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Xu H, Guo Y, Xia M, Yu J, Chi X, Han Y, Li X, Zhang F. An updated phylogeny and adaptive evolution within Amaranthaceae s.l. inferred from multiple phylogenomic datasets. Ecol Evol 2024; 14:e70013. [PMID: 39011133 PMCID: PMC11246835 DOI: 10.1002/ece3.70013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 06/17/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
Amaranthaceae s.l. is a widely distributed family consisting of over 170 genera and 2000 species. Previous molecular phylogenetic studies have shown that Amaranthaceae s.s. and traditional Chenopodiaceae form a monophyletic group (Amaranthaceae s.l.), however, the relationships within this evolutionary branch have yet to be fully resolved. In this study, we assembled the complete plastomes and full-length ITS of 21 Amaranthaceae s.l. individuals and compared them with 38 species of Amaranthaceae s.l. Through plastome structure and sequence alignment analysis, we identified a reverse complementary region approximately 5200 bp long in the genera Atriplex and Chenopodium. Adaptive evolution analysis revealed significant positive selection in eight genes, which likely played a driving role in the evolution of Amaranthaceae s.l., as demonstrated by partitioned evolutionary analysis. Furthermore, we found that about two-thirds of the examined species lack the ycf15 gene, potentially associated with natural selection pressures from their adapted habitats. The phylogenetic tree indicated that some genera (Chenopodium, Halogeton, and Subtr. Salsolinae) are paraphyletic lineages. Our results strongly support the clustering of Amaranthaceae s.l. with monophyletic traditional Chenopodiaceae (Clades I and II) and Amaranthaceae s.s. After a comprehensive analysis, we determined that cytonuclear conflict, gene selection by adapted habitats, and incomplete lineage sorting (ILS) events were the primary reasons for the inconsistent phylogeny of Amaranthaceae s.l. During the last glacial period, certain species within Amaranthaceae s.l. underwent adaptations to different environments and began to differentiate rapidly. Since then, these species may have experienced morphological and genetic changes distinct from those of other genera due to intense selection pressure.
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Affiliation(s)
- Hao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuqin Guo
- Qinghai National Park Research Monitoring and Evaluation CenterXiningChina
| | - Mingze Xia
- School of PharmacyWeifang Medical UniversityWeifangChina
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaofeng Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Yun Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoping Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
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Li W, Dong X, Zhang X, Cao J, Liu M, Zhou X, Long H, Cao H, Lin H, Zhang L. Genome assembly and resequencing shed light on evolution, population selection, and sex identification in Vernicia montana. HORTICULTURE RESEARCH 2024; 11:uhae141. [PMID: 38988615 PMCID: PMC11233859 DOI: 10.1093/hr/uhae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024]
Abstract
Vernicia montana is a dioecious plant widely cultivated for high-quality tung oil production and ornamental purposes in the Euphorbiaceae family. The lack of genomic information has severely hindered molecular breeding for genetic improvement and early sex identification in V. montana. Here, we present a chromosome-level reference genome of a male V. montana with a total size of 1.29 Gb and a contig N50 of 3.69 Mb. Genome analysis revealed that different repeat lineages drove the expansion of genome size. The model of chromosome evolution in the Euphorbiaceae family suggests that polyploidization-induced genomic structural variation reshaped the chromosome structure, giving rise to the diverse modern chromosomes. Based on whole-genome resequencing data and analyses of selective sweep and genetic diversity, several genes associated with stress resistance and flavonoid synthesis such as CYP450 genes and members of the LRR-RLK family, were identified and presumed to have been selected during the evolutionary process. Genome-wide association studies were conducted and a putative sex-linked insertion and deletion (InDel) (Chr 2: 102 799 917-102 799 933 bp) was identified and developed as a polymorphic molecular marker capable of effectively detecting the gender of V. montana. This InDel is located in the second intron of VmBASS4, suggesting a possible role of VmBASS4 in sex determination in V. montana. This study sheds light on the genome evolution and sex identification of V. montana, which will facilitate research on the development of agronomically important traits and genomics-assisted breeding.
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Affiliation(s)
- Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
- College of Biology and Agricultural Resources, Huanggang Normal University, No.146 Xingang 2nd Road, Huangzhou District, Huanggang, Hubei 438000, China
| | - Xiang Dong
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No.7 Pengfei Road, Dapeng New District, Shenzhen 518120, China
| | - Jie Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Xu Zhou
- College of Landscape Architecture, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Hongxu Long
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Heping Cao
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, 1100 Allen Toussaint Blvd, New Orleans, LA 70124-4305, USA
| | - Hai Lin
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
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Morey K, Khakhar A. Exploring the frontier of rapid prototyping technologies for plant synthetic biology and what could lie beyond. THE NEW PHYTOLOGIST 2024; 242:903-908. [PMID: 38426415 DOI: 10.1111/nph.19650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
Realizing the full potential of plant synthetic biology both to elucidate the relationship between genotype and phenotype and to apply these insights to engineer traits requires rapidly iterating through design-build-test cycles. However, the months-long process of transgenesis, the long generation times, and the size-based limitations on experimentation have stymied progress by limiting the speed and scale of these cycles. Herein, we review a representative sample of recent studies that demonstrate a variety of rapid prototyping technologies that overcome some of these bottlenecks and accelerate progress. However, each of them has caveats that limit their broad utility. Their complementary strengths and weaknesses point to the intriguing possibility that these strategies could be combined in the future to enable rapid and scalable deployment of synthetic biology in plants.
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Affiliation(s)
- Kevin Morey
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80525, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80525, USA
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Yan M, Li M, Wang Y, Wang X, Moeinzadeh MH, Quispe-Huamanquispe DG, Fan W, Fang Y, Wang Y, Nie H, Wang Z, Tanaka A, Heider B, Kreuze JF, Gheysen G, Wang H, Vingron M, Bock R, Yang J. Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato. MOLECULAR PLANT 2024; 17:277-296. [PMID: 38155570 DOI: 10.1016/j.molp.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/10/2023] [Accepted: 12/25/2023] [Indexed: 12/30/2023]
Abstract
The hexaploid sweetpotato (Ipomoea batatas) is one of the most important root crops worldwide. However, its genetic origin remains controversial, and its domestication history remains unknown. In this study, we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato. The diploid progenitor was likely closely related to Ipomoea aequatoriensis and contributed the B1 subgenome, IbT-DNA2, and the lineage 1 type of chloroplast genome to sweetpotato. The tetraploid progenitor of sweetpotato was most likely I. batatas 4x, which donated the B2 subgenome, IbT-DNA1, and the lineage 2 type of chloroplast genome. Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors, followed by a subsequent whole-genome duplication. In addition, we detected biased gene exchanges between the subgenomes; the rate of B1 to B2 subgenome conversions was nearly three times higher than that of B2 to B1 subgenome conversions. Our analyses revealed that genes involved in storage root formation, maintenance of genome stability, biotic resistance, sugar transport, and potassium uptake were selected during the speciation and domestication of sweetpotato. This study sheds light on the evolution of sweetpotato and paves the way for improvement of this crop.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Ming Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Yunze Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xinyi Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - M-Hossein Moeinzadeh
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | | | - Weijuan Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yijie Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yuqin Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Haozhen Nie
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Zhangying Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | | | | | | | - Hongxia Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae). Ecol Evol 2024; 14:e10868. [PMID: 38274863 PMCID: PMC10809029 DOI: 10.1002/ece3.10868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
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Li Y, Li X, Nie S, Zhang M, Yang Q, Xu W, Duan Y, Wang X. Reticulate evolution of the tertiary relict Osmanthus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:145-160. [PMID: 37837261 DOI: 10.1111/tpj.16480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
When interspecific gene flow is common, species relationships are more accurately represented by a phylogenetic network than by a bifurcating tree. This study aimed to uncover the role of introgression in the evolution of Osmanthus, the only genus of the subtribe Oleinae (Oleaceae) with its distribution center in East Asia. We built species trees, detected introgression, and constructed networks using multiple kinds of sequencing data (whole genome resequencing, transcriptome sequencing, and Sanger sequencing of nrDNA) combined with concatenation and coalescence approaches. Then, based on well-understood species relationships, historical biogeographic analyses and diversification rate estimates were employed to reveal the history of Osmanthus. Osmanthus originated in mid-Miocene Europe and dispersed to the eastern Tibetan Plateau in the late Miocene. Thereafter, it continued to spread eastwards. Phylogenetic conflict is common within the 'Core Osmanthus' clade and is seen at both early and late stages of diversification, leading to hypotheses of net-like species relationships. Incomplete lineage sorting proved ineffective in explaining phylogenetic conflicts and thus supported introgression as the main cause of conflicts. This study elucidates the diversification history of a relict genus in the subtropical regions of eastern Asia and reveals that introgression had profound effects on its evolutionary history.
