101
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Guo X, Fang D, Sahu SK, Yang S, Guang X, Folk R, Smith SA, Chanderbali AS, Chen S, Liu M, Yang T, Zhang S, Liu X, Xu X, Soltis PS, Soltis DE, Liu H. Chloranthus genome provides insights into the early diversification of angiosperms. Nat Commun 2021; 12:6930. [PMID: 34836973 PMCID: PMC8626473 DOI: 10.1038/s41467-021-26922-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.
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Affiliation(s)
- Xing Guo
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Dongming Fang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Sunil Kumar Sahu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shuai Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Xuanmin Guang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ryan Folk
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762 United States of America
| | - Stephen A. Smith
- grid.214458.e0000000086837370Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 United States of America
| | - Andre S. Chanderbali
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Sisi Chen
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.9227.e0000000119573309South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650 China
| | - Min Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ting Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shouzhou Zhang
- grid.9227.e0000000119573309Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004 China
| | - Xin Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839BGI-Fuyang, BGI-Shenzhen, Fuyang, 236009 China
| | - Xun Xu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pamela S. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Douglas E. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America ,grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, FL 32611 United States of America
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
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102
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Yang Y, Li S, Xing Y, Zhang Z, Liu T, Ao W, Bao G, Zhan Z, Zhao R, Zhang T, Zhang D, Song Y, Bian C, Xu L, Kang T. The first high-quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa. Mol Ecol Resour 2021; 22:1493-1507. [PMID: 34758188 DOI: 10.1111/1755-0998.13547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/11/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022]
Abstract
Arctium lappa has a long medicinal and edible history with great economic importance. Here, the first high-quality chromosome-level draft genome of A. lappa was presented by the Illumina and PacBio sequencing data. The assembled genome was approximately 1.79 Gb with a N50 contig size of 6.88 Mb. Approximately 1.70 Gb (95.4%) of the contig sequences were anchored onto 18 chromosomes using Hi-C data; the scaffold N50 was improved to be 91.64 Mb. Furthermore, we obtained 1.12 Gb (68.46%) of repetitive sequences and 32,771 protein-coding genes; 616 positively selected candidate genes were identified. Among candidate genes related to lignan biosynthesis, the following were found to be highly correlated with the accumulation of arctiin: 4-coumarate-CoA ligase (4CL), dirigent protein (DIR), and hydroxycinnamoyl transferase (HCT). Additionally, we compared the transcriptomes of A. lappa roots at three different developmental stages and identified 8,943 differentially expressed genes (DEGs) in these tissues. These data can be utilized to identify genes related to A. lappa quality or provide a basis for molecular identification and comparative genomics among related species.
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Affiliation(s)
- Yanyun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Shengnan Li
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | | | - Tao Liu
- School of Pharmacy, China Medical University, Shenyang, China
| | - Wuliji Ao
- School of Mongol Medicine, Inner Mongolia University for Nationalities, Tongliao, China
| | - Guihua Bao
- School of Mongol Medicine, Inner Mongolia University for Nationalities, Tongliao, China
| | - Zhilai Zhan
- Traditional Chinese Medicine Resource Center, Chinese Academy of Traditional Chinese Medicine, Beijing, China
| | - Rong Zhao
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Tingting Zhang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Dachuan Zhang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yueyue Song
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Che Bian
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Tingguo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
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103
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Huang Z, Shen F, Chen Y, Cao K, Wang L. Chromosome-scale genome assembly and population genomics provide insights into the adaptation, domestication, and flavonoid metabolism of Chinese plum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1174-1192. [PMID: 34473873 DOI: 10.1111/tpj.15482] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Globally, commercialized plum cultivars are mostly diploid Chinese plums (Prunus salicina Lindl.), also known as Japanese plums, and are one of the most abundant and variable fruit tree species. To advance Prunus genomic research, we present a chromosome-scale P. salicina genome assembly, constructed using an integrated strategy that combines Illumina, Oxford Nanopore, and high-throughput chromosome conformation capture (Hi-C) sequencing. The high-quality genome assembly consists of a 318.6-Mb sequence (contig N50 length of 2.3 Mb) with eight pseudo-chromosomes. The expansion of the P. salicina genome is led by recent segmental duplications and a long terminal repeat burst of approximately 0.2 Mya. This resulted in a significant expansion of gene families associated with flavonoid metabolism and plant resistance, which impacted fruit flavor and increased species adaptability. Population structure and domestication history suggest that Chinese plum may have originated from South China and provides a domestication route with accompanying genomic variations. Selection sweep and genetic diversity analysis enabled the identification of several critical genes associated with flowering time, stress tolerance, and flavonoid metabolism, demonstrating the essential roles of related pathways during domestication. Furthermore, we reconstructed and exploited flavonoid-anthocyanin metabolism using multi-omics analysis in Chinese plum and proposed a complete metabolic pathway. Collectively, our results will facilitate further candidate gene discovery for important agronomic traits in Chinese plum and provide insights into future functional genomic studies and DNA-informed breeding.
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Affiliation(s)
- Zhenyu Huang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou, Henan, 450009, China
| | - Fei Shen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yuling Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou, Henan, 450009, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou, Henan, 450009, China
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou, Henan, 450009, China
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104
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Gonzalez-Ibeas D, Ibanez V, Perez-Roman E, Borredá C, Terol J, Talon M. Shaping the biology of citrus: I. Genomic determinants of evolution. THE PLANT GENOME 2021; 14:e20104. [PMID: 34275210 DOI: 10.1002/tpg2.20104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
We performed genomic analyses on wild species of the genus Citrus to identify major determinants of evolution. The most notable effect occurred on the pathogen-defense genes, as observed in many other plant genera. The gene space was also characterized by changes in gene families intimately related to relevant biochemical properties of citrus fruit, such as pectin modifying enzymes, HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, and O-methyltransferases. Citrus fruits are highly abundant on pectins and secondary metabolites such as terpenoids and flavonoids, the targets of these families. Other gene types under positive selection, expanded through tandem duplications and retained as triplets from whole genome duplications, codified for purple acid phosphatases and MATE-efflux proteins. Although speciation has not been especially rapid in the genus, analyses of selective pressure at the codon level revealed that the extant species evolved from the ancestral citrus radiation show signatures of pervasive adaptive evolution and is therefore potentially responsible for the vast phenotypic differences observed among current species.
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Affiliation(s)
- Daniel Gonzalez-Ibeas
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Victoria Ibanez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Estela Perez-Roman
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Carles Borredá
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Javier Terol
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Manuel Talon
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
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105
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Li J, Fan R, Wu B, Ji X, Hao C. Genome-Wide Identification and Functional Exploration of SBP-Box Gene Family in Black Pepper ( Piper nigrum L.). Genes (Basel) 2021; 12:genes12111740. [PMID: 34828347 PMCID: PMC8625754 DOI: 10.3390/genes12111740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Black pepper (Piper nigrum L.), is dubbed "the King of Spices". However, the lack of genic knowledge has limited the understanding of its physiological processes and hindered the development of its molecular breeding. The SBP-box gene family is an important family in plant development and integrates multiple physiological processes. Here, we made a genome-wide identification of the pepper SBP-box gene family to provide evolutionary and functional information about this conserved transcription factor. In total, 34 SBP genes were identified in pepper. All these pepper SBP genes were clustered into eight groups, and one pepper group was not found in Arabidopsis thaliana. Segment duplications played the most important role in the expansion process of pepper SBP genes, and all these duplications were subjected to purifying selection. Half of pepper SBP genes were found miR156 target sites, and 17 miR156s were predicted. The tissue expression analysis revealed the differential expression of pepper SBP genes. Eleven SBP genes were found in four co-expression networks, and the GO enrichment further provides a functional prediction for pepper SBP genes. This study lays a foundation for further studies of pepper and provides a valuable reference for functional mining of pepper SBP genes.
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Affiliation(s)
- Jing Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Baoduo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Xunzhi Ji
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
- Correspondence:
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106
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Zhao X, Tan L, Wang S, Shen Y, Guo L, Ye X, Liu S, Feng Y, Wu W. The SR Splicing Factors: Providing Perspectives on Their Evolution, Expression, Alternative Splicing, and Function in Populus trichocarpa. Int J Mol Sci 2021; 22:ijms222111369. [PMID: 34768799 PMCID: PMC8583155 DOI: 10.3390/ijms222111369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are important splicing factors in plant development and abiotic/hormone-related stresses. However, evidence that SR proteins contribute to the process in woody plants has been lacking. Using phylogenetics, gene synteny, transgenic experiments, and RNA-seq analysis, we identified 24 PtSR genes and explored their evolution, expression, and function in Popolus trichocarpa. The PtSR genes were divided into six subfamilies, generated by at least two events of genome triplication and duplication. Notably, they were constitutively expressed in roots, stems, and leaves, demonstrating their fundamental role in P. trichocarpa. Additionally, most PtSR genes (~83%) responded to at least one stress (cold, drought, salt, SA, MeJA, or ABA), and, especially, cold stress induced a dramatic perturbation in the expression and/or alternative splicing (AS) of 18 PtSR genes (~75%). Evidentially, the overexpression of PtSCL30 in Arabidopsis decreased freezing tolerance, which probably resulted from AS changes of the genes (e.g., ICE2 and COR15A) critical for cold tolerance. Moreover, the transgenic plants were salt-hypersensitive at the germination stage. These indicate that PtSCL30 may act as a negative regulator under cold and salt stress. Altogether, this study sheds light on the evolution, expression, and AS of PtSR genes, and the functional mechanisms of PtSCL30 in woody plants.
