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Han M, Qie Q, Liu M, Meng H, Wu T, Yang Y, Niu L, Sun G, Wang Y. Clonal growth characteristics and diversity patterns of different Clintonia udensis (Liliaceae) diploid and tetraploid cytotypes in the Hualongshan Mountains. Sci Rep 2024; 14:15509. [PMID: 38969683 DOI: 10.1038/s41598-024-66067-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Polyploidization plays an important role in plant evolution and biodiversity. However, intraspecific polyploidy compared to interspecific polyploidy received less attention. Clintonia udensis (Liliaceae) possess diploid (2n = 2x = 14) and autotetraploid (2n = 4x = 28) cytotypes. In the Hualongshan Mountains, the autotetraploids grew on the northern slope, while the diploids grew on the southern slopes. The clonal growth characteristics and clonal architecture were measured and analyzed by field observations and morphological methods. The diversity level and differentiation patterns for two different cytotypes were investigated using SSR markers. The results showed that the clonal growth parameters, such as the bud numbers of each rhizome node and the ratio of rhizome branches in the autotetraploids were higher than those in the diploids. Both the diploids and autotetraploids appeared phalanx clonal architectures with short internodes between ramets. However, the ramets or genets of the diploids had a relatively scattered distribution, while those of the autotetraploids were relatively clumping. The diploids and autotetraploids all allocated more biomass to their vegetative growth. The diploids had a higher allocation to reproductive organs than that of autotetraploids, which indicated that the tetraploids invested more resources in clonal reproduction than diploids. The clone diversity and genetic diversity of the autotetraploids were higher than that of the diploids. Significant genetic differentiation between two different cytotypes was observed (P < 0.01). During establishment and evolution, C. udensis autotetraploids employed more clumping phalanx clonal architecture and exhibited more genetic variation than the diploids.
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Affiliation(s)
- Mian Han
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Qiyang Qie
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Meilan Liu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Huiqin Meng
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Tiantian Wu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Yadi Yang
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Lingling Niu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Genlou Sun
- Department of Botany, Saint Mary's University, Halifax, NS B3H 3C3, Canada.
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China.
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2
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Galià-Camps C, Pegueroles C, Turon X, Carreras C, Pascual M. Genome composition and GC content influence loci distribution in reduced representation genomic studies. BMC Genomics 2024; 25:410. [PMID: 38664648 PMCID: PMC11046876 DOI: 10.1186/s12864-024-10312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge variability of genomic features. However, their variability and the extent to which genomic content determines the distribution of recovered loci in reduced representation sequencing studies is largely unexplored. RESULTS Here, by using 80 genome assemblies, we observed that whereas plants primarily increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. Loci mapping in introns, exons, and intergenic categories obtained by in silico digestion using 2b-enzymes are positively correlated with the percentage of these regions in the corresponding genomes, suggesting that loci distribution mostly mirrors genomic architecture of the selected taxon. However, exonic regions showed a significant enrichment of loci in all groups regardless of the used enzyme. Moreover, when using selective adaptors to obtain a secondarily reduced loci dataset, the percentage and distribution of retained loci also varied. Adaptors with G/C terminals recovered a lower percentage of selected loci, with a further enrichment of exonic regions, while adaptors with A/T terminals retained a higher percentage of loci and slightly selected more intronic regions than expected. CONCLUSIONS Our results highlight how genome composition, genome GC content, RAD enzyme choice and use of base-selective adaptors influence reduced genome representation techniques. This is important to acknowledge in population and conservation genomic studies, as it determines the abundance and distribution of loci.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain.
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, Blanes, 17300, Spain.