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Affiliation(s)
- Yongfu Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xuan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Qinghua Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Wenbin Xu
- Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yifan Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xianrong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Feng M, Augstein F, Kareem A, Melnyk CW. Plant grafting: Molecular mechanisms and applications. MOLECULAR PLANT 2024; 17:75-91. [PMID: 38102831 DOI: 10.1016/j.molp.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
People have grafted plants since antiquity for propagation, to increase yields, and to improve stress tolerance. This cutting and joining of tissues activates an incredible regenerative ability as different plants fuse and grow as one. For over a hundred years, people have studied the scientific basis for how plants graft. Today, new techniques and a deepening knowledge of the molecular basis for graft formation have allowed a range of previously ungraftable combinations to emerge. Here, we review recent developments in our understanding of graft formation, including the attachment and vascular formation steps. We analyze why plants graft and how biotic and abiotic factors influence successful grafting. We also discuss the ability and inability of plants to graft, and how grafting has transformed both horticulture and fundamental plant science. As our knowledge about plant grafting improves, new combinations and techniques will emerge to allow an expanded use of grafting for horticultural applications and to address fundamental research questions.
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Affiliation(s)
- Ming Feng
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Frauke Augstein
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Abdul Kareem
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Charles W Melnyk
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden.
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Krawczyk K, Paukszto Ł, Maździarz M, Sawicki J. The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1275377. [PMID: 38143577 PMCID: PMC10739336 DOI: 10.3389/fpls.2023.1275377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023]
Abstract
Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Park S, Park S. Intrageneric structural variation in organelle genomes from the genus Dystaenia (Apiaceae): genome rearrangement and mitochondrion-to-plastid DNA transfer. FRONTIERS IN PLANT SCIENCE 2023; 14:1283292. [PMID: 38116150 PMCID: PMC10728875 DOI: 10.3389/fpls.2023.1283292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
Introduction During plant evolution, intracellular DNA transfer (IDT) occurs not only from organelles to the nucleus but also between organelles. To further comprehend these events, both organelle genomes and transcriptomes are needed. Methods In this study, we constructed organelle genomes and transcriptomes for two Dystaenia species and described their dynamic IDTs between their nuclear and mitochondrial genomes, or plastid and mitochondrial genomes (plastome and mitogenome). Results and Discussion We identified the putative functional transfers of the mitochondrial genes 5' rpl2, rps10, rps14, rps19, and sdh3 to the nucleus in both Dystaenia species and detected two transcripts for the rpl2 and sdh3 genes. Additional transcriptomes from the Apicaceae species also provided evidence for the transfers and duplications of these mitochondrial genes, showing lineage-specific patterns. Intrageneric variations of the IDT were found between the Dystaenia organelle genomes. Recurrent plastid-to-mitochondrion DNA transfer events were only identified in the D. takeshimana mitogenome, and a pair of mitochondrial DNAs of plastid origin (MIPTs) may generate minor alternative isoforms. We only found a mitochondrion-to-plastid DNA transfer event in the D. ibukiensis plastome. This event may be linked to inverted repeat boundary shifts in its plastome. We inferred that the insertion region involved an MIPT that had already acquired a plastid sequence in its mitogenome via IDT. We propose that the MIPT acts as a homologous region pairing between the donor and recipient sequences. Our results provide insight into the evolution of organelle genomes across the family Apiaceae.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Republic of Korea
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Tanwar N, Arya SS, Rookes JE, Cahill DM, Lenka SK, Bansal KC. Prospects of chloroplast metabolic engineering for developing nutrient-dense food crops. Crit Rev Biotechnol 2023; 43:1001-1018. [PMID: 35815847 DOI: 10.1080/07388551.2022.2092717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/29/2022] [Indexed: 11/03/2022]
Abstract
Addressing nutritional deficiencies in food crops through biofortification is a sustainable approach to tackling malnutrition. Biofortification is continuously being attempted through conventional breeding as well as through various plant biotechnological interventions, ranging from molecular breeding to genetic engineering and genome editing for enriching crops with various health-promoting metabolites. Genetic engineering is used for the rational incorporation of desired nutritional traits in food crops and predominantly operates through nuclear and chloroplast genome engineering. In the recent past, chloroplast engineering has been deployed as a strategic tool to develop model plants with enhanced nutritional traits due to the various advantages it offers over nuclear genome engineering. However, this approach needs to be extended for the nutritional enhancement of major food crops. Further, this platform could be combined with strategies, such as synthetic biology, chloroplast editing, nanoparticle-mediated rapid chloroplast transformation, and horizontal gene transfer through grafting for targeting endogenous metabolic pathways for overproducing native nutraceuticals, production of biopharmaceuticals, and biosynthesis of designer nutritional compounds. This review focuses on exploring various features of chloroplast genome engineering for nutritional enhancement of food crops by enhancing the levels of existing metabolites, restoring the metabolites lost during crop domestication, and introducing novel metabolites and phytonutrients needed for a healthy daily diet.
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Affiliation(s)
- Neha Tanwar
- TERI-Deakin Nano-Biotechnology Centre, The Energy Resources Institute (TERI), New Delhi, India
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - Sagar S Arya
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - James E Rookes
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - David M Cahill
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - Sangram K Lenka
- TERI-Deakin Nano-Biotechnology Centre, The Energy Resources Institute (TERI), New Delhi, India
- Gujarat Biotechnology University, Gujarat, India
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Ter Steege H, Fortes EA, Rozendaal DMA, Erkens RHJ, Sabatier D, Aymard G, Duijm E, Eurlings M, Grewe F, Pombo MM, Gomes VF, de Mansano VF, de Oliveira SM. Molecular phylogeny and evolution of inflorescence types in Eperua. AMERICAN JOURNAL OF BOTANY 2023; 110:e16229. [PMID: 37661805 DOI: 10.1002/ajb2.16229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
PREMISE The Amazonian hyperdominant genus Eperua (Fabaceae) currently holds 20 described species and has two strongly different inflorescence and flower types, with corresponding different pollination syndrome. The evolution of these vastly different inflorescence types within this genus was unknown and the main topic in this study. METHODS We constructed a molecular phylogeny, based on the full nuclear ribosomal DNA and partial plastome, using Bayesian inference and maximum likelihood methods, to test whether the genus is monophyletic, whether all species are monophyletic and if the shift from bat to bee pollination (or vice versa) occurred once in this genus. RESULTS All but two species are well supported by the nuclear ribosomal phylogeny. The plastome phylogeny, however, shows a strong geographic signal suggesting strong local hybridization or chloroplast capture, rendering chloroplast barcodes meaningless in this genus. CONCLUSIONS With our data, we cannot fully resolve the backbone of the tree to clarify sister genera relationships and confirm monophyly of the genus Eperua. Within the genus, the shift from bat to bee and bee to bat pollination has occurred several times but, with the bee to bat not always leading to a pendant inflorescence.
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Affiliation(s)
- Hans Ter Steege
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Quantitative Biodiversity Dynamics, Dept. of Biology, Utrecht, Utrecht University, The Netherlands
| | - Elenice A Fortes
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Danaë M A Rozendaal
- Plant Production Systems Group, Wageningen University, P.O. Box 430, Wageningen, 6700 AK, the Netherlands
- Centre for Crop Systems Analysis, Wageningen University, P.O. Box 430, Wageningen, 6700 AK, the Netherlands
| | - Roy H J Erkens
- Maastricht Science Programme, Faculty of Science and Engineering, Maastricht University, P.O. Box 616. 6200 MD, Maastricht, The Netherlands
| | - Daniel Sabatier
- AMAP, IRD, Cirad, CNRS, INRA, Université de Montpellier, Montpellier, F-34398, France
| | - Gerardo Aymard
- UNELLEZ-Guanare, Programa de Ciencias del Agro y del Mar, Herbario Universitario (PORT), Mesa de Cavacas, estado Portuguesa, 3350, Venezuela
- Compensation International Progress S.A. Ciprogress-Greenlife, Bogotá D.C., Colombia
| | - Elza Duijm
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Felix Grewe
- Grainger Bioinformatics Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, 60605-2496, IL, USA
| | - Maihyra M Pombo
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Manaus, 69067-375, AM, Brazil
| | - Vitor F Gomes
- Escola de Negócios Tecnologia e Inovação, Centro Universitário do Pará, Belém, PA, Brazil
- Universidade Federal do Pará, Rua Augusto Corrêa 01, Belém, 66075-110, PA, Brazil
| | - Vidal F de Mansano
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915, Rio de Janeiro, 22460-030, RJ, Brazil
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12
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Liu L, Chen M, Folk RA, Wang M, Zhao T, Shang F, Soltis DE, Li P. Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids. Mol Ecol Resour 2023; 23:1673-1688. [PMID: 37449554 DOI: 10.1111/1755-0998.13833] [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: 03/10/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an "expanded" malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.