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Affiliation(s)
- Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Yirong Shen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Xiaoxue Ye
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Ying Feng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- Correspondence: (Y.F.); (W.W.)
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
- Correspondence: (Y.F.); (W.W.)
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107
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Chakraborty A, Mahajan S, Jaiswal SK, Sharma VK. Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. Commun Biol 2021; 4:1193. [PMID: 34654884 PMCID: PMC8521574 DOI: 10.1038/s42003-021-02720-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Curcuma longa, or turmeric, is traditionally known for its immense medicinal properties and has diverse therapeutic applications. However, the absence of a reference genome sequence is a limiting factor in understanding the genomic basis of the origin of its medicinal properties. In this study, we present the draft genome sequence of C. longa, belonging to Zingiberaceae plant family, constructed using 10x Genomics linked reads and Oxford Nanopore long reads. For comprehensive gene set prediction and for insights into its gene expression, transcriptome sequencing of leaf tissue was also performed. The draft genome assembly had a size of 1.02 Gbp with ~70% repetitive sequences, and contained 50,401 coding gene sequences. The phylogenetic position of C. longa was resolved through a comprehensive genome-wide analysis including 16 other plant species. Using 5,388 orthogroups, the comparative evolutionary analysis performed across 17 species including C. longa revealed evolution in genes associated with secondary metabolism, plant phytohormones signaling, and various biotic and abiotic stress tolerance responses. These mechanisms are crucial for perennial and rhizomatous plants such as C. longa for defense and environmental stress tolerance via production of secondary metabolites, which are associated with the wide range of medicinal properties in C. longa.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shubham K Jaiswal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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108
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Zhang Y, Shen Q, Leng L, Zhang D, Chen S, Shi Y, Ning Z, Chen S. Incipient diploidization of the medicinal plant Perilla within 10,000 years. Nat Commun 2021; 12:5508. [PMID: 34535649 PMCID: PMC8448860 DOI: 10.1038/s41467-021-25681-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Perilla is a young allotetraploid Lamiaceae species widely used in East Asia as herb and oil plant. Here, we report the high-quality, chromosome-scale genomes of the tetraploid (Perilla frutescens) and the AA diploid progenitor (Perilla citriodora). Comparative analyses suggest post Neolithic allotetraploidization within 10,000 years, and nucleotide mutation in tetraploid is 10% more than in diploid, both of which are dominated by G:C → A:T transitions. Incipient diploidization is characterized by balanced swaps of homeologous segments, and subsequent homeologous exchanges are enriched towards telomeres, with excess of replacements of AA genes by fractionated BB homeologs. Population analyses suggest that the crispa lines are close to the nascent tetraploid, and involvement of acyl-CoA: lysophosphatidylcholine acyltransferase gene for high α-linolenic acid content of seed oil is revealed by GWAS. These resources and findings provide insights into incipient diploidization and basis for breeding improvement of this medicinal plant.
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Affiliation(s)
- Yujun Zhang
- grid.410318.f0000 0004 0632 3409Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qi Shen
- grid.410318.f0000 0004 0632 3409Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China ,grid.464326.1Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China ,grid.411866.c0000 0000 8848 7685Present Address: Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liang Leng
- grid.410318.f0000 0004 0632 3409Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dong Zhang
- grid.410318.f0000 0004 0632 3409Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sha Chen
- grid.410318.f0000 0004 0632 3409Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuhua Shi
- grid.410318.f0000 0004 0632 3409Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zemin Ning
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Hinxton, UK
| | - Shilin Chen
- grid.410318.f0000 0004 0632 3409Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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109
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Yu Y, Yang S, Bian L, Yu K, Meng X, Zhang G, Xu W, Yao W, Guo D. Identification of C3H2C3-type RING E3 ubiquitin ligase in grapevine and characterization of drought resistance function of VyRCHC114. BMC PLANT BIOLOGY 2021; 21:422. [PMID: 34535070 PMCID: PMC8447581 DOI: 10.1186/s12870-021-03162-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND RING is one of the largest E3 ubiquitin ligase families and C3H2C3 type is the largest subfamily of RING, which plays an important role in plant growth and development, and growth and responses to biotic and abiotic stresses. RESULTS A total of 143 RING C3H2C3-type genes (RCHCs) were discovered from the grapevine genome and separated into groups (I-XI) according to their phylogenetic analysis, and these genes named according to their positions on chromosomes. Gene replication analysis showed that tandem duplications play a predominant role in the expansion of VvRCHCs family together. Structural analysis showed that most VvRCHCs (67.13 %) had no more than 2 introns, while genes clustered together based on phylogenetic trees had similar motifs and evolutionarily conserved structures. Cis-acting element analysis showed the diversity of VvRCHCs regulation. The expression profiles of eight DEGs in RNA-Seq after drought stress were like the results of qRT-PCR analysis. In vitro ubiquitin experiment showed that VyRCHC114 had E3 ubiquitin ligase activity, overexpression of VyRCHC114 in Arabidopsis improved drought tolerance. Moreover, the transgenic plant survival rate increased by 30 %, accompanied by electrolyte leakage, chlorophyll content and the activities of SOD, POD, APX and CAT were changed. The quantitative expression of AtCOR15a, AtRD29A, AtERD15 and AtP5CS1 showed that they participated in the response to drought stress may be regulated by the expression of VyRCHC114. CONCLUSIONS This study provides valuable new information for the evolution of grapevine RCHCs and its relevance for studying the functional characteristics of grapevine VyRCHC114 genes under drought stress.
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Affiliation(s)
- Yihe Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Shengdi Yang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Lu Bian
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Keke Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Xiangxuan Meng
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Guohai Zhang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Weirong Xu
- School of Wine, Ningxia University, Yinchuan, 750021 Ningxia Province China
| | - Wenkong Yao
- School of Wine, Ningxia University, Yinchuan, 750021 Ningxia Province China
| | - Dalong Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
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Feng X, Wang Y, Zhang N, Gao S, Wu J, Liu R, Huang Y, Zhang J, Qi Y. Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum. BMC PLANT BIOLOGY 2021; 21:395. [PMID: 34425748 PMCID: PMC8383383 DOI: 10.1186/s12870-021-03175-3] [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: 05/15/2021] [Accepted: 08/11/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND The identification and functional analysis of genes that improve tolerance to low potassium stress in S. spontaneum is crucial for breeding sugarcane cultivars with efficient potassium utilization. Calcineurin B-like (CBL) protein is a calcium sensor that interacts with specific CBL-interacting protein kinases (CIPKs) upon plants' exposure to various abiotic stresses. RESULTS In this study, nine CBL genes were identified from S. spontaneum. Phylogenetic analysis of 113 CBLs from 13 representative plants showed gene expansion and strong purifying selection in the CBL family. Analysis of CBL expression patterns revealed that SsCBL01 was the most commonly expressed gene in various tissues at different developmental stages. Expression analysis of SsCBLs under low K+ stress indicated that potassium deficiency moderately altered the transcription of SsCBLs. Subcellular localization showed that SsCBL01 is a plasma membrane protein and heterologous expression in yeast suggested that, while SsCBL01 alone could not absorb K+, it positively regulated K+ absorption mediated by the potassium transporter SsHAK1. CONCLUSIONS This study provided insights into the evolution of the CBL gene family and preliminarily demonstrated that the plasma membrane protein SsCBL01 was involved in the response to low K+ stress in S. spontaneum.
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Affiliation(s)
- Xiaomin Feng
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Yongjun Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Shuai Gao
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Jiayun Wu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Rui Liu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Yonghong Huang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yongwen Qi
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007 China
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111
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Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication. Proc Natl Acad Sci U S A 2021; 118:2101780118. [PMID: 34301898 DOI: 10.1073/pnas.2101780118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Teleost fishes comprise one-half of all vertebrate species and possess a duplicated genome. This whole-genome duplication (WGD) occurred on the teleost stem lineage in an ancient common ancestor of all living teleosts and is hypothesized as a trigger of their exceptional evolutionary radiation. Genomic and phylogenetic data indicate that WGD occurred in the Mesozoic after the divergence of teleosts from their closest living relatives but before the origin of the extant teleost groups. However, these approaches cannot pinpoint WGD among the many extinct groups that populate this 50- to 100-million-y lineage, preventing tests of the evolutionary effects of WGD. We infer patterns of genome size evolution in fossil stem-group teleosts using high-resolution synchrotron X-ray tomography to measure the bone cell volumes, which correlate with genome size in living species. Our findings indicate that WGD occurred very early on the teleost stem lineage and that all extinct stem-group teleosts known so far possessed duplicated genomes. WGD therefore predates both the origin of proposed key innovations of the teleost skeleton and the onset of substantial morphological diversification in the clade. Moreover, the early occurrence of WGD allowed considerable time for postduplication reorganization prior to the origin of the teleost crown group. This suggests at most an indirect link between WGD and evolutionary success, with broad implications for the relationship between genomic architecture and large-scale evolutionary patterns in the vertebrate Tree of Life.