| | - Cinta Pegueroles
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, Blanes, 17300, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
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3
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Blume RY, Kalendar R, Guo L, Cahoon EB, Blume YB. Overcoming genetic paucity of Camelina sativa: possibilities for interspecific hybridization conditioned by the genus evolution pathway. FRONTIERS IN PLANT SCIENCE 2023; 14:1259431. [PMID: 37818316 PMCID: PMC10561096 DOI: 10.3389/fpls.2023.1259431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023]
Abstract
Camelina or false flax (Camelina sativa) is an emerging oilseed crop and a feedstock for biofuel production. This species is believed to originate from Western Asian and Eastern European regions, where the center of diversity of the Camelina genus is located. Cultivated Camelina species arose via a series of polyploidization events, serving as bottlenecks narrowing genetic diversity of the species. The genetic paucity of C. sativa is foreseen as the most crucial limitation for successful breeding and improvement of this crop. A potential solution to this challenge could be gene introgression from Camelina wild species or from resynthesized allohexaploid C. sativa. However, both approaches would require a complete comprehension of the evolutionary trajectories that led to the C. sativa origin. Although there are some studies discussing the origin and evolution of Camelina hexaploid species, final conclusions have not been made yet. Here, we propose the most complete integrated evolutionary model for the Camelina genus based on the most recently described findings, which enables efficient improvement of C. sativa via the interspecific hybridization with its wild relatives. We also discuss issues of interspecific and intergeneric hybridization, aimed on improving C. sativa and overcoming the genetic paucity of this crop. The proposed comprehensive evolutionary model of Camelina species indicates that a newly described species Camelina neglecta has a key role in origin of tetra- and hexaploids, all of which have two C. neglecta-based subgenomes. Understanding of species evolution within the Camelina genus provides insights into further research on C. sativa improvements via gene introgression from wild species, and a potential resynthesis of this emerging oilseed crop.
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Affiliation(s)
- Rostyslav Y. Blume
- Institute of Food Biotechnology and Genomics of National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Ruslan Kalendar
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Edgar B. Cahoon
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Yaroslav B. Blume
- Institute of Food Biotechnology and Genomics of National Academy of Science of Ukraine, Kyiv, Ukraine
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4
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Kong X, Zhang Y, Wang Z, Bao S, Feng Y, Wang J, Yu Z, Long F, Xiao Z, Hao Y, Gao X, Li Y, Ding Y, Wang J, Lei T, Xu C, Wang J. Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae. HORTICULTURE RESEARCH 2023; 10:uhad073. [PMID: 37303613 PMCID: PMC10251138 DOI: 10.1093/hr/uhad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/10/2023] [Indexed: 06/13/2023]
Abstract
An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.
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Affiliation(s)
| | | | | | | | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Feng Long
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zejia Xiao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yinfeng Li
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
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5
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Wang J, Yuan M, Feng Y, Zhang Y, Bao S, Hao Y, Ding Y, Gao X, Yu Z, Xu Q, Zhao J, Zhu Q, Wang P, Wu C, Wang J, Li Y, Xu C, Wang J. A common whole-genome paleotetraploidization in Cucurbitales. PLANT PHYSIOLOGY 2022; 190:2430-2448. [PMID: 36053177 PMCID: PMC9706448 DOI: 10.1093/plphys/kiac410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Cucurbitales are an important order of flowering plants known for encompassing edible plants of economic and medicinal value and numerous ornamental plants of horticultural value. By reanalyzing the genomes of two representative families (Cucurbitaceae and Begoniaceae) in Cucurbitales, we found that the previously identified Cucurbitaceae common paleotetraploidization that occurred shortly after the core-eudicot-common hexaploidization event is shared by Cucurbitales, including Begoniaceae. We built a multigenome alignment framework for Cucurbitales by identifying orthologs and paralogs and systematically redating key evolutionary events in Cucurbitales. Notably, characterizing the gene retention levels and genomic fractionation patterns between subgenomes generated from different polyploidizations in Cucurbitales suggested the autopolyploid nature of the Begoniaceae common tetraploidization and the allopolyploid nature of the Cucurbitales common tetraploidization and the Cucurbita-specific tetraploidization. Moreover, we constructed the ancestral Cucurbitales karyotype comprising 17 proto-chromosomes, confirming that the most recent common ancestor of Cucurbitaceae contained 15 proto-chromosomes and rejecting the previous hypothesis for an ancestral Cucurbitaceae karyotype with 12 proto-chromosomes. In addition, we found that the polyploidization and tandem duplication events promoted the expansion of gene families involved in the cucurbitacin biosynthesis pathway; however, gene loss and chromosomal rearrangements likely limited the expansion of these gene families.