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Affiliation(s)
- Luxian Liu
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengzhen Chen
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
| | - Meizhen Wang
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fude Shang
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, Henan, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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13
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Lesica P, Lavin M. Will molecular phylogenetics help decrease nomenclatural instability? AMERICAN JOURNAL OF BOTANY 2023; 110:e16219. [PMID: 37561649 DOI: 10.1002/ajb2.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/12/2023]
Affiliation(s)
- Peter Lesica
- Division of Biological Sciences, University of Montana, Missoula, 59812, Montana, USA
| | - Matt Lavin
- Plant Sciences and Plant Pathology Department, Montana State University, Bozeman, 59717, Montana, USA
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14
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Zhang W, Wang H, Zhang T, Fang X, Liu M, Xiao H. Geographic-genomic and geographic-phenotypic differentiation of the Aquilegia viridiflora complex. HORTICULTURE RESEARCH 2023; 10:uhad041. [PMID: 37159802 PMCID: PMC10163360 DOI: 10.1093/hr/uhad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/05/2023] [Indexed: 05/11/2023]
Abstract
How species diverge into different lineages is a central issue in evolutionary biology. Despite the increasing evidence indicating that such divergences do not need geographic isolation, the correlation between lineage divergence and the adaptive ecological divergence of phenotype corresponding to distribution is still unknown. In addition, gene flow has been widely detected during and through such diverging processes. We used one widely distributed Aquilegia viridiflora complex as a model system to examine genomic differentiation and corresponding phenotypic variations along geographic gradients. Our phenotypic analyses of 20 populations from northwest to northeast China identified two phenotypic groups along the geographic cline. All examined traits are distinct from each other, although a few intermediate individuals occur in their contacting regions. We further sequenced the genomes of representative individuals of each population. However, four distinct genetic lineages were detected based on nuclear genomes. In particular, we recovered numerous genetic hybrids in the contact regions of four lineages. Gene flow is widespread and continuous between four lineages but much higher between contacting lineages than geographically isolated lineages. Gene flow and natural selection might result in inconsistency between heredity and phenotype. Moreover, many genes with fast lineage-specific mutations were identified to be involved in local adaptation. Our results suggest that both geographic isolation and local selection exerted by the environment and pollinators may together create geographic distributions of phenotypic variations as well as the underlying genomic divergences in numerous lineages.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | | | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Xiaoxue Fang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Meiying Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
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15
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Loupit G, Brocard L, Ollat N, Cookson SJ. Grafting in plants: recent discoveries and new applications. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2433-2447. [PMID: 36846896 DOI: 10.1093/jxb/erad061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/14/2023] [Indexed: 06/06/2023]
Abstract
Grafting is a traditional horticultural technique that makes use of plant wound healing mechanisms to join two different genotypes together to form one plant. In many agricultural systems, grafting with rootstocks controls the vigour of the scion and/or provides tolerance to deleterious soil conditions such as the presence of soil pests or pathogens or limited or excessive water or mineral nutrient supply. Much of our knowledge about the limits to grafting different genotypes together comes from empirical knowledge of horticulturalists. Until recently, researchers believed that grafting monocotyledonous plants was impossible, because they lack a vascular cambium, and that graft compatibility between different scion/rootstock combinations was restricted to closely related genotypes. Recent studies have overturned these ideas and open up the possibility of new research directions and applications for grafting in agriculture. The objective of this review is to describe and assess these recent advances in the field of grafting and, in particular, the molecular mechanisms underlining graft union formation and graft compatibility between different genotypes. The challenges of characterizing the different stages of graft union formation and phenotyping graft compatibility are examined.
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Affiliation(s)
- Grégoire Loupit
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Lysiane Brocard
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US4, F-33000 Bordeaux, France
| | - Nathalie Ollat
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Sarah Jane Cookson
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
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16
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New Insights into Plastid and Mitochondria Evolution in Wild Peas (Pisum L.). DIVERSITY 2023. [DOI: 10.3390/d15020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid and mitochondrial genomes of Pisum sativum subsp. elatius and Pisum fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most wild peas from continental southern Europe and a single specimen from Morocco were found to share the same organellar genome constitution; four others, presumably hybrid constitutions, were revealed in Mediterranean islands and Athos Peninsula. A mitochondrial genome closely related to that of Pisum abyssinicum, from Yemen and Ethiopia, was unexpectedly found in an accession of P. sativum subsp. elatius from Israel, their plastid genomes being unrelated. Phylogenetic reconstructions based on plastid and mitochondrial genomes revealed different sets of wild peas to be most related to cultivated P. sativum subsp. sativum, making its wild progenitor and its origin area enigmatic. An accession of P. fulvum representing ‘fulvum-b’ branch, according to a nuclear marker, appeared in the same branch as other fulvum accessions in organellar trees. The results stress the complicated evolution and structure of genetic diversity of pea crop wild relatives.
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17
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Stubbs RL, Theodoridis S, Mora‐Carrera E, Keller B, Yousefi N, Potente G, Léveillé‐Bourret É, Celep F, Kochjarová J, Tedoradze G, Eaton DAR, Conti E. Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot. THE NEW PHYTOLOGIST 2023; 237:656-671. [PMID: 36210520 PMCID: PMC10099377 DOI: 10.1111/nph.18525] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.
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Affiliation(s)
- Rebecca L. Stubbs
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am Main60325Germany
| | - Emiliano Mora‐Carrera
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Étienne Léveillé‐Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV)Université de MontréalQuébecH1X 2B2Canada
| | - Ferhat Celep
- Department of Biology, Faculty of Arts and SciencesKırıkkale UniversityKırıkkale71450Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of ForestryTechnical University in ZvolenZvolen96001Slovak Republic
| | - Giorgi Tedoradze
- Department of Plant Systematics and Geography, Institute of BotanyIlia State UniversityTbilisi0105Georgia
| | - Deren A. R. Eaton
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNY10027USA
| | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
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18
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Chen YP, Zhao F, Paton AJ, Sunojkumar P, Gao LM, Xiang CL. Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:985488. [PMID: 36160976 PMCID: PMC9493350 DOI: 10.3389/fpls.2022.985488] [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: 07/04/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
As one of the largest genera of Lamiaceae and of great medicinal importance, Isodon is also phylogenetically and taxonomically recalcitrant largely ascribed to its recent rapid radiation in the Hengduan Mountains. Previous molecular phylogenetic studies using limited loci have only successfully resolved the backbone topology of the genus, but the interspecific relationships suffered from low resolution, especially within the largest clade (Clade IV) which comprises over 80% species. In this study, we attempted to further elucidate the phylogenetic relationships within Isodon especially Clade IV using plastome sequences with a broad taxon sampling of ca. 80% species of the genus. To reduce systematic errors, twelve different plastome data sets (coding and non-coding regions with ambiguously aligned regions and saturated loci removed or not) were employed to reconstruct phylogeny using maximum likelihood and Bayesian inference. Our results revealed largely congruent topologies of the 12 data sets and recovered major lineages of Isodon consistent with previous studies, but several incongruences are also found among these data sets and among single plastid loci. Most of the shallow nodes within Clade IV were resolved with high support but extremely short branch lengths in plastid trees, and showed tremendous conflicts with the nrDNA tree, morphology and geographic distribution. These incongruences may largely result from stochasticity (due to insufficient phylogenetic signal) and hybridization and plastid capture. Therefore, the uniparental-inherited plastome sequences are insufficient to disentangle relationships within a genus which has undergone recent rapid diversification. Our findings highlight a need for additional data from nuclear genome to resolve the relationships within Clade IV and more focused studies to assess the influences of multiple processes in the evolutionary history of Isodon. Nevertheless, the morphology of the shape and surface sculpture/indumentum of nutlets is of systematic importance that they can distinguish the four major clades of Isodon.
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Affiliation(s)
- Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Fei Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Alan J. Paton
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
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Chloroplast Genome of Lithocarpus dealbatus (Hook.f. & Thomson ex Miq.) Rehder Establishes Monophyletic Origin of the Species and Reveals Mutational Hotspots with Taxon Delimitation Potential. Life (Basel) 2022; 12:life12060828. [PMID: 35743859 PMCID: PMC9225305 DOI: 10.3390/life12060828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022] Open
Abstract
There is phylogenetic ambiguity in the genus Lithocarpus and subfamily Quercoideae (Family: Fagaceae). Lithocarpus dealbatus, an ecologically important tree, is the dominant species among the Quercoideae in India. Although several studies have been conducted on the species' regeneration and ecological and economic significance, limited information is available on its phylo-genomics. To resolve the phylogeny in Quercoideae, we sequenced and assembled the 161,476 bp chloroplast genome of L. dealbatus, which has a large single-copy section of 90,732 bp and a small single-copy region of 18,987 bp, separated by a pair of inverted repeat regions of 25,879 bp. The chloroplast genome contained 133 genes, of which 86 were protein-coding genes, 39 were transfer RNAs, and eight were ribosomal RNAs. Analysis of repeat elements and RNA editing sites revealed interspecific similarities within the Lithocarpus genus. DNA diversity analysis identified five highly diverged coding and noncoding hotspot regions in the four genera, which can be used as polymorphic markers for species/taxon delimitation across the four genera of Quercoideae viz., Lithocarpus, Quercus, Castanea, and Castanopsis. The chloroplast-based phylogenetic analysis among the Quercoideae established a monophyletic origin of Lithocarpus, and a closer evolutionary lineage with a few Quercus species. Besides providing insights into the chloroplast genome architecture of L. dealbatus, the study identified five mutational hotspots having high taxon-delimitation potential across four genera of Quercoideae.