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112
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Guo X, Mandáková T, Trachtová K, Özüdoğru B, Liu J, Lysak MA. Linked by Ancestral Bonds: Multiple Whole-Genome Duplications and Reticulate Evolution in a Brassicaceae Tribe. Mol Biol Evol 2021; 38:1695-1714. [PMID: 33331908 PMCID: PMC8097306 DOI: 10.1093/molbev/msaa327] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pervasive hybridization and whole-genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. Although frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (∼60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring postpolyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.
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Affiliation(s)
- Xinyi Guo
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karolína Trachtová
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Barış Özüdoğru
- Department of Biology, Faculty of Science, Hacettepe University, Beytepe, Ankara, Turkey
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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113
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Cheng J, Wang X, Liu X, Zhu X, Li Z, Chu H, Wang Q, Lou Q, Cai B, Yang Y, Lu X, Peng K, Liu D, Liu Y, Lu L, Liu H, Yang T, Ge Q, Shi C, Liu G, Dong Z, Xu X, Wang W, Jiang H, Ma Y. Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway. MOLECULAR PLANT 2021; 14:1199-1209. [PMID: 33951484 DOI: 10.1016/j.molp.2021.04.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/06/2021] [Accepted: 04/29/2021] [Indexed: 05/21/2023]
Abstract
Taxus, commonly known as yew, is a well-known gymnosperm with great ornamental and medicinal value. In this study, by assembling a chromosome-level genome of the Himalayan yew (Taxus wallichiana) with 10.9 Gb in 12 chromosomes, we revealed that tandem duplication acts as the driving force of gene family evolution in the yew genome, resulting in the main genes for paclitaxel biosynthesis, i.e. those encoding the taxadiene synthase, P450s, and transferases, being clustered on the same chromosome. The tandem duplication may also provide genetic resources for the nature to sculpt the core structure of taxoids at different positions and subsequently establish the complex pathway of paclitaxel by neofunctionalization. Furthermore, we confirmed that there are two genes in the cluster encoding isoenzymes of a known enzyme in the paclitaxel biosynthetic pathway. The reference genome of the Himalayan yew will serve as a platform for decoding the complete biosynthetic pathway of paclitaxel and understanding the chemodiversity of taxoids in gymnosperms.
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Affiliation(s)
- Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Xiao Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Jiaxing Synbiolab Biotechnology Co., Ltd., Jiaxing 314006, China
| | - Xiaonan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiaoxi Zhu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihe Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Huanyu Chu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qian Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - QianQian Lou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bijun Cai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yiqun Yang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyun Lu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Kai Peng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dingyu Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuwan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Lina Lu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ting Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Qijin Ge
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chengcheng Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Guichun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zhiwei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China.
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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Zhang C, Huang CH, Liu M, Hu Y, Panero JL, Luebert F, Gao T, Ma H. Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1273-1293. [PMID: 33559953 DOI: 10.1111/jipb.13078] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/08/2021] [Indexed: 05/29/2023]
Abstract
Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole-genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous-Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower-like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.
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Affiliation(s)
- Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
| | - Mian Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
| | - Jose L Panero
- Department of Integrative Biology, The University of Texas, University Station C0930, Austin, Texas, 78712, USA
| | - Federico Luebert
- Institut für Bodiversität der Pflanzen, Universität Bonn, Bonn, D - 53115, Germany
- Department of Silviculture and Nature Conservation, University of Chile, Santiago, 9206, Chile
| | - Tiangang Gao
- State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
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115
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Bowers JE, Paterson AH. Chromosome number is key to longevity of polyploid lineages. THE NEW PHYTOLOGIST 2021; 231:19-28. [PMID: 33772797 DOI: 10.1111/nph.17361] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Polyploidy is ubiquitous and often recursive in plant lineages, most frequently resulting in extinction but occasionally associated with great evolutionary success. However, instead of chromosome numbers exponentially increasing due to recurrent polyploidy, most angiosperm species have fewer than 14 chromosome pairs. Following genome duplication, diploidisation can render one copy of essential genes nonfunctional without fitness cost. In isolated subpopulations, alternate (homoeologous) gene copies can be lost, creating incompatibilities that reduce fitness of hybrids between subpopulations, constraining exchange of favourable genetic changes and reducing species fitness. When multiple sets of incompatible genes are genetically linked, their deleterious effects are not independent. The effective number of independently acting sets of incompatible loci in hybrids is limited by chromosome number and recombination. Therefore, species with many chromosomes are subject to a higher fitness penalty during diploidisation. Karyotypic changes, especially fusions, that reduce gene flow are normally fitness disadvantages, but during the diploidisation process, can increase fitness by reducing mixing of differentially diploidised alleles. Fitness penalties caused by diploidisation favour accelerated karyotypic change, with each change increasing barriers to gene flow, contributing to speciation. Lower chromosome numbers and increased chromosome fusions confer advantages to surviving the diploidisation process following polyploid formation, by independent mechanisms.
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Affiliation(s)
- John E Bowers
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
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116
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Yin L, Zhu Z, Huang L, Luo X, Li Y, Xiao C, Yang J, Wang J, Zou Q, Tao L, Kang Z, Tang R, Wang M, Fu S. DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.). HORTICULTURE RESEARCH 2021; 8:142. [PMID: 34193846 PMCID: PMC8245426 DOI: 10.1038/s41438-021-00576-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/29/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of B. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in B. napus might be partially regulated by MET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed Brassica polyploids.
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Affiliation(s)
- Liqin Yin
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Liangjun Huang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Xuan Luo
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Yun Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Chaowen Xiao
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Jisheng Wang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Qiong Zou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Lanrong Tao
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zeming Kang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Rong Tang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Maolin Wang
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Shaohong Fu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
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117
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Migicovsky Z, Yeats TH, Watts S, Song J, Forney CF, Burgher-MacLellan K, Somers DJ, Gong Y, Zhang Z, Vrebalov J, van Velzen R, Giovannoni JG, Rose JKC, Myles S. Apple Ripening Is Controlled by a NAC Transcription Factor. Front Genet 2021; 12:671300. [PMID: 34239539 PMCID: PMC8258254 DOI: 10.3389/fgene.2021.671300] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of pre-harvest ripening and associated textural changes following harvest are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from ∼800 apple accessions. In this population, we compared a genetic marker within NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after 3 months of cold storage. By sequencing NAC18.1 across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. NAC18.1 encodes a protein that is orthogolous to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). We introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Trevor H Yeats
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Sophie Watts
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville, NS, Canada
| | | | | | - Daryl J Somers
- Vineland Research and Innovation Centre, Vineland Station, ON, Canada
| | - Yihui Gong
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Zhaoqi Zhang
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Julia Vrebalov
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Robin van Velzen
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - James G Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States.,United States Department of Agriculture, Robert W. Holley Center, Cornell University, Ithaca, NY, United States
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
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118
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Huang J, Li X, Chen X, Guo Y, Liang W, Wang H. Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity. Int J Mol Sci 2021; 22:6556. [PMID: 34207256 PMCID: PMC8234336 DOI: 10.3390/ijms22126556] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.
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Affiliation(s)
| | | | | | | | | | - Huahua Wang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.H.); (X.L.); (X.C.); (Y.G.); (W.L.)
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119
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Li Z, McKibben MTW, Finch GS, Blischak PD, Sutherland BL, Barker MS. Patterns and Processes of Diploidization in Land Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:387-410. [PMID: 33684297 DOI: 10.1146/annurev-arplant-050718-100344] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing and disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Geoffrey S Finch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Brittany L Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
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120
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Fanelli V, Ngo KJ, Thompson VL, Silva BR, Tsai H, Sabetta W, Montemurro C, Comai L, Harmer SL. A TILLING by sequencing approach to identify induced mutations in sunflower genes. Sci Rep 2021; 11:9885. [PMID: 33972605 PMCID: PMC8110748 DOI: 10.1038/s41598-021-89237-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
The Targeting Induced Local Lesions in Genomes (TILLING) technology is a reverse genetic strategy broadly applicable to every kind of genome and represents an attractive tool for functional genomic and agronomic applications. It consists of chemical random mutagenesis followed by high-throughput screening of point mutations in targeted genomic regions. Although multiple methods for mutation discovery in amplicons have been described, next-generation sequencing (NGS) is the tool of choice for mutation detection because it quickly allows for the analysis of a large number of amplicons. The aim of the present work was to screen a previously generated sunflower TILLING population and identify alterations in genes involved in several important and complex physiological processes. Twenty-one candidate sunflower genes were chosen as targets for the screening. The TILLING by sequencing strategy allowed us to identify multiple mutations in selected genes and we subsequently validated 16 mutations in 11 different genes through Sanger sequencing. In addition to addressing challenges posed by outcrossing, our detection and validation of mutations in multiple regulatory loci highlights the importance of this sunflower population as a genetic resource.
