Agroscope, Wädenswil, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | | | - Léa Frachon
- Department of Systematic and Evolutionary Botany and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | - Dario Copetti
- Institute of Agricultural Sciences and Zurich-Basel Plant Science Centre, ETH Zürich, Zurich, Switzerland
| | - Bruno Studer
- Institute of Agricultural Sciences and Zurich-Basel Plant Science Centre, ETH Zürich, Zurich, Switzerland
| | - Jürg E. Frey
- Department of Method Development and Analytics, Agroscope, Wädenswil, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | - Philipp M. Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
- Department of Systematic and Evolutionary Botany and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
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35
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Li MH, Liu KW, Li Z, Lu HC, Ye QL, Zhang D, Wang JY, Li YF, Zhong ZM, Liu X, Yu X, Liu DK, Tu XD, Liu B, Hao Y, Liao XY, Jiang YT, Sun WH, Chen J, Chen YQ, Ai Y, Zhai JW, Wu SS, Zhou Z, Hsiao YY, Wu WL, Chen YY, Lin YF, Hsu JL, Li CY, Wang ZW, Zhao X, Zhong WY, Ma XK, Ma L, Huang J, Chen GZ, Huang MZ, Huang L, Peng DH, Luo YB, Zou SQ, Chen SP, Lan S, Tsai WC, Van de Peer Y, Liu ZJ. Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy. NATURE PLANTS 2022; 8:373-388. [PMID: 35449401 PMCID: PMC9023349 DOI: 10.1038/s41477-022-01127-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 03/09/2022] [Indexed: 05/12/2023]
Abstract
To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.
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Affiliation(s)
- Ming-He Li
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hsiang-Chia Lu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Qin-Liang Ye
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Diyang Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie-Yu Wang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yu-Feng Li
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Zhi-Ming Zhong
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Xuedie Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xia Yu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiong-De Tu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bin Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Hao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing-Yu Liao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Ting Jiang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Hong Sun
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinliao Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan-Qiong Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Ai
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun-Wen Zhai
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sha-Sha Wu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhuang Zhou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Lin Wu
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Fu Lin
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jui-Ling Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Ying Li
- Department of Applied Chemistry, National Pingtung University, Pingtung, Taiwan
| | | | | | | | - Xiao-Kai Ma
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liang Ma
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Huang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gui-Zhen Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ming-Zhong Huang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Laiqiang Huang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Dong-Hui Peng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shuang-Quan Zou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shi-Pin Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan.
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, China.
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36
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Sun Y, Shang L, Zhu QH, Fan L, Guo L. Twenty years of plant genome sequencing: achievements and challenges. TRENDS IN PLANT SCIENCE 2022; 27:391-401. [PMID: 34782248 DOI: 10.1016/j.tplants.2021.10.006] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/15/2021] [Accepted: 10/18/2021] [Indexed: 05/27/2023]
Abstract
Publication of the complete genome sequence of Arabidopsis thaliana, the first plant reference genome, in December 2000 heralded the beginning of the plant genome era. Over the past 20 years reference genomes have been generated for hundreds of plant species, spanning non-vascular to flowering plants. Releasing these plant genomes has dramatically advanced studies in all disciplines of plant biology. Importantly, multiple reference-level genomes have been generated for the major crops and their progenitors, enabling the creation of pan-genomes and exploration of domestication history and natural variations that can be adopted by modern crop breeding. We summarize the progress of plant genome sequencing and the challenges of sequencing more complex plant genomes and generating pan-genomes.
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Affiliation(s)
- Yanqing Sun
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Lianguang Shang
- 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, Shenzhen, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China; Zhejiang University City College School of Medicine, Hangzhou, China.
