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Potente G, Yousefi N, Keller B, Mora-Carrera E, Szövényi P, Conti E. The Primula edelbergii S-locus is an example of a jumping supergene. Mol Ecol Resour 2024; 24:e13988. [PMID: 38946153 DOI: 10.1111/1755-0998.13988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/24/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Research on supergenes, non-recombining genomic regions housing tightly linked genes that control complex phenotypes, has recently gained prominence in genomics. Heterostyly, a floral heteromorphism promoting outcrossing in several angiosperm families, is controlled by the S-locus supergene. The S-locus has been studied primarily in closely related Primula species and, more recently, in other groups that independently evolved heterostyly. However, it remains unknown whether genetic architecture and composition of the S-locus are maintained among species that share a common origin of heterostyly and subsequently diverged across larger time scales. To address this research gap, we present a chromosome-scale genome assembly of Primula edelbergii, a species that shares the same origin of heterostyly with Primula veris (whose S-locus has been characterized) but diverged from it 18 million years ago. Comparative genomic analyses between these two species allowed us to show, for the first time, that the S-locus can 'jump' (i.e. translocate) between chromosomes maintaining its function in controlling heterostyly. Additionally, we found that four S-locus genes were conserved but reshuffled within the supergene, seemingly without affecting their expression, thus we could not detect changes explaining the lack of self-incompatibility in P. edelbergii. Furthermore, we confirmed that the S-locus is not undergoing genetic degeneration. Finally, we investigated P. edelbergii evolutionary history within Ericales in terms of whole genome duplications and transposable element accumulation. In summary, our work provides a valuable resource for comparative analyses aimed at investigating the genetics of heterostyly and the pivotal role of supergenes in shaping the evolution of complex phenotypes.
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Affiliation(s)
- Giacomo Potente
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Emiliano Mora-Carrera
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
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Xie L, Gong X, Yang K, Huang Y, Zhang S, Shen L, Sun Y, Wu D, Ye C, Zhu QH, Fan L. Technology-enabled great leap in deciphering plant genomes. NATURE PLANTS 2024; 10:551-566. [PMID: 38509222 DOI: 10.1038/s41477-024-01655-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.
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Affiliation(s)
- Lingjuan Xie
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
| | - Xiaojiao Gong
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Kun Yang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Yujie Huang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Shiyu Zhang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Leti Shen
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
| | - Yanqing Sun
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China.
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Attikora AJP, Silué S, Yao SDM, De Clerck C, Shumbe L, Diarrassouba N, Fofana IJ, Alabi T, Lassois L. An innovative optimized protocol for high-quality genomic DNA extraction from recalcitrant Shea tree (Vitellaria paradoxa, C.F. Gaertn) plant and its suitability for downstream applications. Mol Biol Rep 2024; 51:171. [PMID: 38252378 DOI: 10.1007/s11033-023-09098-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND It is not always easy to find a universal protocol for the extraction of genomic DNA (gDNA) from plants. Extraction of gDNA from plants such as shea with a lot of polysaccharides in their leaves is done in two steps: a first step to remove the polysaccharides and a second step for the extraction of the gDNA. In this work, we designed a protocol for extracting high-quality gDNA from shea tree and demonstrate its suitability for downstream molecular applications. METHODS Fifty milligrams of leaf and root tissues were used to test the efficiency of our protocol. The quantity of gDNA was measured with the NanoDrop spectrometer and the quality was checked on agarose gel. Its suitability for use in downstream applications was tested with restriction enzymes, SSRs and RAPD polymerase chain reactions and Sanger sequencing. RESULTS The average yield of gDNA was 5.17; 3.96; 2.71 and 2.41 µg for dry leaves, dry roots, fresh leaves and fresh roots respectively per 100 mg of tissue. Variance analysis of the yield showed significant difference between all tissue types. Leaf gDNA quality was better compared to root gDNA at the absorbance ratio A260/280 and A260/230. The minimum amplifiable concentration of leaf gDNA was 1 pg/µl while root gDNA remained amplifiable at 10 pg/µl. Genomic DNA obtained was also suitable for sequencing. CONCLUSION This protocol provides an efficient, convenient and cost effective DNA extraction method suitable for use in various vitellaria paradoxa genomic studies.