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Chen YP, Turdimatovich TO, Nuraliev MS, Lazarević P, Drew BT, Xiang CL. Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae). Cladistics 2022; 38:429-451. [PMID: 35358338 DOI: 10.1111/cla.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/28/2022] Open
Abstract
The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns, and the biogeographical history of the three genera (defined as Dracocephalum s.l.). Based on a sampling of 66 taxa comprising more than 80% from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognizes nine sections within the genus.
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Affiliation(s)
- Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | - Maxim S Nuraliev
- Department of Higher Plants, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Predrag Lazarević
- Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, Kearney, 68849, USA
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Li W, Chen S, Liu Y, Wang L, Jiang J, Zhao S, Fang W, Chen F, Guan Z. Long-distance transport RNAs between rootstocks and scions and graft hybridization. PLANTA 2022; 255:96. [PMID: 35348893 DOI: 10.1007/s00425-022-03863-w] [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: 08/15/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
The present review addresses the advances of the identification methods, functions, and transportation mechanism of long-distance transport RNAs between rootstock and scion. In addition, we highlight the cognitive processes and potential mechanisms of graft hybridization. Phloem, the main transport channel of higher plants, plays an important role in the growth and development of plants. Numerous studies have identified a large number of RNAs, including mRNAs, miRNAs, siRNAs, and lncRNAs, in the plant phloem. They can not only be transported to long distances across the grafting junction in the phloem, but also act as signal molecules to regulate the growth, development, and stress resistance of remote cells or tissues, resulting in changes in the traits of rootstocks and scions. Many mobile RNAs have been discovered, but their detection methods, functions, and long-distance transport mechanisms remain to be elucidated. In addition, grafting hybridization, a phenomenon that has been questioned before, and which has an important role in selecting for superior traits, is gradually being recognized with the emergence of new evidence and the prevalence of horizontal gene transfer between parasitic plants. In this review, we outline the species, functions, identification methods, and potential mechanisms of long-distance transport RNAs between rootstocks and scions after grafting. In addition, we summarize the process of recognition and the potential mechanisms of graft hybridization. This study aimed to emphasize the role of grafting in the study of long-distance signals and selection for superior traits and to provide ideas and clues for further research on long-distance transport RNAs and graft hybridization.
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Affiliation(s)
- Wenjie Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ye Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Likai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuang Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Liu R, Wang H, Yang JB, Corlett RT, Randle CP, Li DZ, Yu WB. Cryptic Species Diversification of the Pedicularis siphonantha Complex (Orobanchaceae) in the Mountains of Southwest China Since the Pliocene. FRONTIERS IN PLANT SCIENCE 2022; 13:811206. [PMID: 35401620 PMCID: PMC8987768 DOI: 10.3389/fpls.2022.811206] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Morphological approaches often fail to delimit species in recently derived species complexes. This can be exacerbated in historical collections which may have lost key features in specimen preparation and preservation. Here, we examine the Pedicularis siphonantha complex, endemic to the Mountains of Southwest China. This complex is characterized by its red/purple/pink and long-tubular corolla, and twisted, beaked galea. However, herbarium specimens are often difficult to identify to species. Molecular approaches using nrITS or nuclear ribosomal internal transcribed spacer (nrITS) + plastid DNA (ptDNA) have been successfully used for species identification in Pedicularis. To resolve taxonomic confusion in the Pedicularis siphonantha complex, we reconstructed phylogenies of the complex using nrITS and four plastid DNA loci (matK, rbcL, trnH-psbA, and trnL-F). To recover as much of the phylogenetic history as possible, we sampled individuals at the population level. Topological incongruence between the nrITS and ptDNA datasets was recovered in clades including two widely distributed species, Pedicularis milliana and Pedicularis tenuituba. Based on morphological, geographical, and genetic evidence, we suggest that hybridization/introgression has occurred between P. milliana and Pedicularis sigmoidea/Pedicularis sp. 1 in the Yulong Snow Mountain of Lijiang, northwest Yunnan, and between P. tenuituba and Pedicularis leptosiphon in Ninglang, northwest Yunnan. After removing conflicting DNA regions in Pedicularis dolichosiphon (nrITS) and P. milliana (ptDNA), the concatenated nrITS and ptDNA phylogenies distinguish 11 species in the P. siphonantha complex, including two undescribed species, from the Jiaozi and Yulong Snow Mountains, respectively. Phylogeographical analyses indicate that the P. siponantha complex originated from south of the Hengduan Mountains, expanding north to the Himalayas and the Yunnan-Guizhou Plateau. Moreover, the uplift of the Qinghai-Tibet Plateau and climate oscillations may have driven further diversification in the complex.
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Affiliation(s)
- Rong Liu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Plant Germplasm and Genomics Centre, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Richard T. Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Christopher P. Randle
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States
| | - De-Zhu Li
- Plant Germplasm and Genomics Centre, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
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Xia MZ, Li Y, Zhang FQ, Yu JY, Khan G, Chi XF, Xu H, Chen SL. Reassessment of the Phylogeny and Systematics of Chinese Parnassia (Celastraceae): A Thorough Investigation Using Whole Plastomes and Nuclear Ribosomal DNA. FRONTIERS IN PLANT SCIENCE 2022; 13:855944. [PMID: 35371115 PMCID: PMC8971841 DOI: 10.3389/fpls.2022.855944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Parnassia L., a perennial herbaceous genus in the family Celastraceae, consists of about 60 species and is mainly distributed in the Pan-Himalayan and surrounding mountainous regions. The taxonomic position and phylogenetic relationships of the genus are still controversial. Herein, we reassessed the taxonomic status of Parnassia and its intra- and inter-generic phylogeny within Celastraceae. To that end, we sequenced and assembled the whole plastid genomes and nuclear ribosomal DNA (nrDNA) of 48 species (74 individuals), including 25 species of Parnassia and 23 species from other genera of Celastraceae. We integrated high throughput sequence data with advanced statistical toolkits and performed the analyses. Our results supported the Angiosperm Phylogeny Group IV (APG IV) taxonomy which kept the genus to the family Celastraceae. Although there were topological conflicts between plastid and nrDNA phylogenetic trees, Parnassia was fully supported as a monophyletic group in all cases. We presented a first attempt to estimate the divergence of Parnassia, and molecular clock analysis indicated that the diversification occurred during the Eocene. The molecular phylogenetic results confirmed numerous taxonomic revisions, revealing that the morphological characters used in Parnassia taxonomy and systematics might have evolved multiple times. In addition, we speculated that hybridization/introgression might exist during genus evolution, which needs to be further studied. Similarly, more in-depth studies will clarify the diversification of characters and species evolution models of this genus.
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Affiliation(s)
- Ming-Ze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- School of Pharmacy, Weifang Medical University, Weifang, China
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Jing-Ya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Xiao-Feng Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
| | - Hao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
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Dong D, Shi YN, Mou ZM, Chen SY, Zhao DK. Grafting: a potential method to reveal the differential accumulation mechanism of secondary metabolites. HORTICULTURE RESEARCH 2022; 9:uhac050. [PMID: 35591927 PMCID: PMC9113227 DOI: 10.1093/hr/uhac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/14/2022] [Indexed: 06/15/2023]
Abstract
Plant secondary metabolites make a great contribution to the agricultural and pharmaceutical industries. Their accumulation is determined by the integrated transport of target compounds and their biosynthesis-related RNA, protein, or DNA. However, it is hard to track the movement of these biomolecules in vivo. Grafting may be an ideal method to solve this problem. The differences in genetic and metabolic backgrounds between rootstock and scion, coupled with multiple omics approaches and other molecular tools, make it feasible to determine the movement of target compounds, RNAs, proteins, and DNAs. In this review, we will introduce methods of using the grafting technique, together with molecular biological tools, to reveal the differential accumulation mechanism of plant secondary metabolites at different levels. Details of the case of the transport of one diterpene alkaloid, fuziline, will be further illustrated to clarify how the specific accumulation model is shaped with the help of grafting and multiple molecular biological tools.