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
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37
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Abramson BW, Novotny M, Hartwick NT, Colt K, Aevermann BD, Scheuermann RH, Michael TP. The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness. PLANT PHYSIOLOGY 2022; 188:879-897. [PMID: 34893913 PMCID: PMC8825320 DOI: 10.1093/plphys/kiab564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/16/2021] [Indexed: 05/13/2023]
Abstract
The ability to trace every cell in some model organisms has led to the fundamental understanding of development and cellular function. However, in plants the complexity of cell number, organ size, and developmental time makes this a challenge even in the diminutive model plant Arabidopsis (Arabidopsis thaliana). Duckweed, basal nongrass aquatic monocots, provide an opportunity to follow every cell of an entire plant due to their small size, reduced body plan, and fast clonal growth habit. Here we present a chromosome-resolved genome for the highly invasive Lesser Duckweed (Lemna minuta) and generate a preliminary cell atlas leveraging low cell coverage single-nuclei sequencing. We resolved the 360 megabase genome into 21 chromosomes, revealing a core nonredundant gene set with only the ancient tau whole-genome duplication shared with all monocots, and paralog expansion as a result of tandem duplications related to phytoremediation. Leveraging SMARTseq2 single-nuclei sequencing, which provided higher gene coverage yet lower cell count, we profiled 269 nuclei covering 36.9% (8,457) of the L. minuta transcriptome. Since molecular validation was not possible in this nonmodel plant, we leveraged gene orthology with model organism single-cell expression datasets, gene ontology, and cell trajectory analysis to define putative cell types. We found that the tissue that we computationally defined as mesophyll expressed high levels of elemental transport genes consistent with this tissue playing a role in L. minuta wastewater detoxification. The L. minuta genome and preliminary cell map provide a paradigm to decipher developmental genes and pathways for an entire plant.
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Affiliation(s)
- Bradley W Abramson
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Nolan T Hartwick
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Kelly Colt
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Brian D Aevermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, California 92093, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, USA
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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38
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Xu Y, Lei Y, Su Z, Zhao M, Zhang J, Shen G, Wang L, Li J, Qi J, Wu J. A chromosome-scale Gastrodia elata genome and large-scale comparative genomic analysis indicate convergent evolution by gene loss in mycoheterotrophic and parasitic plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1609-1623. [PMID: 34647389 DOI: 10.1111/tpj.15528] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 05/27/2023]
Abstract
Mycoheterotrophic and parasitic plants are heterotrophic and parasitize on fungi and plants, respectively, to obtain nutrients. Large-scale comparative genomics analysis has not been conducted in mycoheterotrophic or parasitic plants or between these two groups of parasites. We assembled a chromosome-level genome of the fully mycoheterotrophic plant Gastrodia elata (Orchidaceae) and performed comparative genomic analyses on the genomes of G. elata and four orchids (initial mycoheterotrophs), three parasitic plants (Cuscuta australis, Striga asiatica, and Sapria himalayana), and 36 autotrophs from various angiosperm lineages. It was found that while in the hemiparasite S. asiatica and initial mycoheterotrophic orchids, approximately 4-5% of the conserved orthogroups were lost, the fully heterotrophic G. elata and C. australis both lost approximately 10% of the conserved orthogroups, indicating that increased heterotrophy is positively associated with gene loss. Importantly, many genes that are essential for autotrophs, including those involved in photosynthesis, the circadian clock, flowering time regulation, immunity, nutrient uptake, and root and leaf development, were convergently lost in both G. elata and C. australis. The high-quality genome of G. elata will facilitate future studies on the physiology, ecology, and evolution of mycoheterotrophic plants, and our findings highlight the critical role of gene loss in the evolution of plants with heterotrophic lifestyles.
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Affiliation(s)
- Yuxing Xu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yunting Lei
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhongxiang Su
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Man Zhao
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jingxiong Zhang
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guojing Shen
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Lei Wang
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jing Li
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jinfeng Qi
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jianqiang Wu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
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39
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de Oliveira Bustamante F, do Nascimento TH, Montenegro C, Dias S, do Vale Martins L, Braz GT, Benko-Iseppon AM, Jiang J, Pedrosa-Harand A, Brasileiro-Vidal AC. Oligo-FISH barcode in beans: a new chromosome identification system. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3675-3686. [PMID: 34368889 DOI: 10.1007/s00122-021-03921-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
An Oligo-FISH barcode system was developed for two model legumes, allowing the identification of all cowpea and common bean chromosomes in a single FISH experiment, and revealing new chromosome rearrangements. The FISH barcode system emerges as an effective tool to understand the chromosome evolution of economically important legumes and their related species. Current status on plant cytogenetic and cytogenomic research has allowed the selection and design of oligo-specific probes to individually identify each chromosome of the karyotype in a target species. Here, we developed the first chromosome identification system for legumes based on oligo-FISH barcode probes. We selected conserved genomic regions between Vigna unguiculata (Vu, cowpea) and Phaseolus vulgaris (Pv, common bean) (diverged ~ 9.7-15 Mya), using cowpea as a reference, to produce a unique barcode pattern for each species. We combined our oligo-FISH barcode pattern with a set of previously developed FISH probes based on BACs and ribosomal DNA sequences. In addition, we integrated our FISH maps with genome sequence data. Based on this integrated analysis, we confirmed two translocation events (involving chromosomes 1, 5, and 8; and chromosomes 2 and 3) between both species. The application of the oligo-based probes allowed us to demonstrate the participation of chromosome 5 in the translocation complex for the first time. Additionally, we detailed a pericentric inversion on chromosome 4 and identified a new paracentric inversion on chromosome 10. We also detected centromere repositioning associated with chromosomes 2, 3, 5, 7, and 9, confirming previous results for chromosomes 2 and 3. This first barcode system for legumes can be applied for karyotyping other Phaseolinae species, especially non-model, orphan crop species lacking genomic assemblies and cytogenetic maps, expanding our understanding of the chromosome evolution and genome organization of this economically important legume group.