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Affiliation(s)
- Valentina Fanelli
- grid.7644.10000 0001 0120 3326Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, 70124 Bari, Italy ,grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Kathie J. Ngo
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Veronica L. Thompson
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Brennan R. Silva
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Helen Tsai
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Wilma Sabetta
- grid.5326.20000 0001 1940 4177National Research Council, Institute of Bioscience and BioResources-IBBR, 70124 Bari, Italy
| | - Cinzia Montemurro
- grid.7644.10000 0001 0120 3326Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, 70124 Bari, Italy
| | - Luca Comai
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Stacey L. Harmer
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
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121
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Zhao Y, Zhang R, Jiang KW, Qi J, Hu Y, Guo J, Zhu R, Zhang T, Egan AN, Yi TS, Huang CH, Ma H. Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae. MOLECULAR PLANT 2021; 14:748-773. [PMID: 33631421 DOI: 10.1016/j.molp.2021.02.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/31/2020] [Accepted: 02/19/2021] [Indexed: 05/20/2023]
Abstract
Fabaceae are the third largest angiosperm family, with 765 genera and ∼19 500 species. They are important both economically and ecologically, and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability. However, resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive, precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae. Here, we report a highly resolved phylogeny using >1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species, along with other datasets, for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 genera. The subfamilies are maximally supported as monophyletic. The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes, and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae. Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary, marked by mass extinction, and subsequent divergence of most tribe-level clades within ∼15 million years. Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae, including those at the ancestors of Fabaceae and five of the subfamilies, and further analyses supported the Fabaceae ancestral polyploidy. The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switch(es) to rhizobial nodulation followed by multiple losses. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.
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Affiliation(s)
- Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China; Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, PR China; Ningbo Botanical Garden Herbarium, Ningbo 315201, PR China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Yi Hu
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Renbin Zhu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, PR China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Ashley N Egan
- Department of Biology, Utah Valley University, Orem, UT 84058, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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122
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Szövényi P, Gunadi A, Li FW. Charting the genomic landscape of seed-free plants. NATURE PLANTS 2021; 7:554-565. [PMID: 33820965 DOI: 10.1038/s41477-021-00888-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 05/02/2023]
Abstract
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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123
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Abstract
Aims:
The discontinuous pattern of genome size variation in angiosperms is an unsolved
problem related to genome evolution. In this study, we introduced a genome evolution operator
and solved the related eigenvalue equation to deduce the discontinuous pattern.
Background:
Genome is a well-defined system for studying the evolution of species. One of the
basic problems is the genome size evolution. The DNA amounts for angiosperm species are highly
variable, differing over 1000-fold. One big surprise is the discovery of the discontinuous
distribution of nuclear DNA amounts in many angiosperm genera.
Objective:
The discontinuous distribution of nuclear DNA amounts has certain regularity, much
like a group of quantum states in atomic physics. The quantum pattern has not been explained by
all the evolutionary theories so far and we shall interpret it through the quantum simulation of
genome evolution.
Methods:
We introduced a genome evolution operator H to deduce the distribution of DNA
amount. The nuclear DNA amount in angiosperms is studied from the eigenvalue equation of the
genome evolution operator H. The operator H is introduced by physical simulation and it is
defined as a function of the genome size N and the derivative with respect to the size.
Results:
The discontinuity of DNA size distribution and its synergetic occurrence in related
angiosperms species are successfully deduced from the solution of the equation. The results agree
well with the existing experimental data of Aloe, Clarkia, Nicotiana, Lathyrus, Allium and other
genera.
Conclusion:
The success of our approach may infer the existence of a set of genomic evolutionary
equations satisfying classical-quantum duality. The classical phase of evolution means it obeys the
classical deterministic law, while the quantum phase means it obeys the quantum stochastic law.
The discontinuity of DNA size distribution provides novel evidences on the quantum evolution of
angiosperms. It has been realized that the discontinuous pattern is due to the existence of some
unknown evolutionary constraints. However, our study indicates that these constraints on the
angiosperm genome essentially originate from quantum.
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Affiliation(s)
- Liaofu Luo
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Lirong Zhang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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124
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Zhang C, Zhang T, Luebert F, Xiang Y, Huang CH, Hu Y, Rees M, Frohlich MW, Qi J, Weigend M, Ma H. Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications. Mol Biol Evol 2021; 37:3188-3210. [PMID: 32652014 DOI: 10.1093/molbev/msaa160] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/16/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023] Open
Abstract
Asterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number of important crops. Despite their biological prominence and value to humans, the deep asterid phylogeny has not been fully resolved, and the evolutionary landscape underlying their radiation remains unknown. To resolve the asterid phylogeny, we sequenced 213 transcriptomes/genomes and combined them with other data sets, representing all accepted orders and nearly all families of asterids. We show fully supported monophyly of asterids, Berberidopsidales as sister to asterids, monophyly of all orders except Icacinales, Aquifoliales, and Bruniales, and monophyly of all families except Icacinaceae and Ehretiaceae. Novel taxon placements benefited from the expanded sampling with living collections from botanical gardens, resolving hitherto uncertain relationships. The remaining ambiguous placements here are likely due to limited sampling and could be addressed in the future with relevant additional taxa. Using our well-resolved phylogeny as reference, divergence time estimates support an Aptian (Early Cretaceous) origin of asterids and the origin of all orders before the Cretaceous-Paleogene boundary. Ancestral state reconstruction at the family level suggests that the asterid ancestor was a woody terrestrial plant with simple leaves, bisexual, and actinomorphic flowers with free petals and free anthers, a superior ovary with a style, and drupaceous fruits. Whole-genome duplication (WGD) analyses provide strong evidence for 33 WGDs in asterids and one in Berberidopsidales, including four suprafamilial and seven familial/subfamilial WGDs. Our results advance the understanding of asterid phylogeny and provide numerous novel evolutionary insights into their diversification and morphological evolution.
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Affiliation(s)
- Caifei Zhang
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Taikui Zhang
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Federico Luebert
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany.,Department of Silviculture and Nature Conservation, University of Chile, Santiago, Chile
| | - Yezi Xiang
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chien-Hsun Huang
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Hu
- Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Mathew Rees
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | | | - Ji Qi
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Maximilian Weigend
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Hong Ma
- Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
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125
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Liu B, Jin C, De Storme N, Schotte S, Schindfessel C, De Meyer T, Geelen D. A Hypomorphic Mutant of PHD Domain Protein Male Meiocytes Death 1. Genes (Basel) 2021; 12:516. [PMID: 33916197 PMCID: PMC8066392 DOI: 10.3390/genes12040516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 01/04/2023] Open
Abstract
Meiosis drives reciprocal genetic exchanges and produces gametes with halved chromosome number, which is important for the genetic diversity, plant viability, and ploidy consistency of flowering plants. Alterations in chromosome dynamics and/or cytokinesis during meiosis may lead to meiotic restitution and the formation of unreduced microspores. In this study, we isolated an Arabidopsis mutant male meiotic restitution 1 (mmr1), which produces a small subpopulation of diploid or polyploid pollen grains. Cytological analysis revealed that mmr1 produces dyads, triads, and monads indicative of male meiotic restitution. Both homologous chromosomes and sister chromatids in mmr1 are separated normally, but chromosome condensation at metaphase I is slightly affected. The mmr1 mutant displayed incomplete meiotic cytokinesis. Supportively, immunostaining of the microtubular cytoskeleton showed that the spindle organization at anaphase II and mini-phragmoplast formation at telophase II are aberrant. The causative mutation in mmr1 was mapped to chromosome 1 at the chromatin regulator Male Meiocyte Death 1 (MMD1/DUET) locus. mmr1 contains a C-to-T transition at the third exon of MMD1/DUET at the genomic position 2168 bp from the start codon, which causes an amino acid change G618D that locates in the conserved PHD-finger domain of histone binding proteins. The F1 progenies of mmr1 crossing with knockout mmd1/duet mutant exhibited same meiotic defects and similar meiotic restitution rate as mmr1. Taken together, we here report a hypomorphic mmd1/duet allele that typically shows defects in microtubule organization and cytokinesis.
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Affiliation(s)
- Bing Liu
- College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
- Unit HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (C.J.); (N.D.S.); (S.S.); (C.S.)
| | - Chunlian Jin
- Unit HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (C.J.); (N.D.S.); (S.S.); (C.S.)
| | - Nico De Storme
- Unit HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (C.J.); (N.D.S.); (S.S.); (C.S.)
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Sébastien Schotte
- Unit HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (C.J.); (N.D.S.); (S.S.); (C.S.)
| | - Cédric Schindfessel
- Unit HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (C.J.); (N.D.S.); (S.S.); (C.S.)