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Affiliation(s)
- Ding Dong
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, 650504, China
- Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, 650504, China
- School of Life Science, Yunnan University, Kunming, 650204, China
| | - Ya-Na Shi
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, 650000, China
| | - Zong-Min Mou
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, 650504, China
- Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, 650504, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650504, China
| | - Sui-Yun Chen
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, 650504, China
- Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, 650504, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650504, China
| | - Da-Ke Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, 650504, China
- Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, 650504, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650504, China
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Wu H, Yang JB, Liu JX, Li DZ, Ma PF. Organelle Phylogenomics and Extensive Conflicting Phylogenetic Signals in the Monocot Order Poales. FRONTIERS IN PLANT SCIENCE 2022; 12:824672. [PMID: 35173754 PMCID: PMC8841755 DOI: 10.3389/fpls.2021.824672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The Poales is one of the largest orders of flowering plants with significant economic and ecological values. Reconstructing the phylogeny of the Poales is important for understanding its evolutionary history that forms the basis for biological studies. However, due to sparse taxon sampling and limited molecular data, previous studies have resulted in a variety of contradictory topologies. In particular, there are three nodes surrounded by incongruence: the phylogenetic ambiguity near the root of the Poales tree, the sister family of Poaceae, and the delimitation of the xyrid clade. We conducted a comprehensive sampling and reconstructed the phylogenetic tree using plastid and mitochondrial genomic data from 91 to 66 taxa, respectively, representing all the 16 families of Poales. Our analyses support the finding of Bromeliaceae and Typhaceae as the earliest diverging groups within the Poales while having phylogenetic relationships with the polytomy. The clade of Ecdeiocoleaceae and Joinvilleaceae is recovered as the sister group of Poaceae. The three families, Mayacaceae, Eriocaulaceae, and Xyridaceae, of the xyrid assembly diverged successively along the backbone of the Poales phylogeny, and thus this assembly is paraphyletic. Surprisingly, we find substantial phylogenetic conflicts within the plastid genomes of the Poales, as well as among the plastid, mitochondrial, and nuclear data. These conflicts suggest that the Poales could have a complicated evolutionary history, such as rapid radiation and polyploidy, particularly allopolyploidy through hybridization. In sum, our study presents a new perspicacity into the complex phylogenetic relationships and the underlying phylogenetic conflicts within the Poales.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Casola C, Li J. Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C 4 plants. PeerJ 2022; 10:e12791. [PMID: 35127287 PMCID: PMC8801178 DOI: 10.7717/peerj.12791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/22/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL. METHODS Our study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages. RESULTS The reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacements in C4 lineages, with both RbcL and RpoC1 (the RNA polymerase beta' subunit 1) showing a significantly higher convergent/non-convergent replacements ratio in C4 branches. Notably, more C4:C4 reference branches showed higher numbers of convergent vs. non-convergent replacements than C3:C3 and C3:C4 branches. Our results suggest that, in the PACMAD clade, C4 grasses experienced higher levels of molecular convergence than C3 species across multiple chloroplast genes. These findings have important implications for our understanding of the evolution of the C4 photosynthesis pathway.
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Affiliation(s)
- Claudio Casola
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States of America
- Interdisciplinary Graduate Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, United States of America
| | - Jingjia Li
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States of America
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Chambaud C, Cookson SJ, Ollat N, Bayer E, Brocard L. A correlative light electron microscopy approach reveals plasmodesmata ultrastructure at the graft interface. PLANT PHYSIOLOGY 2022; 188:44-55. [PMID: 34687300 PMCID: PMC8774839 DOI: 10.1093/plphys/kiab485] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/21/2021] [Indexed: 06/01/2023]
Abstract
Despite recent progress in our understanding of graft union formation, we still know little about the cellular events underlying the grafting process. This is partially due to the difficulty of reliably targeting the graft interface in electron microscopy to study its ultrastructure and three-dimensional architecture. To overcome this technological bottleneck, we developed a correlative light electron microscopy (CLEM) approach to study the graft interface with high ultrastructural resolution. Grafting hypocotyls of Arabidopsis thaliana lines expressing yellow FP or monomeric red FP in the endoplasmic reticulum (ER) allowed efficient targeting of the grafting interface for examination under light and electron microscopy. To explore the potential of our method to study sub-cellular events at the graft interface, we focused on the formation of secondary plasmodesmata (PD) between the grafted partners. We showed that four classes of PD were formed at the interface and that PD introgression into the cell wall was initiated equally by both partners. Moreover, the success of PD formation appeared not systematic with a third of PD not spanning the cell wall entirely. Characterizing the ultrastructural characteristics of these incomplete PD gives us insights into the process of secondary PD biogenesis. We found that the establishment of successful symplastic connections between the scion and rootstock occurred predominantly in the presence of thin cell walls and ER-plasma membrane tethering. The resolution reached in this work shows that our CLEM method advances the study of biological processes requiring the combination of light and electron microscopy.
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Affiliation(s)
- Clément Chambaud
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882 Villenave d’Ornon, France
| | - Sarah Jane Cookson
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882 Villenave d’Ornon, France
| | - Nathalie Ollat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882 Villenave d’Ornon, France
| | - Emmanuelle Bayer
- Laboratoire de Biogénèse Membranaire (LBM), CNRS, Univ. Bordeaux, UMR 5200, F-33882 Villenave d’Ornon, France
| | - Lysiane Brocard
- Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, F-33000 Bordeaux, France
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Ulaszewski B, Jankowska-Wróblewska S, Świło K, Burczyk J. Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112534. [PMID: 34834899 PMCID: PMC8618278 DOI: 10.3390/plants10112534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Several genera formerly contained within the genus Sorbus L. sensu lato have been proposed as separate taxa, including Aria, Chamaemespilus and Torminalis. However, molecular evidence for such distinctions are rather scarce. We assembled the complete chloroplast genome of Sorbus aucuparia, another representative of Sorbus s.s., and performed detailed comparisons with the available genomes of Aria edulis, Chamaemespilus alpina and Torminalis glaberrima. Additionally, using 110 complete chloroplast genomes of the Maleae representatives, we constructed the phylogenetic tree of the tribe using Maximum Likelihood methods. The chloroplast genome of S. aucuparia was found to be similar to other species within Maleae. The phylogenetic tree of the Maleae tribe indicated that A. edulis, C. alpina and T. glaberrima formed a concise group belonging to a different clade (related to Malus) than the one including Sorbus s.s. (related to Pyrus). However, Aria and Chamaemespilus appeared to be more closely related to each other than to Torminalis. Our results provide additional support for considering Aria, Chamaemespilus and Torminalis as separate genera different from Sorbus s.s.
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Hunter P. The molecular biology of grafting: Recent research may provide new applications for a millennia-old agricultural technology. EMBO Rep 2021; 22:e54098. [PMID: 34648669 DOI: 10.15252/embr.202154098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
Plant biologists have begun to unravel the molecular mechanisms behind grafting, yielding insights into plant evolution and expanding the scope of this technique.
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Bantis F, Tsiolas G, Mouchtaropoulou E, Tsompanoglou I, Polidoros AN, Argiriou A, Koukounaras A. Comparative Transcriptome Analysis in Homo- and Hetero-Grafted Cucurbit Seedlings. FRONTIERS IN PLANT SCIENCE 2021; 12:691069. [PMID: 34777405 PMCID: PMC8582762 DOI: 10.3389/fpls.2021.691069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Watermelon (Citrullus lanatus) is a valuable horticultural crop with nutritional benefits grown worldwide. It is almost exclusively cultivated as grafted scions onto interspecific squash rootstock (Cucurbita maxima × Cucurbita moschata) to improve the growth and yield and to address the problems of soilborne diseases and abiotic stress factors. This study aimed to examine the effect of grafting (homo- and hetero-grafting) on the transcriptome level of the seedlings. Therefore, we compared homo-grafted watermelon (WW) with non-grafted watermelon control (W), homo-grafted squash (SS) with non-grafted squash control (S), hetero-grafted watermelon onto squash (WS) with SS, and WS with WW. Different numbers of differentially expressed genes (DEGs) were identified in each comparison. In total, 318 significant DEGs were detected between the transcriptomes of hetero-grafts and homo-grafts at 16 h after grafting. Overall, a significantly higher number of downregulated transcripts was detected among the DEGs. Only one gene showing increased expression related to the cytokinin synthesis was common in three out of four comparisons involving WS, SS, and S. The highest number of differentially expressed (DE) transcripts (433) was detected in the comparison between SS and S, followed by the 127 transcripts between WW and W. The study provides a description of the transcriptomic nature of homo- and hetero-grafted early responses, while the results provide a start point for the elucidation of the molecular mechanisms and candidate genes for the functional analyses of hetero-graft and homo-graft systems in Cucurbitaceae and generally in the plants.
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Affiliation(s)
- Filippos Bantis
- School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - George Tsiolas
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
| | | | - Ioanna Tsompanoglou
- School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexios N. Polidoros
- School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
- Department of Food Science and Nutrition, University of the Aegean, Myrina, Greece
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Zhu X, Liu X, Liu T, Wang Y, Ahmed N, Li Z, Jiang H. Synthetic biology of plant natural products: From pathway elucidation to engineered biosynthesis in plant cells. PLANT COMMUNICATIONS 2021; 2:100229. [PMID: 34746761 PMCID: PMC8553972 DOI: 10.1016/j.xplc.2021.100229] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 04/11/2021] [Accepted: 08/06/2021] [Indexed: 05/10/2023]
Abstract
Plant natural products (PNPs) are the main sources of drugs, food additives, and new biofuels and have become a hotspot in synthetic biology. In the past two decades, the engineered biosynthesis of many PNPs has been achieved through the construction of microbial cell factories. Alongside the rapid development of plant physiology, genetics, and plant genetic modification techniques, hosts have now expanded from single-celled microbes to complex plant systems. Plant synthetic biology is an emerging field that combines engineering principles with plant biology. In this review, we introduce recent advances in the biosynthetic pathway elucidation of PNPs and summarize the progress of engineered PNP biosynthesis in plant cells. Furthermore, a future vision of plant synthetic biology is proposed. Although we are still a long way from overcoming all the bottlenecks in plant synthetic biology, the ascent of this field is expected to provide a huge opportunity for future agriculture and industry.