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Affiliation(s)
- Fernanda de Oliveira Bustamante
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade do Estado de Minas Gerais, Unidade Divinópolis, Divinópolis, MG, Brazil
| | | | - Claudio Montenegro
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Sibelle Dias
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Lívia do Vale Martins
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Departamento de Biologia, Universidade Federal do Piauí, Teresina, PI, Brazil
| | | | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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40
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Chambers A, Cibrián-Jaramillo A, Karremans AP, Moreno Martinez D, Hernandez-Hernandez J, Brym M, Resende MFR, Moloney R, Sierra SN, Hasing T, Alomia YA, Hu Y. Genotyping-By-Sequencing diversity analysis of international Vanilla collections uncovers hidden diversity and enables plant improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 311:111019. [PMID: 34482920 DOI: 10.1016/j.plantsci.2021.111019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Genomics-based diversity analysis of natural vanilla populations is important in order to guide conservation efforts and genetic improvement through plant breeding. Vanilla is a cultivated, undomesticated spice that originated in Mesoamerica prior to spreading globally through vegetative cuttings. Vanilla extract from the commercial species, mainly V. planifolia and V. × tahitensis, is used around the world as an ingredient in foods, beverages, cosmetics, and pharmaceuticals. The global reliance on descendants of a few foundational clones in commercial production has resulted in an industry at heightened risk of catastrophic failure due to extremely narrow genetic diversity. Conversely, national and institutional collections including those near the center of cultivation contain previously undiscovered diversity that could bolster the genetic improvement of vanilla and guide conservation efforts. Towards this goal, an international vanilla genotyping effort generated and analyzed 431,204 single nucleotide polymorphisms among 412 accessions and 27 species from eight collections. Phylogenetic and STRUCTURE analysis sorted vanilla by species and identified hybrid accessions. Principal Component Analysis and the Fixation Index (FST) were used to refine relationships among accessions and showed differentiation among species. Analysis of the commercial species split V. planifolia into three types with all V. × tahitensis accessions being most similar to V. planifolia type 2. Finally, an in-depth analysis of V. × tahitensis identified seven V. planifolia and six V. odorata accessions as most similar to the estimated parental genotypes providing additional data in support of the current hybrid theory. The prevalence of probable V. × tahitensis parental accessions from Belize suggests that V. × tahitensis could have originated from this area and highlights the need for vanilla conservation throughout Central and South America. The genetic groupings among accessions, particularly for V. planifolia, can now be used to focus breeding efforts on fewer accessions that capture the greatest diversity.
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Affiliation(s)
- Alan Chambers
- Tropical Research and Education Center, Horticultural Sciences Department, University of Florida, 18905 SW 280th St, Homestead, FL, 33033, USA.
| | - Angélica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), CINVESTAV, Km 9.6 Carretera Irapuato-León, Guanajuato, CP 36824, Mexico.
| | - Adam P Karremans
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica; Naturalis Biodiversity Center, Endless Forms Group, Sylviusweg 72, Leiden, 2333 BE, the Netherlands.
| | - David Moreno Martinez
- Posgrado en Ecología Tropical, Centro de Investigaciones Tropicales, Universidad Veracruzana, José María Morelos 44, Zona Centro, CP 91000, Xalapa, Veracruz, Mexico.
| | - Juan Hernandez-Hernandez
- Campo Experimental Ixtacuaco, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Km 4.5 Carretera Martínez de la Torre-Tlapacoyan, Veracruz, CP 93600, Mexico.