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links, 9000 Ghent, Belgium;
| | - Danny Geelen
- Unit HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (C.J.); (N.D.S.); (S.S.); (C.S.)
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126
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Costello R, Emms DM, Kelly S. Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles. Mol Biol Evol 2021; 37:969-981. [PMID: 31750917 PMCID: PMC7086175 DOI: 10.1093/molbev/msz275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the Plant Kingdom arise, in part, as a result of differences in the cohort of nuclear-encoded proteins that are targeted to them. However, neither the rate at which differences in protein targeting accumulate nor the evolutionary consequences of these changes are known. Using phylogenomic approaches coupled to ancestral state estimation, we show that the plant organellar proteome has diversified in proportion with molecular sequence evolution such that the proteomes of plant chloroplasts and mitochondria lose or gain on average 3.6 proteins per million years. We further demonstrate that changes in organellar protein targeting are associated with an increase in the rate of molecular sequence evolution and that such changes predominantly occur in genes with regulatory rather than metabolic functions. Finally, we show that gain and loss of protein target signals occurs at a higher rate following gene duplication, revealing that gene and genome duplication are a key facilitator of plant organelle evolution.
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Affiliation(s)
- Rona Costello
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - David M Emms
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Li J, Wang Y, Dong Y, Zhang W, Wang D, Bai H, Li K, Li H, Shi L. The chromosome-based lavender genome provides new insights into Lamiaceae evolution and terpenoid biosynthesis. HORTICULTURE RESEARCH 2021; 8:53. [PMID: 33642593 PMCID: PMC7917091 DOI: 10.1038/s41438-021-00490-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 05/05/2023]
Abstract
The aromatic shrub Lavandula angustifolia produces various volatile terpenoids that serve as resources for essential oils and function in plant-insect communication. To better understand the genetic basis of the terpenoid diversity in lavender, we present a high-quality reference genome for the Chinese lavender cultivar "Jingxun 2" using PacBio and Hi-C technologies to anchor the 894.50 Mb genome assembly into 27 pseudochromosomes. In addition to the γ triplication event, lavender underwent two rounds of whole-genome duplication (WGD) during the Eocene-Oligocene (29.6 MYA) and Miocene-Pliocene (6.9 MYA) transitions. As a result of tandem duplications and lineage-specific WGDs, gene families related to terpenoid biosynthesis in lavender are substantially expanded compared to those of five other species in Lamiaceae. Many terpenoid biosynthesis transcripts are abundant in glandular trichomes. We further integrated the contents of ecologically functional terpenoids and coexpressed terpenoid biosynthetic genes to construct terpenoid-gene networks. Typical gene clusters, including TPS-TPS, TPS-CYP450, and TPS-BAHD, linked with compounds that primarily function as attractants or repellents, were identified by their similar patterns of change during flower development or in response to methyl jasmonate. Comprehensive analysis of the genetic basis of the production of volatiles in lavender could serve as a foundation for future research into lavender evolution, phytochemistry, and ecology.
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Affiliation(s)
- Jingrui Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100015, Beijing, China
| | - Yiming Wang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Yanmei Dong
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100015, Beijing, China
| | - Wenying Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100015, Beijing, China
| | - Di Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
| | - Hongtong Bai
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
| | - Kui Li
- Novogene Bioinformatics Institute, 100083, Beijing, China.
| | - Hui Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China.
| | - Lei Shi
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China.
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Zeng L, Dehesh K. The eukaryotic MEP-pathway genes are evolutionarily conserved and originated from Chlaymidia and cyanobacteria. BMC Genomics 2021; 22:137. [PMID: 33637041 PMCID: PMC7912892 DOI: 10.1186/s12864-021-07448-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
Background Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes. Results Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development. Conclusion Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07448-x.
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Affiliation(s)
- Liping Zeng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
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Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi. Commun Biol 2021; 4:201. [PMID: 33589695 PMCID: PMC7884421 DOI: 10.1038/s42003-021-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.
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Dar MS, Dholakia BB, Kulkarni AP, Oak PS, Shanmugam D, Gupta VS, Giri AP. Influence of domestication on specialized metabolic pathways in fruit crops. PLANTA 2021; 253:61. [PMID: 33538903 DOI: 10.1007/s00425-020-03554-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 12/23/2020] [Indexed: 05/08/2023]
Abstract
During the process of plant domestication, the selection and traditional breeding for desired characters such as flavor, juiciness and nutritional value of fruits, probably have resulted in gain or loss of specialized metabolites contributing to these traits. Their appearance in fruits is likely due to the acquisition of novel and specialized metabolic pathways and their regulation, driven by systematic molecular evolutionary events facilitated by traditional breeding. Plants change their armory of specialized metabolism to adapt and survive in diverse ecosystems. This may occur through molecular evolutionary events, such as single nucleotide polymorphism, gene duplication and transposition, leading to convergent or divergent evolution of biosynthetic pathways producing such specialized metabolites. Breeding and selection for improved specific and desired traits (fruit size, color, taste, flavor, etc.) in fruit crops through conventional breeding approaches may further alter content and profile of specialized metabolites. Biosynthetic routes of these metabolites have been studied in various plants. Here, we explore the influence of plant domestication and breeding processes on the selection of biosynthetic pathways of favorable specialized metabolites in fruit crops. An orderly clustered arrangement of genes associated with their production is observed in many fruit crops. We further analyzed selection-based acquisition of specialized metabolic pathways comparing first the metabolic profiles and genes involved in their biosynthesis, followed by the genomic organization of such genes between wild and domesticated horticultural crops. Domestication of crop plants favored the acquisition and retention of metabolic pathways that enhanced the fruit value while eliminated those which produced toxic or unfavorable metabolites. Interestingly, unintentional reorganization of complex metabolic pathways by selection and traditional breeding processes has endowed us with flavorful, juicy and nutritionally rich fruits.
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Affiliation(s)
- M Saleem Dar
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Bhushan B Dholakia
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
| | - Abhijeet P Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS, 411007, India
| | - Pranjali S Oak
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Dhanasekaran Shanmugam
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Vidya S Gupta
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Ashok P Giri
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India.
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Zheng Y, Wang LB, Sun SF, Liu SY, Liu MJ, Lin J. Phylogenetic and ion-response analyses reveal a relationship between gene expansion and functional divergence in the Ca 2+/cation antiporter family in Angiosperms. PLANT MOLECULAR BIOLOGY 2021; 105:303-320. [PMID: 33123851 DOI: 10.1007/s11103-020-01088-7] [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: 02/20/2020] [Accepted: 10/21/2020] [Indexed: 05/28/2023]
Abstract
Plant CaCA superfamily genes with higher tendency to retain after WGD are more gene expression and function differentiated in ion-response. Plants and animals face different environmental stresses but share conserved Ca2+ signaling pathways, such as Ca2+/Cation transport. The Ca2+/cation antiporters superfamily (CaCAs) is an ancient and widespread family of ion-coupled cation transporters found in all kingdoms of life. We analyzed the molecular evolution progress of the family through comparative genomics and phylogenetics of CaCAs genes from plants and animals, grouping these genes into several families and clades, and identified multiple gene duplication retention events, particularly in the CAX (H+/cation exchanger), CCX (cation/Ca2+ exchanger), and NCL (Na+/Ca2+ exchanger-like) families. The tendency of duplication retention differs between families and gene clades. The gene duplication events were probably the result of whole-genome duplication (WGD) in plants and might have led to functional divergence. Tissue and ion-response expression analyses revealed that CaCAs genes with more highly differentiated expression patterns are more likely to be retained as duplicates than those with more conserved expression profiles. Phenotype of Arabidopsis thaliana mutants showed that loss of genes with a greater tendency to be retained after duplication resulted in more severe growth deficiency. CaCAs genes in salt-tolerant species tended to inherit the expression characteristics of their most recent common ancestral genes, with conservative ion-response expression. This study indicates a possible evolutionary scheme for cation transport and illustrates distinct fates and a mechanism for the evolution of gene duplicates. The increased copy numbers of genes and divergences in expression might have contributed to the divergent functions of CaCAs protein, allowing plants to cope with environmental stresses and adapt to a larger number of ecological niches.
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Affiliation(s)
- Ye Zheng
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Lin-Bo Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Shu-Feng Sun
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Shi-Ying Liu
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Ming-Jia Liu
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Juan Lin
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China.