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Affiliation(s)
- Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Min Yuan
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yan Zhang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Shoutong Bao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qiang Xu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Junxin Zhao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qianwen Zhu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Ping Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Chunyang Wu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
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6
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Islam MM, Deepo DM, Nasif SO, Siddique AB, Hassan O, Siddique AB, Paul NC. Cytogenetics and Consequences of Polyploidization on Different Biotic-Abiotic Stress Tolerance and the Potential Mechanisms Involved. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202684. [PMID: 36297708 PMCID: PMC9609754 DOI: 10.3390/plants11202684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 06/12/2023]
Abstract
The application of polyploidy in sustainable agriculture has already brought much appreciation among researchers. Polyploidy may occur naturally or can be induced in the laboratory using chemical or gaseous agents and results in complete chromosome nondisjunction. This comprehensive review described the potential of polyploidization on plants, especially its role in crop improvement for enhanced production and host-plant resistance development against pests and diseases. An in-depth investigation on techniques used in the induction of polyploidy, cytogenetic evaluation methods of different ploidy levels, application, and current research trends is also presented. Ongoing research has mainly aimed to bring the recurrence in polyploidy, which is usually detected by flow cytometry, chromosome counting, and cytogenetic techniques such as fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). Polyploidy can bring about positive consequences in the growth and yield attributes of crops, making them more tolerant to abiotic and biotic stresses. However, the unexpected change in chromosome set and lack of knowledge on the mechanism of stress alleviation is hindering the application of polyploidy on a large scale. Moreover, a lack of cost-benefit analysis and knowledge gaps on the socio-economic implication are predominant. Further research on polyploidy coupling with modern genomic technologies will help to bring real-world market prospects in the era of changing climate. This review on polyploidy provides a solid foundation to do next-generation research on crop improvement.
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Affiliation(s)
- Md Mazharul Islam
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
- Research and Development, Horticultural Crop Breeding, Quality Feeds Limited, Dhaka 1230, Bangladesh
| | - Deen Mohammad Deepo
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Saifullah Omar Nasif
- Global Centre for Environmental Remediation (GCER), College of Engineering Science and Environment, The University of Newcastle, Newcastle, NSW 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building, The University of Newcastle, Newcastle, NSW 2308, Australia
| | - Abu Bakar Siddique
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Oliul Hassan
- Department of Ecology and Environmental System, College of Ecology and Environmental Sciences, Kyungpook National University, Sangju 37224, Korea
| | - Abu Bakar Siddique
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Narayan Chandra Paul
- Kumho Life Science Laboratory, Department of Integrative Food Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea
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7
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Zhang Y, Zhang L, Xiao Q, Wu C, Zhang J, Xu Q, Yu Z, Bao S, Wang J, Li Y, Wang L, Wang J. Two independent allohexaploidizations and genomic fractionation in Solanales. FRONTIERS IN PLANT SCIENCE 2022; 13:1001402. [PMID: 36212355 PMCID: PMC9538396 DOI: 10.3389/fpls.2022.1001402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Solanales, an order of flowering plants, contains the most economically important vegetables among all plant orders. To date, many Solanales genomes have been sequenced. However, the evolutionary processes of polyploidization events in Solanales and the impact of polyploidy on species diversity remain poorly understood. We compared two representative Solanales genomes (Solanum lycopersicum L. and Ipomoea triloba L.) and the Vitis vinifera L. genome and confirmed two independent polyploidization events. Solanaceae common hexaploidization (SCH) and Convolvulaceae common hexaploidization (CCH) occurred ∼43-49 and ∼40-46 million years ago (Mya), respectively. Moreover, we identified homologous genes related to polyploidization and speciation and constructed multiple genomic alignments with V. vinifera genome, providing a genomic homology framework for future Solanales research. Notably, the three polyploidization-produced subgenomes in both S. lycopersicum and I. triloba showed significant genomic fractionation bias, suggesting the allohexaploid nature of the SCH and CCH events. However, we found that the higher genomic fractionation bias of polyploidization-produced subgenomes in Solanaceae was likely responsible for their more abundant species diversity than that in Convolvulaceae. Furthermore, through genomic fractionation and chromosomal structural variation comparisons, we revealed the allohexaploid natures of SCH and CCH, both of which were formed by two-step duplications. In addition, we found that the second step of two paleohexaploidization events promoted the expansion and diversity of β-amylase (BMY) genes in Solanales. These current efforts provide a solid foundation for future genomic and functional exploration of Solanales.