| | - Maria Brym
- Tropical Research and Education Center, Horticultural Sciences Department, University of Florida, 18905 SW 280th St, Homestead, FL, 33033, USA.
| | - Marcio F R Resende
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
| | - Ruth Moloney
- Corridgeree Belize Ltd, Mile 6, Southern Highway, Silk Grass, Stann Creek District, Belize.
| | - Sheryl N Sierra
- College of Agriculture, Food, Environment and Natural Resources, Cavite State University, Indang, Cavite, 4122, Philippines.
| | | | - Yasmin A Alomia
- Department of Biological Sciences, Faculty of Sciences, Universidad de Los Andes, Cra. 1 Nº 18A - 12, Bogotá, Colombia.
| | - Ying Hu
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
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41
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Li HL, Wu L, Dong Z, Jiang Y, Jiang S, Xing H, Li Q, Liu G, Tian S, Wu Z, Bin Wu, Li Z, Zhao P, Zhang Y, Tang J, Xu J, Huang K, Liu X, Zhang W, Liao Q, Ren Y, Huang X, Li Q, Li C, Wang Y, Xavier-Ravi B, Li H, Liu Y, Wan T, Liu Q, Zou Y, Jian J, Xia Q, Liu Y. Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway. HORTICULTURE RESEARCH 2021; 8:189. [PMID: 34354044 PMCID: PMC8342499 DOI: 10.1038/s41438-021-00627-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/20/2021] [Accepted: 07/13/2021] [Indexed: 05/18/2023]
Abstract
Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger 'Zhugen', a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3'H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.
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Affiliation(s)
- Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Lin Wu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Zhaoming Dong
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
| | - Yusong Jiang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Sanjie Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Haitao Xing
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Qiang Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Guocheng Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Shuming Tian
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- College of Biology and Food Engineering, Chongqign Three Gorges University, Wanzhou, Chongqing, China
| | - Zhangyan Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Bin Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhexin Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
| | - Yan Zhang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
| | - Jianmin Tang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Ke Huang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Xia Liu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Wenlin Zhang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Qinhong Liao
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yun Ren
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Xinzheng Huang
- Department of Entomology and MOAKey Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian, Beijing, China
| | - Qingzhi Li
- Jinan Second Agricultural Science Research Institute, Jinan, Shandong, China
| | - Chengyong Li
- Jinan Second Agricultural Science Research Institute, Jinan, Shandong, China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
| | | | - Honghai Li
- Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Yang Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
- Fairy Lake Botanical Garden and Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Tao Wan
- Fairy Lake Botanical Garden and Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Qinhu Liu
- Ningyang Science and Technology Bureau, Taian, Shandong, China
| | - Yong Zou
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China.
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China.
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China.
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China.
| | - Yiqing Liu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China.
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China.
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Huang LM, Huang H, Chuang YC, Chen WH, Wang CN, Chen HH. Evolution of Terpene Synthases in Orchidaceae. Int J Mol Sci 2021; 22:6947. [PMID: 34203299 PMCID: PMC8268431 DOI: 10.3390/ijms22136947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Terpenoids are the largest class of plant secondary metabolites and are one of the major emitted volatile compounds released to the atmosphere. They have functions of attracting pollinators or defense function, insecticidal properties, and are even used as pharmaceutical agents. Because of the importance of terpenoids, an increasing number of plants are required to investigate the function and evolution of terpene synthases (TPSs) that are the key enzymes in terpenoids biosynthesis. Orchidacea, containing more than 800 genera and 28,000 species, is one of the largest and most diverse families of flowering plants, and is widely distributed. Here, the diversification of the TPSs evolution in Orchidaceae is revealed. A characterization and phylogeny of TPSs from four different species with whole genome sequences is available. Phylogenetic analysis of orchid TPSs indicates these genes are divided into TPS-a, -b, -e/f, and g subfamilies, and their duplicated copies are increased in derived orchid species compared to that in the early divergence orchid, A. shenzhenica. The large increase of both TPS-a and TPS-b copies can probably be attributed to the pro-duction of different volatile compounds for attracting pollinators or generating chemical defenses in derived orchid lineages; while the duplications of TPS-g and TPS-e/f copies occurred in a species-dependent manner.
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Affiliation(s)
- Li-Min Huang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Yu-Chen Chuang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Wen-Huei Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Neng Wang
- Department of Life Sciences, Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106, Taiwan;
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
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