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Wan WL, Kim ST, Castel B, Charoennit N, Chae E. Genetics of autoimmunity in plants: an evolutionary genetics perspective. THE NEW PHYTOLOGIST 2021; 229:1215-1233. [PMID: 32970825 DOI: 10.1111/nph.16947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/12/2020] [Indexed: 05/14/2023]
Abstract
Autoimmunity in plants has been found in numerous hybrids as a form of hybrid necrosis and mutant panels. Uncontrolled cell death is a main cellular outcome of autoimmunity, which negatively impacts growth. Its occurrence highlights the vulnerable nature of the plant immune system. Genetic investigation of autoimmunity in hybrid plants revealed that extreme variation in the immune receptor repertoire is a major contributor, reflecting an evolutionary conundrum that plants face in nature. In this review, we discuss natural variation in the plant immune system and its contribution to fitness. The value of autoimmunity genetics lies in its ability to identify combinations of a natural immune receptor and its partner that are predisposed to triggering autoimmunity. The network of immune components for autoimmunity becomes instrumental in revealing mechanistic details of how immune receptors recognize cellular invasion and activate signaling. The list of autoimmunity-risk variants also allows us to infer evolutionary processes contributing to their maintenance in the natural population. Our approach to autoimmunity, which integrates mechanistic understanding and evolutionary genetics, has the potential to serve as a prognosis tool to optimize immunity in crops.
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Affiliation(s)
- Wei-Lin Wan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Sang-Tae Kim
- Department of Life Sciences, The Catholic University of Korea, Bucheon, Gyeonggi-do, 14662, South Korea
| | - Baptiste Castel
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Nuri Charoennit
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
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Zeng X, Li H, Li K, Yuan R, Zhao S, Li J, Luo J, Li X, Ma H, Wu G, Yan X. Evolution of the Brassicaceae-specific MS5-Like family and neofunctionalization of the novel MALE STERILITY 5 gene essential for male fertility in Brassica napus. THE NEW PHYTOLOGIST 2021; 229:2339-2356. [PMID: 33128826 PMCID: PMC7894334 DOI: 10.1111/nph.17053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 10/08/2020] [Indexed: 05/22/2023]
Abstract
New genes (or lineage-specific genes) can facilitate functional innovations. MALE STERILITY 5 (MS5) in Brassica napus is a fertility-related new gene, which has two wild-type alleles (BnMS5a and BnMS5c ) and two mutant alleles (BnMS5b and BnMS5d ) that could induce male sterility. Here, we studied the history and functional evolution of MS5 homologs in plants by phylogenetic analysis and molecular genetic experiments. We identified 727 MS5 homologs and found that they define a Brassicaceae-specific gene family that has expanded partly via multiple tandem gene duplications and also probably transpositions. The MS5 in B. napus is inherited from a basic diploid ancestor of B. rapa. Molecular genetic experiments indicate that BnMS5a and BnMS5c are functionally distinct in B. napus and that BnMS5d can inhibit BnMS5a in B. napus in a dosage-dependent manner. The BnMS5a protein can move in coordination with meiotic telomeres and interact with the nuclear envelope protein SUN1, with a possible crucial role in meiotic chromosome behavior. In summary, BnMS5 belongs to a Brassicaceae-specific new gene family, and has gained a novel function that is essential for male fertility in B. napus through neofunctionalization that has likely occurred since the origin of B. rapa.
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Affiliation(s)
- Xinhua Zeng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Hao Li
- Department of Biologythe Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Keqi Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Rong Yuan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Shengbo Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Jun Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Junling Luo
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Xiaofei Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Hong Ma
- Department of Biologythe Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Gang Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Xiaohong Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
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Cheng J, Chen J, Liu X, Li X, Zhang W, Dai Z, Lu L, Zhou X, Cai J, Zhang X, Jiang H, Ma Y. The origin and evolution of the diosgenin biosynthetic pathway in yam. PLANT COMMUNICATIONS 2021; 2:100079. [PMID: 33511341 PMCID: PMC7816074 DOI: 10.1016/j.xplc.2020.100079] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 05/21/2023]
Abstract
Diosgenin, mainly produced by Dioscorea species, is a traditional precursor of most hormonal drugs in the pharmaceutical industry. The mechanisms that underlie the origin and evolution of diosgenin biosynthesis in plants remain unclear. After sequencing the whole genome of Dioscorea zingiberensis, we revealed the evolutionary trajectory of the diosgenin biosynthetic pathway in Dioscorea and demonstrated the de novo biosynthesis of diosgenin in a yeast cell factory. First, we found that P450 gene duplication and neo-functionalization, driven by positive selection, played important roles in the origin of the diosgenin biosynthetic pathway. Subsequently, we found that the enrichment of diosgenin in the yam lineage was regulated by CpG islands, which evolved to regulate gene expression in the diosgenin pathway and balance the carbon flux between the biosynthesis of diosgenin and starch. Finally, by integrating genes from plants, animals, and yeast, we heterologously synthesized diosgenin to 10 mg/l in genetically-engineered yeast. Our study not only reveals the origin and evolutionary mechanisms of the diosgenin biosynthetic pathway in Dioscorea, but also introduces an alternative approach for the production of diosgenin through synthetic biology.
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Affiliation(s)
- Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jing Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaonan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiangchen Li
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weixiong Zhang
- Research Center for Ecology and Environmental Sciences, Northwestern Polytechnical University, Xian, China
| | - Zhubo Dai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lina Lu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiang Zhou
- Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi 330004, China
| | - Jing Cai
- Research Center for Ecology and Environmental Sciences, Northwestern Polytechnical University, Xian, China
- Corresponding author
| | - Xueli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Corresponding author
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Corresponding author
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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Liu C, Zhao Y, Zhao X, Dong J, Yuan Z. Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance. BMC PLANT BIOLOGY 2020; 20:560. [PMID: 33308157 PMCID: PMC7733266 DOI: 10.1186/s12870-020-02771-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/02/2020] [Indexed: 06/09/2023]
Abstract
BACKGROUNDS Pomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl- and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl-, NO3-, HCO3- and I-, but its characteristics have not been reported on pomegranate. RESULTS In this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which was suspected to be a NO3-/H+ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl-. We determined the content of Cl-, NO3-, H2PO4-, and SO42- in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl- content increased sharply in pomegranate tissues. Salinity inhibited the uptake of NO3- and SO42-, but accelerated H2PO4- uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl- into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl- from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO3- was transported into leaves to mitigate the nitrogen deficiency. CONCLUSIONS Our findings suggested that the PgCLC genes played important roles in balancing of Cl- and NO3- in pomegranate tissues under salt stress. This study established a theoretical foundation for the further functional characterization of the CLC genes in pomegranate.
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Affiliation(s)
- Cuiyu Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yujie Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianmei Dong
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
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The Puzzling Fate of a Lupin Chromosome Revealed by Reciprocal Oligo-FISH and BAC-FISH Mapping. Genes (Basel) 2020; 11:genes11121489. [PMID: 33322080 PMCID: PMC7764521 DOI: 10.3390/genes11121489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022] Open
Abstract
Old World lupins constitute an interesting model for evolutionary research due to diversity in genome size and chromosome number, indicating evolutionary genome reorganization. It has been hypothesized that the polyploidization event which occurred in the common ancestor of the Fabaceae family was followed by a lineage-specific whole genome triplication (WGT) in the lupin clade, driving chromosome rearrangements. In this study, chromosome-specific markers were used as probes for heterologous fluorescence in situ hybridization (FISH) to identify and characterize structural chromosome changes among the smooth-seeded (Lupinus angustifolius L., Lupinus cryptanthus Shuttlew., Lupinus micranthus Guss.) and rough-seeded (Lupinus cosentinii Guss. and Lupinus pilosus Murr.) lupin species. Comparative cytogenetic mapping was done using FISH with oligonucleotide probes and previously published chromosome-specific bacterial artificial chromosome (BAC) clones. Oligonucleotide probes were designed to cover both arms of chromosome Lang06 of the L. angustifolius reference genome separately. The chromosome was chosen for the in-depth study due to observed structural variability among wild lupin species revealed by BAC-FISH and supplemented by in silico mapping of recently released lupin genome assemblies. The results highlighted changes in synteny within the Lang06 region between the lupin species, including putative translocations, inversions, and/or non-allelic homologous recombination, which would have accompanied the evolution and speciation.
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Zhang L, Wu S, Chang X, Wang X, Zhao Y, Xia Y, Trigiano RN, Jiao Y, Chen F. The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress. PLANT, CELL & ENVIRONMENT 2020; 43:2847-2856. [PMID: 33001478 DOI: 10.1111/pce.13898] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/22/2020] [Accepted: 09/26/2020] [Indexed: 05/24/2023]
Abstract
Flowering plants, or angiosperms, consist of more than 300,000 species, far more than any other land plant lineages. The accumulated evidence indicates that multiple ancient polyploidy events occurred around 100 to 120 million years ago during the Cretaceous and drove the early diversification of four major clades of angiosperms: gamma whole-genome triplication in the common ancestor of core eudicots, tau whole-genome duplication during the early diversification of monocots, lambda whole-genome duplication during the early diversification of magnoliids, and pi whole-genome duplication in the Nymphaeales lineage. These four polyploidy events have played essential roles in the adaptive evolution and diversification of major clades of flowering plants. Here, we specifically review the current understanding of this wave of ancient whole-genome duplications and their evolutionary significance. Notably, although these ancient whole-genome duplications occurred independently, they have contributed to the expansion of many stress-related genes (e.g., heat shock transcription factors and Arabidopsis response regulators),and these genes could have been selected for by global environmental changes in the Cretaceous. Therefore, this ancient wave of paleopolyploidy events could have significantly contributed to the adaptation of angiosperms to environmental changes, and potentially promoted the wide diversification of flowering plants.