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Affiliation(s)
- 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
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Xiaonan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Tian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Life Science and Technology College, Guangxi University, Nanning, Guangxi 530004, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yina Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Nida Ahmed
- 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
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zhichao Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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Savage Z, Duggan C, Toufexi A, Pandey P, Liang Y, Segretin ME, Yuen LH, Gaboriau DCA, Leary AY, Tumtas Y, Khandare V, Ward AD, Botchway SW, Bateman BC, Pan I, Schattat M, Sparkes I, Bozkurt TO. Chloroplasts alter their morphology and accumulate at the pathogen interface during infection by Phytophthora infestans. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1771-1787. [PMID: 34250673 DOI: 10.1111/tpj.15416] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 05/22/2023]
Abstract
Upon immune activation, chloroplasts switch off photosynthesis, produce antimicrobial compounds and associate with the nucleus through tubular extensions called stromules. Although it is well established that chloroplasts alter their position in response to light, little is known about the dynamics of chloroplast movement in response to pathogen attack. Here, we report that during infection with the Irish potato famine pathogen Phytophthora infestans, chloroplasts accumulate at the pathogen interface, associating with the specialized membrane that engulfs the pathogen haustorium. The chemical inhibition of actin polymerization reduces the accumulation of chloroplasts at pathogen haustoria, suggesting that this process is partially dependent on the actin cytoskeleton. However, chloroplast accumulation at haustoria does not necessarily rely on movement of the nucleus to this interface and is not affected by light conditions. Stromules are typically induced during infection, embracing haustoria and facilitating chloroplast interactions, to form dynamic organelle clusters. We found that infection-triggered stromule formation relies on BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1)-mediated surface immune signaling, whereas chloroplast repositioning towards haustoria does not. Consistent with the defense-related induction of stromules, effector-mediated suppression of BAK1-mediated immune signaling reduced stromule formation during infection. On the other hand, immune recognition of the same effector stimulated stromules, presumably via a different pathway. These findings implicate chloroplasts in a polarized response upon pathogen attack and point to more complex functions of these organelles in plant-pathogen interactions.
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Affiliation(s)
- Zachary Savage
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Cian Duggan
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Alexia Toufexi
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Pooja Pandey
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Yuxi Liang
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - María Eugenia Segretin
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular 'Dr Héctor N. Torres' (INGEBI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Vuelta de Obligado 2490, Ciudad Autónoma de Buenos Aires, C1428ADN, Argentina
| | - Lok Him Yuen
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - David C A Gaboriau
- Facility for Imaging by Light Microscopy, Faculty of Medicine, National Heart & Lung Institute (NHLI), Imperial College London, South Kensington, SAF building, London, SW7 2AZ, UK
| | - Alexandre Y Leary
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Yasin Tumtas
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Virendrasinh Khandare
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Andrew D Ward
- Central Laser Facility, Science and Technology Facilities Council Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0QX, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0QX, UK
| | - Benji C Bateman
- Central Laser Facility, Science and Technology Facilities Council Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0QX, UK
| | - Indranil Pan
- Centre for Process Systems Engineering and Centre for Environmental Policy, Imperial College London, South Kensington Campus, London, London, SW7 2AZ, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London, London, NW1 2DB, UK
| | - Martin Schattat
- Martin Luther Universität Halle-Wittenberg, Halle, 06108 Halle, Germany
| | - Imogen Sparkes
- School of Biological Sciences, University of Bristol, University of Bristol, St Michael's Hill, Bristol, BS8 8DZ, UK
| | - Tolga O Bozkurt
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
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Molina-Hidalgo FJ, Vazquez-Vilar M, D'Andrea L, Demurtas OC, Fraser P, Giuliano G, Bock R, Orzáez D, Goossens A. Engineering Metabolism in Nicotiana Species: A Promising Future. Trends Biotechnol 2021; 39:901-913. [PMID: 33341279 DOI: 10.1016/j.tibtech.2020.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/31/2022]
Abstract
Molecular farming intends to use crop plants as biofactories for high value-added compounds following application of a wide range of biotechnological tools. In particular, the conversion of nonfood crops into efficient biofactories is expected to be a strong asset in the development of a sustainable bioeconomy. The 'nonfood' status combined with the high metabolic versatility and the capacity of high-yield cultivation highlight the plant genus Nicotiana as one of the most appropriate 'chassis' for molecular farming. Nicotiana species are a rich source of valuable industrial, active pharmaceutical ingredients and nutritional compounds, synthesized from highly complex biosynthetic networks. Here, we review and discuss approaches currently used to design enriched Nicotiana species for molecular farming using new plant breeding techniques (NPBTs).
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Affiliation(s)
- Francisco Javier Molina-Hidalgo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Lucio D'Andrea
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Olivia C Demurtas
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, London, UK
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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Park M, Christin PA, Bennetzen JL. Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses. Mol Biol Evol 2021; 38:3664-3675. [PMID: 33964159 PMCID: PMC8382918 DOI: 10.1093/molbev/msab133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Limited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a nontargeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and data sets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants.
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Affiliation(s)
- Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - Jeffrey L Bennetzen
- Department of Genetics, University of Georgia, Athens, GA, USA
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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36
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Aubin E, El Baidouri M, Panaud O. Horizontal Gene Transfers in Plants. Life (Basel) 2021; 11:life11080857. [PMID: 34440601 PMCID: PMC8401529 DOI: 10.3390/life11080857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
In plants, as in all eukaryotes, the vertical transmission of genetic information through reproduction ensures the maintenance of the integrity of species. However, many reports over the past few years have clearly shown that horizontal gene transfers, referred to as HGTs (the interspecific transmission of genetic information across reproductive barriers) are very common in nature and concern all living organisms including plants. The advent of next-generation sequencing technologies (NGS) has opened new perspectives for the study of HGTs through comparative genomic approaches. In this review, we provide an up-to-date view of our current knowledge of HGTs in plants.
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Park I, Song JH, Yang S, Chae S, Moon BC. Plastid Phylogenomic Data Offers Novel Insights Into the Taxonomic Status of the Trichosanthes kirilowii Complex (Cucurbitaceae) in South Korea. FRONTIERS IN PLANT SCIENCE 2021; 12:559511. [PMID: 34386020 PMCID: PMC8353159 DOI: 10.3389/fpls.2021.559511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Trichosanthes is a genus in Cucurbitaceae comprising 90-100 species. Trichosanthes species are valuable as herbaceous medicinal ingredients. The fruits, seeds, and roots of species such as T. kirilowii and T. rosthornii are used in Korean traditional herbal medicines. T. rosthornii is only found in China, whereas in South Korea two varieties, T. kirilowii var. kirilowii and T. kirilowii var. japonica, are distributed. T. kirilowii var. kirilowii and T. kirilowii var. japonica have different fruit and leaf shapes but are recognized as belonging to the same species. Furthermore, although its members have herbal medicine applications, genomic information of the genus is still limited. The broad goals of this study were (i) to evaluate the taxonomy of Trichosanthes using plastid phylogenomic data and (ii) provide molecular markers specific for T. kirilowii var. kirilowii and T. kirilowii var. japonica, as these have differences in their pharmacological effectiveness and thus should not be confused and adulterated. Comparison of five Trichosanthes plastid genomes revealed locally divergent regions, mainly within intergenic spacer regions (trnT-UGU-trnL-UAA: marker name Tri, rrn4.5-rrn5: TRr, trnE-UUC-trnT-GGU: TRtt). Using these three markers as DNA-barcodes for important herbal medicine species in Trichosanthes, the identity of Trichosanthes material in commercial medicinal products in South Korea could be successfully determined. Phylogenetic analysis of the five Trichosanthes species revealed that the species are clustered within tribe Sicyoeae. T. kirilowii var. kirilowii and T. rosthornii formed a clade with T. kirilowii var. japonica as their sister group. As T. kirilowii in its current circumscription is paraphyletic and as the two varieties can be readily distinguished morphologically (e.g., in leaf shape), T. kirilowii var. japonica should be treated (again) as an independent species, T. japonica.