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Affiliation(s)
- Affi Jean Paul Attikora
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium.
| | - Souleymane Silué
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Saraka Didier Martial Yao
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro Bio-Tech, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Leonard Shumbe
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Nafan Diarrassouba
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Inza Jésus Fofana
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Taofic Alabi
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
- Functional and Evolutive Entomology, Gembloux Agro Bio-Tech, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Ludivine Lassois
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
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Tchokponhoué DA, Achigan-Dako EG, Sognigbé N, Nyadanu D, Hale I, Odindo AO, Sibiya J. Genome-wide diversity analysis suggests divergence among Upper Guinea and the Dahomey Gap populations of the Sisrè berry (Syn: miracle fruit) plant (Synsepalum dulcificum [Schumach. & Thonn.] Daniell) in West Africa. THE PLANT GENOME 2023; 16:e20299. [PMID: 36661287 DOI: 10.1002/tpg2.20299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 11/20/2022] [Indexed: 05/10/2023]
Abstract
Although Synsepalum dulcificum is viewed as one of the most economically promising orphan tree crops worldwide, its genetic improvement and sustainable conservation are hindered by a lack of understanding of its evolutionary history and current population structure. Here, we report for the first time the application of genome-wide single nucleotide polymorphism genotyping to a diverse panel of S. dulcificum accessions to depict the genetic diversity and population structure of the species in the Dahomey Gap (DG) and Upper Guinea (UG) regions to infer its evolutionary history. Our findings suggest low overall genetic diversity but strong population divergence within the species. Neighbor-joining analysis detected two genetic groups in the UG and DG regions, while STRUCTURE distinguished three genetic groups, corresponding to the UG, Western DG, and Central DG regions. Application of Monmonier's algorithm revealed the existence of a barrier disrupting connectivity between the UG and DG groups. The Western DG group consistently exhibited the highest levels of nucleotide and haplotype diversities, while that of the Central DG exhibited the lowest. Analyses of Tajima's D, Fu's Fs, and Achaz Y* statistics suggest that while both UG and Central DG groups likely experienced recent expansions, the Western DG group is at equilibrium. These findings suggest a geographical structuring of genetic variation which supports the conclusion of differential evolutionary histories among West African groups of S. dulcificum. These results provide foundational insights to guide informed breeding population development and design sustainable conservation strategies for this species.
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Affiliation(s)
- Dèdéou A Tchokponhoué
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - Enoch G Achigan-Dako
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - N'Danikou Sognigbé
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
- Ecole d'Horticulture et d'Aménagement des Espaces Verts, Université Nationale d'Agriculture, Kétou, Republic of Benin
- World Vegetable Center, East and Southern Africa, Arusha, Tanzania
| | - Daniel Nyadanu
- Cocoa Research Institute of Ghana (CRIG), Akim Tafo, Ghana
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - Alfred O Odindo
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Julia Sibiya
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Zhang T, Zhou J, Gao W, Jia Y, Wei Y, Wang G. Complex genome assembly based on long-read sequencing. Brief Bioinform 2022; 23:6657663. [PMID: 35940845 DOI: 10.1093/bib/bbac305] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/20/2022] [Accepted: 07/06/2022] [Indexed: 11/12/2022] Open
Abstract
High-quality genome chromosome-scale sequences provide an important basis for genomics downstream analysis, especially the construction of haplotype-resolved and complete genomes, which plays a key role in genome annotation, mutation detection, evolutionary analysis, gene function research, comparative genomics and other aspects. However, genome-wide short-read sequencing is difficult to produce a complete genome in the face of a complex genome with high duplication and multiple heterozygosity. The emergence of long-read sequencing technology has greatly improved the integrity of complex genome assembly. We review a variety of computational methods for complex genome assembly and describe in detail the theories, innovations and shortcomings of collapsed, semi-collapsed and uncollapsed assemblers based on long reads. Among the three methods, uncollapsed assembly is the most correct and complete way to represent genomes. In addition, genome assembly is closely related to haplotype reconstruction, that is uncollapsed assembly realizes haplotype reconstruction, and haplotype reconstruction promotes uncollapsed assembly. We hope that gapless, telomere-to-telomere and accurate assembly of complex genomes can be truly routinely achieved using only a simple process or a single tool in the future.
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Affiliation(s)
- Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Jie Zhou
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Wentao Gao
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yuran Jia
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yanan Wei
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
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