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Affiliation(s)
- Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shengdan Wu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Xiaojun Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiuyun Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yunpeng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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138
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Bhardwaj E, Lal M, Anand S, Das S. Independent recurrent evolution of MICRORNA genes converging onto similar non-canonical organisation across green plant lineages is driven by local and segmental duplication events in species, family and lineages. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110661. [PMID: 33218629 DOI: 10.1016/j.plantsci.2020.110661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
The relationship between evolutionary history, organisation and transcriptional regulation of genes are intrinsically linked. These have been well studied in canonically organised protein-coding genes but not of MIRNAs. In the present study, we investigated the non-canonical arrangement of MIRNAs across taxonomic boundaries from algae to angiosperms employing a combination of genome organization, phylogeny and synteny. We retrieved the complete dataset of MIRNA from twenty-five species to identify and classify based on organisational patterns. The median size of cluster was between 2-5 kb and between 1-20 % of all MIRNAs are organized in head-to-head (with bidirectional promoter), head-to-tail (tandem), and overlapping manner. Although majority of the clusters are composed of MIRNA homologs, 25% of all clusters comprises of non-homologous genes with a potential of generating functional and regulatory complexity. A comparison of phylogeny and organizational patterns revealed that multiple independent events, some of which are species-specific, and some ancient, in different lineages, are responsible for non-canonical organization. Detailed investigation of MIR395 family across the plants revealed a complex origin of non-canonical arrangement through ancient and recent, segmental and local duplications; analysis of MIR399 family revealed major expansion occurred prior to monocot-dicot split, with few lineage-specific events. Evolution of "convergent" organization pattern of non-canonical arrangement originating from independent loci through recurrent event highlights our poor understanding of evolutionary process of MIRNA genes. The present investigation thus paves way for comparative functional genomics to understand the role of non-canonical organization on transcriptional regulation and regulatory diversity in MIRNA gene families.
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Affiliation(s)
- Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - S Anand
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110 007, India.
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139
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Tao J, Hao Z, Huang C. Molecular evolution of GDP-L-galactose phosphorylase, a key regulatory gene in plant ascorbate biosynthesis. AOB PLANTS 2020; 12:plaa055. [PMID: 33173574 PMCID: PMC7640755 DOI: 10.1093/aobpla/plaa055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Ascorbic acid (AsA) is a widespread antioxidant in living organisms, and plays essential roles in the growth and development of animals and plants as well as in the response to abiotic stress tolerance. The GDP-L-galactose phosphorylase (GGP) is a key regulatory gene in plant AsA biosynthesis that can regulate the concentration of AsA at the transcriptional and translational levels. The function and regulation mechanisms of GGP have been well understood; however, the molecular evolutionary patterns of the gene remain unclear. In this study, a total of 149 homologous sequences of GGP were sampled from 71 plant species covering the major groups of Viridiplantae, and the phylogenetic relationships, gene duplication and molecular evolution analyses of the genes were systematically investigated. Results showed that GGP genes are present throughout the plant kingdom and five shared whole-genome duplications and several lineage-specific whole-genome duplications were found, which led to the rapid expansion of GGPs in seed plants, especially in angiosperms. The structure of GGP genes was more conserved in land plants, but varied greatly in green algae, indicating that GGP may have undergone great differentiation in the early stages of plant evolution. Most GGP proteins had a conserved motif arrangement and composition, suggesting that plant GGPs have similar catalytic functions. Molecular evolutionary analyses showed that GGP genes were predominated by purifying selection, indicating that the gene is functionally conserved due to its vital importance in AsA biosynthesis. Most of the branches under positive selection identified by the branch-site model were mainly in the chlorophytes lineage, indicating episodic diversifying selection may contribute to the evolution of GGPs, especially in the chlorophyte lineage. The conserved function of GGP and its rapid expansion in angiosperms maybe one of the reasons for the increase of AsA content in angiosperms, enabling angiosperms to adapt to changing environments.
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Affiliation(s)
- Junjie Tao
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, China
| | - Zhuan Hao
- College of Chemistry and Materials, Weinan Normal University, Weinan, China
| | - Chunhui Huang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, China
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140
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Becher H, Brown MR, Powell G, Metherell C, Riddiford NJ, Twyford AD. Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island. PLANT COMMUNICATIONS 2020; 1:100105. [PMID: 33367265 PMCID: PMC7748025 DOI: 10.1016/j.xplc.2020.100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/24/2020] [Accepted: 08/27/2020] [Indexed: 05/02/2023]
Abstract
Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation. However, polyploid groups are understudied due to complex sequence homology, challenging genome assembly, and taxonomic complexity. Here, we study adaptive divergence in taxonomically complex eyebrights (Euphrasia), where recent divergence, phenotypic plasticity, and hybridization blur species boundaries. We focus on three closely related tetraploid species with contrasting ecological preferences that are sympatric on Fair Isle, a small isolated island in the British Isles. Using a common garden experiment, we show a genetic component to the morphological differences present between these species. Using whole-genome sequencing and a novel k-mer approach we call "Tetmer", we demonstrate that the species are of allopolyploid origin, with a sub-genome divergence of approximately 5%. Using ∼2 million SNPs, we show sub-genome homology across species, with a very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland Euphrasia micrantha, while grassland Euphrasia arctica and coastal Euphrasia foulaensis are more closely related. Overall, we show that tetraploid Euphrasia is a system of allopolyploids of postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.
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Affiliation(s)
- Hannes Becher
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- Corresponding author
| | - Max R. Brown
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Gavin Powell
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, 4 High Firs Crescent, Harpenden, Hertfordshire AL5 1NA, UK
| | | | - Alex D. Twyford
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
- Corresponding author
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141
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Xu S, Wang J, Guo Z, He Z, Shi S. Genomic Convergence in the Adaptation to Extreme Environments. PLANT COMMUNICATIONS 2020; 1:100117. [PMID: 33367270 PMCID: PMC7747959 DOI: 10.1016/j.xplc.2020.100117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 05/08/2023]
Abstract
Convergent evolution is especially common in plants that have independently adapted to the same extreme environments (i.e., extremophile plants). The recent burst of omics data has alleviated many limitations that have hampered molecular convergence studies of non-model extremophile plants. In this review, we summarize cases of genomic convergence in these taxa to examine the extent and type of genomic convergence during the process of adaptation to extreme environments. Despite being well studied by candidate gene approaches, convergent evolution at individual sites is rare and often has a high false-positive rate when assessed in whole genomes. By contrast, genomic convergence at higher genetic levels has been detected during adaptation to the same extreme environments. Examples include the convergence of biological pathways and changes in gene expression, gene copy number, amino acid usage, and GC content. Higher convergence levels play important roles in the adaptive evolution of extremophiles and may be more frequent and involve more genes. In several cases, multiple types of convergence events have been found to co-occur. However, empirical and theoretical studies of this higher level convergent evolution are still limited. In conclusion, both the development of powerful approaches and the detection of convergence at various genetic levels are needed to further reveal the genetic mechanisms of plant adaptation to extreme environments.
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Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiayan Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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142
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Comprehensive analysis of polygalacturonase genes offers new insights into their origin and functional evolution in land plants. Genomics 2020; 113:1096-1108. [PMID: 33171205 DOI: 10.1016/j.ygeno.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/22/2020] [Accepted: 11/04/2020] [Indexed: 11/21/2022]
Abstract
Polygalacturonase (PG) is a hydrolase that participates in pectin degradation, pod shattering and fruit softening. Here, we identified 2786 PG genes across 54 plants, which could be divided into three groups. Evolutionary analysis suggested that PG family originated from the charophyte green algae, and Subgroups A2-A4 evolved from the Subgroup A1 after the tracheophyte-angiosperm split. Whole-genome duplication was the major force leading to PG gene expansion. Interestingly, the PG genes continuously expanded in eudicots, whereas it contracted in monocots after the eudicot-monocot split. PG genes in Group A are expressed at high levels in floral organs, whereas genes in Groups B and C are expressed at high levels in various tissues. Moreover, three BnaPG15 members were found for their potential possibility in pod shattering in Brassica napus. Our results provide new insight into the evolutionary history of PG family, and their potentially functional role in plants.