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Affiliation(s)
- Yan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Lan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qimeng Xiao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Chunyang Wu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jiaqi Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qiang Xu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Zijian Yu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Shoutong Bao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jianyu Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yu Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Li Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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8
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Grover CE, Forsythe ES, Sharbrough J, Miller ER, Conover JL, DeTar RA, Chavarro C, Arick MA, Peterson DG, Leal-Bertioli SCM, Sloan DB, Wendel JF. Variation in cytonuclear expression accommodation among allopolyploid plants. Genetics 2022; 222:6661348. [PMID: 35951749 PMCID: PMC9526054 DOI: 10.1093/genetics/iyac118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution. The hybrid nature of allopolyploids may result in cytonuclear incompatibilities, but the massive nuclear redundancy created during polyploidy affords additional avenues for resolving cytonuclear conflict (i.e., cytonuclear accommodation). Here we evaluate expression changes in organelle-targeted nuclear genes for six allopolyploid lineages that represent four genera (i.e., Arabidopsis, Arachis, Chenopodium, and Gossypium) and encompass a range in polyploid ages. Because incompatibilities between the nucleus and cytoplasm could potentially result in biases toward the maternal homoeolog and/or maternal expression level, we evaluate patterns of homoeolog usage, expression bias, and expression-level dominance in cytonuclear genes relative to the background of non-cytonuclear expression changes and to the diploid parents. Although we find subsets of cytonuclear genes in most lineages that match our expectations of maternal preference, these observations are not consistent among either allopolyploids or categories of organelle-targeted genes. Our results indicate that cytonuclear expression evolution may be subtle and variable among genera and genes, likely reflecting a diversity of mechanisms to resolve nuclear-cytoplasmic incompatibilities in allopolyploid species.
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Affiliation(s)
- Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Dept., Iowa State University, Ames, IA 50010, USA
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Joel Sharbrough
- Biology Dept., New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA
| | - Emma R Miller
- Ecology, Evolution, and Organismal Biology Dept., Iowa State University, Ames, IA 50010, USA
| | - Justin L Conover
- Ecology, Evolution, and Organismal Biology Dept., Iowa State University, Ames, IA 50010, USA
| | - Rachael A DeTar
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Carolina Chavarro
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Soraya C M Leal-Bertioli
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA.,Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jonathan F Wendel
- Ecology, Evolution, and Organismal Biology Dept., Iowa State University, Ames, IA 50010, USA
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9
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Dogan M, Mandáková T, Guo X, Lysak MA. Idahoa and Subularia: Hidden polyploid origins of two enigmatic genera of crucifers. AMERICAN JOURNAL OF BOTANY 2022; 109:1273-1289. [PMID: 35912547 DOI: 10.1002/ajb2.16042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The monotypic Idahoa (I. scapigera) and the bispecific Subularia (S. aquatica and S. monticola) belong to Brassicaceae with unclear phylogenetic relationships and no tribal assignment. To fill this knowledge gap, we investigated these species and their closest relatives by combining cytogenomic and phylogenomic methods. METHODS We used whole plastome sequences in maximum likelihood and Bayesian inference analyses. We tested the phylogenetic informativeness of shared genomic repeats. We combined nuclear gene tree reconciliation and comparative chromosome painting (CCP) to examine the occurrence of past whole-genome duplications (WGDs). RESULTS The plastid data set corroborated the sister relationship between Idahoa and Subularia within the crucifer Lineage V but failed to resolve consistent topologies using both inference methods. The shared repetitive sequences provided conflicting pwhylogenetic signals. CCP analysis unexpectedly revealed that Idahoa (2n = 16) has a diploidized mesotetraploid genome, whereas two Subularia species (2n = 28 and 30) have diploidized mesoctoploid genomes. Several ancient allopolyploidy events have also been detected in closely related taxa (Chamira circaeoides, Cremolobeae, Eudemeae, and Notothlaspideae). CONCLUSIONS Our results suggest that the contentious phylogenetic placement of Idahoa and Subularia is best explained by two WGDs involving one or more shared parental genomes. The newly identified mesopolyploid genomes highlight the challenges of studying plant clades with complex polyploidy histories and provide a better framework for understanding genome evolution in the crucifer family.