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Affiliation(s)
- Inkyu Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Jun-Ho Song
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Sungyu Yang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Sungwook Chae
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Byeong Cheol Moon
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
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38
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Deklerck V, Price E, Vanden Abeele S, Lievens K, Espinoza E, Beeckman H. Timber identification of Autranella, Baillonella and Tieghemella in the taxonomically challenging Sapotaceae family. PLANT METHODS 2021; 17:64. [PMID: 34158085 PMCID: PMC8220841 DOI: 10.1186/s13007-021-00766-x] [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: 02/13/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND To enforce timber import laws and perform timber species identification, the identity of the botanical species must be well-defined. Since the Sapotaceae family is known as a taxonomically challenging family, we focus in this study on the four most valuable Sapotaceae timber species from tropical Africa: Autranella congolensis (De Wild.) A.Chev., Baillonella toxisperma Pierre, Tieghemella africana Pierre and Tieghemella heckelii (A.Chev.) Pierre ex Dubard. The wood anatomical characteristic fiber lumen fraction and Direct Analysis in Real Time-Time of Flight Mass Spectrometry (DART-TOFMS) were used to differentiate the four species and to make inferences on species delineation and taxonomic identity. RESULTS We observed differences in the fiber lumen fraction measurements and discerned two groups: (1) A. congolensis and B. toxisperma, and (2) T. africana and T. heckelii. In addition, all Mann-Whitney U comparisons and differences in distributions (Kolmogorov-Smirnov) for the fiber lumen fraction measurements were significant between all species. When permutating the data between species within those two groups, significant differences were still found between the species within those groups. This could indicate that the fiber lumen fraction is not diagnostic to discern the species. DART-TOFMS analysis showed that A. congolensis and B. toxisperma have distinct chemotypes, while T. heckelii and T. africana have remarkably similar chemotypes. CONCLUSIONS Based on our observations of similar chemotype and weakly differentiated fiber lumen ratio, we support an alternative taxonomic hypothesis that considers Tieghemella monotypic, because of the strong resemblance between T. heckelii and T. africana. Larger sample sizes and further research is required to develop methodology for the identification of these species. A taxonomic study utilizing molecular genetics would be beneficial to assess the status of the genus and the species limits. This could have implications towards their potential inclusion on CITES appendices if there is ever need for them to be listed. If Tieghemella africana and T. heckelii remain two distinct species, they should both be listed. Screening agents should be aware that the morphological and chemical differences between T. africana and T. heckelii are minimal.
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Affiliation(s)
- V Deklerck
- Service of Wood Biology, Royal Museum for Central Africa (RMCA), Leuvensesteensweg 13, 3080, Tervuren, Belgium.
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, United Kingdom.
| | - E Price
- U.S. Forest Service International Programs Wood Identification & Screening Center, Richardson Hall 109, 3180 SW Jefferson Way, Corvallis, OR, 97331, USA
- U.S. Fish and Wildlife Forensic Laboratory, 1490 East Main Street, Ashland, OR, 97520, USA
| | - S Vanden Abeele
- School of Integrative Plant Science, Section of Plant Biology and the L.H.Bailey Hortorium, Cornell University, Ithaca, NY, USA
| | - K Lievens
- Service of Wood Biology, Royal Museum for Central Africa (RMCA), Leuvensesteensweg 13, 3080, Tervuren, Belgium
| | - E Espinoza
- U.S. Fish and Wildlife Forensic Laboratory, 1490 East Main Street, Ashland, OR, 97520, USA
| | - H Beeckman
- Service of Wood Biology, Royal Museum for Central Africa (RMCA), Leuvensesteensweg 13, 3080, Tervuren, Belgium
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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40
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Skalický T, Alves JMP, Morais AC, Režnarová J, Butenko A, Lukeš J, Serrano MG, Buck GA, Teixeira MMG, Camargo EP, Sanders M, Cotton JA, Yurchenko V, Kostygov AY. Endosymbiont Capture, a Repeated Process of Endosymbiont Transfer with Replacement in Trypanosomatids Angomonas spp. Pathogens 2021; 10:pathogens10060702. [PMID: 34200026 PMCID: PMC8229890 DOI: 10.3390/pathogens10060702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Trypanosomatids of the subfamily Strigomonadinae bear permanent intracellular bacterial symbionts acquired by the common ancestor of these flagellates. However, the cospeciation pattern inherent to such relationships was revealed to be broken upon the description of Angomonas ambiguus, which is sister to A. desouzai, but bears an endosymbiont genetically close to that of A. deanei. Based on phylogenetic inferences, it was proposed that the bacterium from A. deanei had been horizontally transferred to A. ambiguus. Here, we sequenced the bacterial genomes from two A. ambiguus isolates, including a new one from Papua New Guinea, and compared them with the published genome of the A. deanei endosymbiont, revealing differences below the interspecific level. Our phylogenetic analyses confirmed that the endosymbionts of A. ambiguus were obtained from A. deanei and, in addition, demonstrated that this occurred more than once. We propose that coinfection of the same blowfly host and the phylogenetic relatedness of the trypanosomatids facilitate such transitions, whereas the drastic difference in the occurrence of the two trypanosomatid species determines the observed direction of this process. This phenomenon is analogous to organelle (mitochondrion/plastid) capture described in multicellular organisms and, thereafter, we name it endosymbiont capture.
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Affiliation(s)
- Tomáš Skalický
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; (T.S.); (A.B.); (J.L.)
| | - João M. P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (J.M.P.A.); (A.C.M.); (M.M.G.T.); (E.P.C.)
| | - Anderson C. Morais
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (J.M.P.A.); (A.C.M.); (M.M.G.T.); (E.P.C.)
| | - Jana Režnarová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (J.R.); (V.Y.)
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; (T.S.); (A.B.); (J.L.)
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (J.R.); (V.Y.)
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; (T.S.); (A.B.); (J.L.)
- Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Myrna G. Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298-0678, USA; (M.G.S.); (G.A.B.)
| | - Gregory A. Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298-0678, USA; (M.G.S.); (G.A.B.)
| | - Marta M. G. Teixeira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (J.M.P.A.); (A.C.M.); (M.M.G.T.); (E.P.C.)
| | - Erney P. Camargo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (J.M.P.A.); (A.C.M.); (M.M.G.T.); (E.P.C.)
| | - Mandy Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; (M.S.); (J.A.C.)
| | - James A. Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; (M.S.); (J.A.C.)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (J.R.); (V.Y.)
- Martsinovsky Institute of Medical Parasitology, Sechenov University, 119435 Moscow, Russia
| | - Alexei Y. Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (J.R.); (V.Y.)
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
- Correspondence:
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Yousef AF, Ali MM, Rizwan HM, Gad AG, Liang D, Binqi L, Kalaji HM, Wróbel J, Xu Y, Chen F. Light quality and quantity affect graft union formation of tomato plants. Sci Rep 2021; 11:9870. [PMID: 33972562 PMCID: PMC8110817 DOI: 10.1038/s41598-021-88971-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
It is already known that there are many factors responsible for the successful formation of a graft union. However, the role of light has been little studied. In an anatomical study, Scanning Electronic Microscope (SEM) was used to explore the effects of different light-emitting diodes (LEDs) on graft union formation in grafted tomato. In addition, the expression genes related to Auxin hormone signaling pathway (SAUR67, AUX1, ARF30, and LAX3) was investigated. The obtained results showed that the concrescence process occurred faster under R7:B3 light conditions, as compared to blue (B) and white fluorescent (WFL) lights. Red light application caused a delay in the vascular tissue differentiation, which may lead to callus development on both sides, causing junctional failure and resulting in ineffective graft junctional arrangement. The expression of genes related to Auxin hormone significantly increased by R7:B3 application. We suggest that LED spectra affects the graft development of tomato plants and can improve the performance of grafted tomato seedlings.
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Affiliation(s)
- Ahmed Fathy Yousef
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Department of Horticulture, College of Agriculture, University of Al-Azhar (Branch Assiut), Assiut, 71524, Egypt
| | - Muhammad Moaaz Ali
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hafiz Muhammad Rizwan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ahmed Gomaa Gad
- Plant Pathology Department, Faculty of Agriculture, Alexandria University, El-Shatby, Alexandria, 21545, Egypt
| | - Dangdi Liang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li Binqi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hazem M Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw, University of Life Sciences SGGW, 159 Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Jacek Wróbel
- Department of Bioengineering, West Pomeranian University of Technology in Szczecin, 17 Słowackiego Street, 71-434, Szczecin, Poland
| | - Yong Xu
- College of Mechanical and Electronic Engineering, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Institute of Machine Learning and Intelligent Science, Fujian University of Technology, 33 Xuefu South Road, Fuzhou, 350118, China.
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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42
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Rascón-Cruz Q, González-Barriga CD, Iglesias-Figueroa BF, Trejo-Muñoz JC, Siqueiros-Cendón T, Sinagawa-García SR, Arévalo-Gallegos S, Espinoza-Sánchez EA. Plastid transformation: Advances and challenges for its implementation in agricultural crops. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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43
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Yang Y, Zhou T, Qian Z, Zhao G. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing. Genomics 2021; 113:1438-1447. [PMID: 33744343 DOI: 10.1016/j.ygeno.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 01/29/2023]
Abstract
China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree supported Quercus section Ilex as not monophyletic, in which Quercus section Cyclobalanopsis and Quercus section Cerris were nested. Most likely, incomplete lineage sorting and/or introgression among ancestral lineages in these three sections resulted in this complex pattern. The current distribution, diversification and molecular differentiation of Q. sect. Ilex in China are likely consequences of local adaptation to the geographic and paleoclimatic changes, which were driven by the uplift of Tibetan Plateau, the Hengduan Mountains and the Himalayas.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China; School of Biological Science and Technology, Baotou Teachers' College, Baotou, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zengqiang Qian
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.