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143
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Genome-Wide Duplication of Allotetraploid Brassica napus Produces Novel Characteristics and Extensive Ploidy Variation in Self-Pollinated Progeny. G3-GENES GENOMES GENETICS 2020; 10:3687-3699. [PMID: 32753368 PMCID: PMC7534442 DOI: 10.1534/g3.120.401493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Whole genome duplications (WGDs) have played a major role in angiosperm species evolution. Polyploid plants have undergone multiple cycles of ancient WGD events during their evolutionary history. However, little attention has been paid to the additional WGD of the existing allopolyploids. In this study, we explored the influences of additional WGD on the allopolyploid Brassica napus. Compared to tetraploid B. napus, octoploid B. napus (AAAACCCC, 2n = 8x =76) showed significant differences in phenotype, reproductive ability and the ploidy of self-pollinated progeny. Genome duplication also altered a key reproductive organ feature in B. napus, that is, increased the number of pollen apertures. Unlike autopolyploids produced from the diploid Brassica species, the octoploid B. napus produced from allotetraploid B. napus had a relatively stable meiotic process, high pollen viability and moderate fertility under self-pollination conditions, indicating that sub-genomic interactions may be important for the successful establishment of higher-order polyploids. Doubling the genome of B. napus provided us with an opportunity to gain insight into the flexibility of the Brassica genomes. The genome size of self-pollinated progeny of octoploid B. napus varied greatly, and was accompanied by extensive genomic instability, such as aneuploidy, mixed-ploidy and mitotic abnormality. The octoploid B. napus could go through any of genome reduction, equilibrium or expansion in the short-term, thus providing a novel karyotype library for the Brassica genus. Our results reveal the short-term evolutionary consequences of recurrent polyploidization events, and help to deepen our understanding of polyploid plant evolution.
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144
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Jiménez-Morales E, Aguilar-Hernández V, Aguilar-Henonin L, Guzmán P. Molecular basis for neofunctionalization of duplicated E3 ubiquitin ligases underlying adaptation to drought tolerance in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:474-492. [PMID: 33164265 DOI: 10.1111/tpj.14938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Multigene families in plants expanded from ancestral genes via gene duplication mechanisms constitute a significant fraction of the coding genome. Although most duplicated genes are lost over time, many are retained in the genome. Clusters of tandemly arrayed genes are commonly found in the plant genome where they can promote expansion of gene families. In the present study, promoter fusion to the GUS reporter gene was used to examine the promoter architecture of duplicated E3 ligase genes that are part of group C in the Arabidopsis thaliana ATL family. Acquisition of gene expression by AtATL78, possibly generated from defective AtATL81 expression, is described. AtATL78 expression was purportedly enhanced by insertion of a TATA box within the core promoter region after a short tandem duplication that occurred during evolution of Brassicaceae lineages. This gene is associated with an adaptation to drought tolerance of A. thaliana. These findings also suggest duplicated genes could serve as a reservoir of tacit genetic information, and expression of these duplicated genes is activated upon acquisition of core promoter sequences. Remarkably, drought transcriptome profiling in response to rehydration suggests that ATL78-dependent gene expression predominantly affects genes with root-specific activities.
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Affiliation(s)
- Estela Jiménez-Morales
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, 36824, México
| | - Victor Aguilar-Hernández
- CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
| | - Laura Aguilar-Henonin
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, 36824, México
| | - Plinio Guzmán
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, 36824, México
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145
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Guo J, Xu W, Hu Y, Huang J, Zhao Y, Zhang L, Huang CH, Ma H. Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations. MOLECULAR PLANT 2020; 13:1117-1133. [PMID: 32445889 DOI: 10.1016/j.molp.2020.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/03/2020] [Accepted: 05/18/2020] [Indexed: 05/04/2023]
Abstract
The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering plants. Most members of the Cucurbitaceae, a family containing ∼1000 species and many important crops, are climbers and have characteristic tendrils and pepo fruits. Here, we present 127 newly sequenced transcriptomes and genomes along with other datasets for a total of 136 cucurbits representing all tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major clades. We analyzed whole-genome duplication, diversification dynamics, and ancestral morphologies, and found that after early genome duplication event(s), a burst of diversification and morphological innovations in flower, fruit, and root characters occurred under the climate optimum in the Early Eocene. Species radiation during the Mid-Eocene Climatic Optimum also coincided with several morphological changes shared by 80% of cucurbits. We found that the cucurbit-specific tendril identity gene TEN originated from a paleo-polyploidization event at the origin of the family. Our results support the hypothesis that cucurbit diversifications were probably driven by increased genetic diversity following polyploidizations and by trait morphological innovations under paleo-climate upheavals. Our study provides a phylogenetic framework and new insights into morphological and genomic changes underlying the adaptive evolution of Cucurbitaceae.
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Affiliation(s)
- Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Weibin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA 16802, USA
| | - Jie Huang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yiyong Zhao
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Lin Zhang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Chien-Hsun Huang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China.
| | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA 16802, USA.
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146
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Feng C, Wang J, Wu L, Kong H, Yang L, Feng C, Wang K, Rausher M, Kang M. The genome of a cave plant, Primulina huaijiensis, provides insights into adaptation to limestone karst habitats. THE NEW PHYTOLOGIST 2020; 227:1249-1263. [PMID: 32274804 DOI: 10.1111/nph.16588] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/29/2020] [Indexed: 05/22/2023]
Abstract
Although whole genome duplication (WGD) has been suggested to facilitate adaptive evolution and diversification, the role of specific WGD events in promoting diversification and adaptation in angiosperms remains poorly understood. Primulina, a species-rich genus with > 180 species associated with limestone karst habitat, constitutes an ideal system for studying the impact of WGD events on speciation and evolutionary adaptation. We sequenced and assembled a chromosome-level genome of the cave-dwelling species P. huaijiensis to study gene family expansion and gene retention following WGDs. We provide evidence that P. huaijiensis has undergone two WGDs since the γ triplication event shared by all eudicots. In addition to a WGD shared by almost all Lamiales (L event), we identified a lineage-specific WGD (D event) that occurred in the early Miocene around 20.6-24.2 Myr ago and that is shared by almost the entire subtribe Didymocarpinae. We found that gene retentions following the D event led to gene family proliferation (e.g. WRKYs) that probably facilitated adaptation to the high salinity and drought stress in limestone karst. Our study highlights the role of lineage-specific WGD in species diversification and adaptation of plants from special habitats.
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Affiliation(s)
- Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lingqing Wu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Chen Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Mark Rausher
- Department of Biology, Duke University, 125 Science Drive, Durham, NC, 27705, USA
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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147
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Zhou S, Chen Y, Guo C, Qi J. PhyloMCL: Accurate clustering of hierarchical orthogroups guided by phylogenetic relationship and inference of polyploidy events. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shengyu Zhou
- State key Laboratory of Genetic Engineering Institute of Plant Biology School of Life Sciences Fudan University Shanghai China
| | - Yamao Chen
- State key Laboratory of Genetic Engineering Institute of Plant Biology School of Life Sciences Fudan University Shanghai China
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization Forestry College Jiangxi Agricultural University Nanchang China
| | - Ji Qi
- State key Laboratory of Genetic Engineering Institute of Plant Biology School of Life Sciences Fudan University Shanghai China
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148
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Nymphaea colorata (Blue-Petal Water Lily). Trends Genet 2020; 36:718-719. [PMID: 32631632 DOI: 10.1016/j.tig.2020.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/15/2020] [Indexed: 11/22/2022]
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149
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Lian S, Zhou Y, Liu Z, Gong A, Cheng L. The differential expression patterns of paralogs in response to stresses indicate expression and sequence divergences. BMC PLANT BIOLOGY 2020; 20:277. [PMID: 32546126 PMCID: PMC7298774 DOI: 10.1186/s12870-020-02460-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/24/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Theoretically, paralogous genes generated through whole genome duplications should share identical expression levels due to their identical sequences and chromatin environments. However, functional divergences and expression differences have arisen due to selective pressures throughout evolution. A comprehensive investigation of the expression patterns of paralogous gene pairs in response to various stresses and a study of correlations between the expression levels and sequence divergences of the paralogs are needed. RESULTS In this study, we analyzed the expression patterns of paralogous genes under different types of stress and investigated the correlations between the expression levels and sequence divergences of the paralogs. We analyzed the differential expression patterns of the paralogs under four different types of stress (drought, cold, infection, and herbivory) and classified them into three main types according to their expression patterns. We then further analyzed the differential expression patterns under various degrees of stress and constructed corresponding co-expression networks of differentially expressed paralogs and transcription factors. Finally, we investigated the correlations between the expression levels and sequence divergences of the paralogs and identified positive correlations between expression level and sequence divergence. With regard to sequence divergence, we identified correlations between selective pressures and phylogenetic relationships. CONCLUSIONS These results shed light on differential expression patterns of paralogs in response to environmental stresses and are helpful for understanding the relationships between expression levels and sequences divergences.
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Affiliation(s)
- Shuaibin Lian
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Yongjie Zhou
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Zixiao Liu
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Andong Gong
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Lin Cheng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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Wang Y, Nie F, Shahid MQ, Baloch FS. Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset. BMC PLANT BIOLOGY 2020; 20:250. [PMID: 32493212 PMCID: PMC7268529 DOI: 10.1186/s12870-020-02461-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/24/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species. RESULTS We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species. CONCLUSION Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
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Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, 556011 Guizhou Province China
| | - Fei Nie
- Biological institute of Guizhou Province, Guiyang City, 556000 Guizhou Province China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong Province China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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