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Affiliation(s)
- Mert Dogan
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Xinyi Guo
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
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10
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Zhang T, Qiao Q, Du X, Zhang X, Hou Y, Wei X, Sun C, Zhang R, Yun Q, Crabbe MJC, Van de Peer Y, Dong W. Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1487-1501. [PMID: 35748532 DOI: 10.1111/jipb.13318] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome-level genome sequence of the hawthorn cultivar "Qiu Jinxing." We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo-chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected in hawthorn. The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high-quality reference genome provides a useful resource for the horticultural improvement of hawthorn.
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Affiliation(s)
- Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, 650091, China
| | - Xiao Du
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Guangxi, Nanning, 530001, China
| | - Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yali Hou
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Wei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Chao Sun
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Rengang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Quanzheng Yun
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, UK
- Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, University of Bedfordshire, Park Square, Luton, UK
- School of Life Sciences, Shanxi University, Taiyuan, 030006, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Center for Plant Systems Biology, Ghent University, VIB, 9052, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
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11
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Wang J, Zhang L, Wang J, Hao Y, Xiao Q, Teng J, Shen S, Zhang Y, Feng Y, Bao S, Li Y, Yan Z, Wei C, Wang L, Wang J. Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow. BMC PLANT BIOLOGY 2022; 22:298. [PMID: 35710333 PMCID: PMC9205023 DOI: 10.1186/s12870-022-03684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remains poorly understood. RESULTS Here, through genomic synteny analyses, we identified duplicate genes generated by the Salicaceae common tetraploidization (SCT) in the poplar and willow genomes. We estimated that at least 0.58% and 0.25% of poplar and willow duplicates were affected by whole-gene conversion after the poplar-willow divergence, with more (5.73% and 2.66%) affected by partial-gene conversion. Moreover, we found that the converted duplicated genes were unevenly distributed on each chromosome in the two genomes, and the well-preserved homoeologous chromosome regions may facilitate the conversion of duplicates. Notably, we found that conversion maintained the similarity of duplicates, likely contributing to the conservation of certain sequences, but is essentially accelerated the rate of evolution and increased species divergence. In addition, we found that converted duplicates tended to have more similar expression patterns than nonconverted duplicates. We found that genes associated with multigene families were preferentially converted. We also found that the genes encoding conserved structural domains associated with specific traits exhibited a high frequency of conversion. CONCLUSIONS Extensive conversion between duplicate genes generated from the SCT contributes to the diversification of the family Salicaceae and has had long-lasting effects on those genes with important biological functions.
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Affiliation(s)
- Jianyu Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Lan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jiaqi Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yanan Hao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Qimeng Xiao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jia Teng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shaoqi Shen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yishan Feng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shoutong Bao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yu Li
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Zimo Yan
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Chendan Wei
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Li Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
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12
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Teng J, Wang J, Zhang L, Wei C, Shen S, Xiao Q, Yue Y, Hao Y, Ge W, Wang J. Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades. FRONTIERS IN PLANT SCIENCE 2022; 13:883140. [PMID: 35712579 PMCID: PMC9194900 DOI: 10.3389/fpls.2022.883140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Eudicots account for ~75% of living angiosperms, containing important food and energy crops. Recently, high-quality genome sequences of several eudicots including Aquilegia coerulea and Nelumbo nucifera have become available, providing an opportunity to investigate the early evolutionary characteristics of eudicots. We performed genomic hierarchical and event-related alignments to infer homology within and between representative species of eudicots. The results provide strong evidence for multiple independent polyploidization events during the early diversification of eudicots, three of which are likely to be allopolyploids: The core eudicot-common hexaploidy (ECH), Nelumbo-specific tetraploidy (NST), and Ranunculales-common tetraploidy (RCT). Using different genomes as references, we constructed genomic alignment to list the orthologous and paralogous genes produced by polyploidization and speciation. This could provide a fundamental framework for studying other eudicot genomes and gene(s) evolution. Further, we revealed significantly divergent evolutionary rates among these species. By performing evolutionary rate correction, we dated RCT to be ~118-134 million years ago (Mya), after Ranunculales diverged with core eudicots at ~123-139 Mya. Moreover, we characterized genomic fractionation resulting from gene loss and retention after polyploidizations. Notably, we revealed a high degree of divergence between subgenomes. In particular, synonymous nucleotide substitutions at synonymous sites (Ks) and phylogenomic analyses implied that A. coerulea might provide the subgenome(s) for the gamma-hexaploid hybridization.
