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Sloan DB, Conover JL, Grover CE, Wendel JF, Sharbrough J. Polyploid plants take cytonuclear perturbations in stride. THE PLANT CELL 2024; 36:829-839. [PMID: 38267606 PMCID: PMC10980399 DOI: 10.1093/plcell/koae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/26/2024]
Abstract
Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and organellar (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived organellar genomes and the half of the allopolyploid nuclear genome from the paternal progenitor. Several evolutionary responses have been predicted to ameliorate these effects, including selection for changes in protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal nuclear gene copies; and fine-tuning of relative cytonuclear genome copy numbers and expression levels. Numerous recent studies, however, have found that evolutionary responses are inconsistent and rarely scale to genome-wide generalities. The apparent robustness of plant cytonuclear interactions to allopolyploidy may reflect features that are general to allopolyploids such as the lack of F2 hybrid breakdown under disomic inheritance, and others that are more plant-specific, including slow sequence divergence in organellar genomes and preexisting regulatory responses to changes in cell size and endopolyploidy during development. Thus, cytonuclear interactions may only rarely act as the main barrier to establishment of allopolyploid lineages, perhaps helping to explain why allopolyploidy is so pervasive in plant evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University,
Fort Collins, CO, USA
| | - Justin L Conover
- Department of Ecology and Evolutionary Biology, University of
Arizona, Tucson, AZ, USA
- Department of Molecular and Cellular Biology, University of
Arizona, Tucson, AZ, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and
Technology, Socorro, NM, USA
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Farhat P, Mandáková T, Divíšek J, Kudoh H, German DA, Lysak MA. The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella. FRONTIERS IN PLANT SCIENCE 2023; 14:1165140. [PMID: 37223809 PMCID: PMC10200890 DOI: 10.3389/fpls.2023.1165140] [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: 02/13/2023] [Accepted: 04/04/2023] [Indexed: 05/25/2023]
Abstract
The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genus Capsella has become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genus Catolobus is native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability of Catolobus pendulus throughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that the Catolobus genome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK, n = 8). In contrast to the much younger Capsella allotetraploid genomes, the presumably autotetraploid Catolobus genome (2n = 32) arose early after the Catolobus/Capsella divergence. Since its origin, the tetraploid Catolobus genome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n = 32 to 2n = 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploid Catolobus cytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship between Catolobus and Capsella allows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.
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Affiliation(s)
- Perla Farhat
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Divíšek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Dmitry A. German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Russia
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
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Huang F, Chen P, Tang X, Zhong T, Yang T, Nwafor CC, Yang C, Ge X, An H, Li Z, Cahoon EB, Zhang C. Genome assembly of the Brassicaceae diploid Orychophragmus violaceus reveals complex whole-genome duplication and evolution of dihydroxy fatty acid metabolism. PLANT COMMUNICATIONS 2023; 4:100432. [PMID: 36071666 PMCID: PMC10030321 DOI: 10.1016/j.xplc.2022.100432] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/27/2022] [Accepted: 09/05/2022] [Indexed: 05/04/2023]
Abstract
Orychophragmus violaceus is a Brassicaceae species widely cultivated in China, particularly as a winter cover crop in northern China because of its low-temperature tolerance and low water demand. Recently, O. violaceus has also been cultivated as a potential industrial oilseed crop because of its abundant 24-carbon dihydroxy fatty acids (diOH-FAs), which contribute to superior high-temperature lubricant properties. In this study, we performed de novo assembly of the O. violaceus genome. Whole-genome synteny analysis of the genomes of its relatives demonstrated that O. violaceus is a diploid that has undergone an extra whole-genome duplication (WGD) after the Brassicaceae-specific α-WGD event, with a basic chromosome number of x = 12. Formation of diOH-FAs is hypothesized to have occurred after the WGD event. Based on the genome and the transcriptome data from multiple stages of seed development, we predicted that OvDGAT1-1 and OvDGAT1-2 are candidate genes for the regulation of diOH-FA storage in O. violaceus seeds. These results may greatly facilitate the development of heat-tolerant and eco-friendly plant-based lubricants using O. violaceus seed oil and improve our understanding of the genomic evolution of Brassicaceae.
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Affiliation(s)
- Fan Huang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Peng Chen
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Tang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ting Zhong
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Taihua Yang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chinedu Charles Nwafor
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chao Yang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianhong Ge
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri-Columbia, Columbia, MO, USA
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Edgar B Cahoon
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Chunyu Zhang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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