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Enfissi EMA, Drapal M, Perez-Fons L, Nogueira M, Berry HM, Almeida J, Fraser PD. New plant breeding techniques and their regulatory implications: An opportunity to advance metabolomics approaches. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153378. [PMID: 33631493 DOI: 10.1016/j.jplph.2021.153378] [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: 11/14/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 05/21/2023]
Abstract
Over the previous decades, biotechnological innovations have led to improved agricultural productivity, more nutritious foods and lower chemical usage. Both in western societies and Low Medium Income Countries (LMICs). However, the projected increases in the global population, means the production of nutritious food stuffs must increase dramatically. Building on existing genetic modification technologies a series of New Plant Breeding Technologies (NPBT) has recently emerged. These approaches include, Agro-infiltration, grafting, cis and intragenesis and gene editing technologies. How these new techniques should be regulated has fostered considerable debate. Concerns have also been raised, to ensure over-regulation does not arise, creating administrative and economic burden. In this article the existing landscape of genetically modified crops is reviewed and the potential of several New Plant Breeding Techniques (NPBT) described. Metabolomics is an omic technology that has developed in a concurrent manner with biotechnological advances in plant breeding. There is potentially further opportunities to advance our metabolomic technologies to characterise the outputs of New Plant Breeding Technologies, in a manner that is beneficial both from an academic, biosafety and industrial perspective.
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Affiliation(s)
- Eugenia M A Enfissi
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Margit Drapal
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Laura Perez-Fons
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Marilise Nogueira
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Harriet M Berry
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Juliana Almeida
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Paul D Fraser
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom.
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Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, Manickam S, Sasirat S, Nikolov LA, Mathews S, Sackton TB, Davis CC. Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae). Curr Biol 2021; 31:1002-1011.e9. [DOI: 10.1016/j.cub.2020.12.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022]
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46
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Kapazoglou A, Tani E, Avramidou EV, Abraham EM, Gerakari M, Megariti S, Doupis G, Doulis AG. Epigenetic Changes and Transcriptional Reprogramming Upon Woody Plant Grafting for Crop Sustainability in a Changing Environment. FRONTIERS IN PLANT SCIENCE 2021; 11:613004. [PMID: 33510757 PMCID: PMC7835530 DOI: 10.3389/fpls.2020.613004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/10/2020] [Indexed: 05/07/2023]
Abstract
Plant grafting is an ancient agricultural practice widely employed in crops such as woody fruit trees, grapes, and vegetables, in order to improve plant performance. Successful grafting requires the interaction of compatible scion and rootstock genotypes. This involves an intricate network of molecular mechanisms operating at the graft junction and associated with the development and the physiology of the scion, ultimately leading to improved agricultural characteristics such as fruit quality and increased tolerance/resistance to abiotic and biotic factors. Bidirectional transfer of molecular signals such as hormones, nutrients, proteins, and nucleic acids from the rootstock to the scion and vice versa have been well documented. In recent years, studies on rootstock-scion interactions have proposed the existence of an epigenetic component in grafting reactions. Epigenetic changes such as DNA methylation, histone modification, and the action of small RNA molecules are known to modulate chromatin architecture, leading to gene expression changes and impacting cellular function. Mobile small RNAs (siRNAs) migrating across the graft union from the rootstock to the scion and vice versa mediate modifications in the DNA methylation pattern of the recipient partner, leading to altered chromatin structure and transcriptional reprogramming. Moreover, graft-induced DNA methylation changes and gene expression shifts in the scion have been associated with variations in graft performance. If these changes are heritable they can lead to stably altered phenotypes and affect important agricultural traits, making grafting an alternative to breeding for the production of superior plants with improved traits. However, most reviews on the molecular mechanisms underlying this process comprise studies related to vegetable grafting. In this review we will provide a comprehensive presentation of the current knowledge on the epigenetic changes and transcriptional reprogramming associated with the rootstock-scion interaction focusing on woody plant species, including the recent findings arising from the employment of advanced-omics technologies as well as transgrafting methodologies and their potential exploitation for generating superior quality grafts in woody species. Furthermore, will discuss graft-induced heritable epigenetic changes leading to novel plant phenotypes and their implication to woody crop improvement for yield, quality, and stress resilience, within the context of climate change.
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Affiliation(s)
- Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-Demeter (HAO-Demeter), Athens, Greece
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Athens, Hellenic Agricultural Organization-Demeter (HAO-Demeter), Athens, Greece
| | - Eleni M. Abraham
- Laboratory of Range Science, Faculty of Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Stamatia Megariti
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Georgios Doupis
- Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Sub-Tropical Crops and Viticulture, Hellenic Agricultural Organization-Demeter (HAO-Demeter) (fr. NAGREF), Heraklion, Greece
| | - Andreas G. Doulis
- Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Sub-Tropical Crops and Viticulture, Hellenic Agricultural Organization-Demeter (HAO-Demeter) (fr. NAGREF), Heraklion, Greece
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Tsaballa A, Xanthopoulou A, Madesis P, Tsaftaris A, Nianiou-Obeidat I. Vegetable Grafting From a Molecular Point of View: The Involvement of Epigenetics in Rootstock-Scion Interactions. FRONTIERS IN PLANT SCIENCE 2021; 11:621999. [PMID: 33488662 PMCID: PMC7817540 DOI: 10.3389/fpls.2020.621999] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/07/2020] [Indexed: 05/25/2023]
Abstract
Vegetable grafting is extensively used today in agricultural production to control soil-borne pathogens, abiotic and biotic stresses and to improve phenotypic characteristics of the scion. Commercial vegetable grafting is currently practiced in tomato, watermelon, melon, eggplant, cucumber, and pepper. It is also regarded as a rapid alternative to the relatively slow approach of breeding for increased environmental-stress tolerance of fruit vegetables. However, even though grafting has been used for centuries, until today, there are still many issues that have not been elucidated. This review will emphasize on the important mechanisms taking place during grafting, especially the genomic interactions between grafting partners and the impact of rootstocks in scion's performance. Special emphasis will be drawn on the relation between vegetable grafting, epigenetics, and the changes in morphology and quality of the products. Recent advances in plant science such as next-generation sequencing provide new information regarding the molecular interactions between rootstock and scion. It is now evidenced that genetic exchange is happening across grafting junctions between rootstock and scion, potentially affecting grafting-mediated effects already recorded in grafted plants. Furthermore, significant changes in DNA methylation are recorded in grafted scions, suggesting that these epigenetic mechanisms could be implicated in grafting effects. In this aspect, we also discuss the process and the molecular aspects of rootstock scion communication. Finally, we provide with an extensive overview of gene expression changes recorded in grafted plants and how these are related to the phenotypic changes observed. Τhis review finally seeks to elucidate the dynamics of rootstock-scion interactions and thus stimulate more research on grafting in the future. In a future where sustainable agricultural production is the way forward, grafting could play an important role to develop products of higher yield and quality in a safe and "green" way.
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Affiliation(s)
- Aphrodite Tsaballa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO-Dimitra), Thessaloniki, Greece
| | - Aliki Xanthopoulou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO-Dimitra), Thessaloniki, Greece
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, Volos, Greece
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Athanasios Tsaftaris
- Perrotis College, American Farm School, Thessaloniki, Greece
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
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48
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Hertle AP, Haberl B, Bock R. Horizontal genome transfer by cell-to-cell travel of whole organelles. SCIENCE ADVANCES 2021; 7:7/1/eabd8215. [PMID: 33523859 PMCID: PMC7775762 DOI: 10.1126/sciadv.abd8215] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 05/10/2023]
Abstract
Recent work has revealed that both plants and animals transfer genomes between cells. In plants, horizontal transfer of entire plastid, mitochondrial, or nuclear genomes between species generates new combinations of nuclear and organellar genomes, or produces novel species that are allopolyploid. The mechanisms of genome transfer between cells are unknown. Here, we used grafting to identify the mechanisms involved in plastid genome transfer from plant to plant. We show that during proliferation of wound-induced callus, plastids dedifferentiate into small, highly motile, amoeboid organelles. Simultaneously, new intercellular connections emerge by localized cell wall disintegration, forming connective pores through which amoeboid plastids move into neighboring cells. Our work uncovers a pathway of organelle movement from cell to cell and provides a mechanistic framework for horizontal genome transfer.
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Affiliation(s)
- Alexander P Hertle
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Benedikt Haberl
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany.
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49
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Bartusch K, Melnyk CW. Insights Into Plant Surgery: An Overview of the Multiple Grafting Techniques for Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:613442. [PMID: 33362838 PMCID: PMC7758207 DOI: 10.3389/fpls.2020.613442] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/20/2020] [Indexed: 05/28/2023]
Abstract
Plant grafting, the ancient practice of cutting and joining different plants, is gaining popularity as an elegant way to generate chimeras that combine desirable traits. Grafting was originally developed in woody species, but the technique has evolved over the past century to now encompass a large number of herbaceous species. The use of plant grafting in science is accelerating in part due to the innovative techniques developed for the model plant Arabidopsis thaliana. Here, we review these developments and discuss the advantages and limitations associated with grafting various Arabidopsis tissues at diverse developmental stages.
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Affiliation(s)
- Kai Bartusch
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Zurich, Switzerland
| | - Charles W. Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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50
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Horizontal Gene Transfer in Eukaryotes: Not if, but How Much? Trends Genet 2020; 36:915-925. [DOI: 10.1016/j.tig.2020.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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