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Affiliation(s)
- Jia Teng
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Lan Zhang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Shaoqi Shen
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Qimeng Xiao
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuanshuai Yue
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Weina Ge
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinpeng Wang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China
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13
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Fang Y, Jiang J, Hou X, Guo J, Li X, Zhao D, Xie X. Plant protein-coding gene families: Their origin and evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:995746. [PMID: 36160967 PMCID: PMC9490259 DOI: 10.3389/fpls.2022.995746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/15/2022] [Indexed: 05/13/2023]
Abstract
Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Jiyuan Guo
- Department of Resources and Environment, Moutai Institute, Zunyi, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Degang Zhao
- Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Ministry of Education, College of Life Sciences, Institute of Agricultural Bioengineering, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- *Correspondence: Degang Zhao,
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- Xin Xie,
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14
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Reis AC, Chester M, de Sousa SM, Campos VR, de Queiroz Nascimento LS, Pacheco Júnior S, Franco AL, Viccini LF. Chromosomal view of Lippia alba, a tropical polyploid complex under genome stabilization process. PROTOPLASMA 2022; 259:33-46. [PMID: 33760982 DOI: 10.1007/s00709-021-01636-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Lippia alba is a phenotypically variable tropical shrub thought to comprise a young autopolyploid complex. Chromosome numbers in L. alba include 2n = 30, 38, 45, 60, and 90. High levels of chemical and phenotypic variation associated with economic and medicinal importance were reported. However, the genetic background including chromosome composition remains under-explored. Furthermore, the occurrence of at least four ploidal levels in L. alba and the lack of data for polyploid plants in tropical areas also merit further study of L. alba. Here we assessed the chromosome composition using two new satellite repeats (CL98 and CL66) applied as FISH probes to mitotic chromosomes, and we proposed to calculate the degree of homozygosis for CL66 satDNA (named as index h) and to associate it to meiotic instability. The CL98 mapping showed few variations in both number of signals and position. However, the levels of structural homozygosity for a satellite repeat CL66 were very variable. The numbers of CL66-bearing-chromosomes were under-represented in tetraploids relative to diploids implying that CL66 arrays have been lost in tetraploid lineages as a result of increased meiotic instability. High percentage of irregularities was observed in meiotic cells, especially in polyploids. L. alba complex comprised a mixture of homomorphic and heteromorphic chromosomes. Overall, the polyploid complex presents features typical of both young and older stable polyploids. It seems that L. alba genome is still in the process of stabilization.
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Affiliation(s)
- Aryane Campos Reis
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | | | - Saulo Marçal de Sousa
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | - Victória Rabelo Campos
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | | | | | - Ana Luiza Franco
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | - Lyderson Facio Viccini
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil.
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15
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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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16
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Singh S, Singh A. A prescient evolutionary model for genesis, duplication and differentiation of MIR160 homologs in Brassicaceae. Mol Genet Genomics 2021; 296:985-1003. [PMID: 34052911 DOI: 10.1007/s00438-021-01797-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/21/2021] [Indexed: 12/18/2022]
Abstract
MicroRNA160 is a class of nitrogen-starvation responsive genes which governs establishment of root system architecture by down-regulating AUXIN RESPONSE FACTOR genes (ARF10, ARF16 and ARF17) in plants. The high copy number of MIR160 variants discovered by us from land plants, especially polyploid crop Brassicas, posed questions regarding genesis, duplication, evolution and function. Absence of studies on impact of whole genome and segmental duplication on retention and evolution of MIR160 homologs in descendent plant lineages prompted us to undertake the current study. Herein, we describe ancestry and fate of MIR160 homologs in Brassicaceae in context of polyploidy driven genome re-organization, copy number and differentiation. Paralogy amongst Brassicaceae MIR160a, MIR160b and MIR160c was inferred using phylogenetic analysis of 468 MIR160 homologs from land plants. The evolutionarily distinct MIR160a was found to represent ancestral form and progenitor of MIR160b and MIR160c. Chronology of evolutionary events resulting in origin and diversification of genomic loci containing MIR160 homologs was delineated using derivatives of comparative synteny. A prescient model for causality of segmental duplications in establishment of paralogy in Brassicaceae MIR160, with whole genome duplication accentuating the copy number increase, is being posited in which post-segmental duplication events viz. differential gene fractionation, gene duplications and inversions are shown to drive divergence of chromosome segments. While mutations caused the diversification of MIR160a, MIR160b and MIR160c, duplicated segments containing these diversified genes suffered gene rearrangements via gene loss, duplications and inversions. Yet the topology of phylogenetic and phenetic trees were found congruent suggesting similar evolutionary trajectory. Over 80% of Brassicaceae genomes and subgenomes showed a preferential retention of single copy each of MIR160a, MIR160b and MIR160c suggesting functional relevance. Thus, our study provides a blue-print for reconstructing ancestry and phylogeny of MIRNA gene families at genomics level and analyzing the impact of polyploidy on organismal complexity. Such studies are critical for understanding the molecular basis of agronomic traits and deploying appropriate candidates for crop improvement.
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Affiliation(s)
- Swati Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, 110070, India.,Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Plot no. 32-34, Knowledge Park III, Greater Noida, Uttar Pradesh, 201310, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, 110070, India.
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17
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Mahelka V, Krak K, Fehrer J, Caklová P, Nagy Nejedlá M, Čegan R, Kopecký D, Šafář J. A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1141-1164. [PMID: 33484020 DOI: 10.1111/tpj.15167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Intra-specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeum bogdanii and 219 kb in the South American Hordeum pubiflorum, resides on a pair of nucleolar organizer region (NOR)-bearing chromosomes. Conserved synteny and micro-collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5-1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress-related protein-coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein-coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non-synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein-coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species.
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Affiliation(s)
- Václav Mahelka
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Karol Krak
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6, 16500, Czech Republic
| | - Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Petra Caklová
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | | | - Radim Čegan
- Institute of Biophysics, Czech Academy of Sciences, Brno, 61265, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
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Didelon M, Khafif M, Godiard L, Barbacci A, Raffaele S. Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens. Front Genet 2020; 11:491. [PMID: 32547597 PMCID: PMC7272662 DOI: 10.3389/fgene.2020.00491] [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: 01/15/2020] [Accepted: 04/20/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogen infection triggers extensive reprogramming of the plant transcriptome, including numerous genes the function of which is unknown. Due to their wide taxonomic distribution, genes encoding proteins with Domains of Unknown Function (DUFs) activated upon pathogen challenge likely play important roles in disease. In Arabidopsis thaliana, we identified thirteen genes harboring a DUF4228 domain in the top 10% most induced genes after infection by the fungal pathogen Sclerotinia sclerotiorum. Based on functional information collected through homology and contextual searches, we propose to refer to this domain as the pathogen and abiotic stress response, cadmium tolerance, disordered region-containing (PADRE) domain. Genome-wide and phylogenetic analyses indicated that PADRE is specific to plants and diversified into 10 subfamilies early in the evolution of Angiosperms. PADRE typically occurs in small single-domain proteins with a bipartite architecture. PADRE N-terminus harbors conserved sequence motifs, while its C-terminus includes an intrinsically disordered region with multiple phosphorylation sites. A pangenomic survey of PADRE genes expression upon S. sclerotiorum inoculation in Arabidopsis, castor bean, and tomato indicated consistent expression across species within phylogenetic groups. Multi-stress expression profiling and co-expression network analyses associated AtPADRE genes with the induction of anthocyanin biosynthesis and responses to chitin and to hypoxia. Our analyses reveal patterns of sequence and expression diversification consistent with the evolution of a role in disease resistance for an uncharacterized family of plant genes. These findings highlight PADRE genes as prime candidates for the functional dissection of mechanisms underlying plant disease resistance to fungi.
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Affiliation(s)
| | | | | | | | - Sylvain Raffaele
- Université de Toulouse, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) – Centre National de la Recherche Scientifique (CNRS), Castanet-Tolosan, France
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