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Campos M, Pérez-Collazos E, Díaz-Pérez A, López-Alvarez D, Oumouloud A, Mur LAJ, Vogel JP, Catalán P. Repeated migration, interbreeding and bottlenecking shaped the phylogeography of the selfing grass Brachypodium stacei. Mol Ecol 2024:e17513. [PMID: 39188107 DOI: 10.1111/mec.17513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 07/24/2024] [Accepted: 08/13/2024] [Indexed: 08/28/2024]
Abstract
Brachypodium stacei is the most ancestral lineage in the genus Brachypodium, a model system for grass functional genomics. B. stacei shows striking and sometimes contradictory biological and evolutionary features, including a high selfing rate yet extensive admixture, an ancient Miocene origin yet with recent evolutionary radiation, and adaptation to different dry climate conditions in its narrow distribution range. Therefore, it constitutes an ideal system to study these life history traits. We studied the phylogeography of 17 native circum-Mediterranean B. stacei populations (39 individuals) using genome-wide RADseq SNP data and complete plastome sequences. Nuclear SNP data revealed the existence of six distinct genetic clusters, low levels of intra-population genetic diversity and high selfing rates, albeit with signatures of admixture. Coalescence-based dating analysis detected a recent split between crown lineages in the Late Quaternary. Plastome sequences showed incongruent evolutionary relationships with those recovered by the nuclear data, suggesting interbreeding and chloroplast capture events between genetically distant populations. Demographic and population dispersal coalescent models identified an ancestral origin of B. stacei in the western-central Mediterranean islands, followed by an early colonization of the Canary Islands and two independent colonization events of the eastern Mediterranean region through long-distance dispersal and bottleneck events as the most likely evolutionary history. Climate niche data identified three arid niches of B. stacei in the southern Mediterranean region. Our findings indicate that the phylogeography of B. stacei populations was shaped by recent radiations, frequent extinctions, long-distance dispersal events, occasional interbreeding, and adaptation to local climates.
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Affiliation(s)
- Miguel Campos
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Ernesto Pérez-Collazos
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Antonio Díaz-Pérez
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- GESPLAN S.A. C, Las Palmas de Gran Canaria, Spain
- Instituto de Genética, Facultad de Agronomía, Universidad Central de Venezuela, Maracay, Venezuela
| | - Diana López-Alvarez
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Facultad de Ciencias Agropecuarias, Departamento de Ciencias Biológicas, Universidad Nacional de Colombia, Palmira, Colombia
| | - Ali Oumouloud
- Institute Agronomique et Vétérinaire Hassan II, Agadir, Morocco
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - John P Vogel
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Pilar Catalán
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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Beringer M, Choudhury RR, Mandáková T, Grünig S, Poretti M, Leitch IJ, Lysak MA, Parisod C. Biased Retention of Environment-Responsive Genes Following Genome Fractionation. Mol Biol Evol 2024; 41:msae155. [PMID: 39073781 PMCID: PMC11306978 DOI: 10.1093/molbev/msae155] [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: 01/10/2024] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles.
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Affiliation(s)
- Marc Beringer
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Rimjhim Roy Choudhury
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Sandra Grünig
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Manuel Poretti
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | | | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Christian Parisod
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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3
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Chen BZ, Li DW, Luo KY, Jiu ST, Dong X, Wang WB, Li XZ, Hao TT, Lei YH, Guo DZ, Liu XT, Duan SC, Zhu YF, Chen W, Dong Y, Yu WB. Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales. FRONTIERS IN PLANT SCIENCE 2024; 15:1444234. [PMID: 39157518 PMCID: PMC11327160 DOI: 10.3389/fpls.2024.1444234] [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: 06/05/2024] [Accepted: 07/16/2024] [Indexed: 08/20/2024]
Abstract
Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing a significant role in the cultivation of horticultural, ornamental, and medicinal plant varieties. Whole-genome duplication (WGD) and its subsequent post-polyploid diploidization (PPD) process represent the most drastic type of karyotype evolution, injecting significant potential for promoting the diversity of this lineage. However, polyploidization histories, as well as genome and subgenome fractionation following WGD events in Lamiales species, are still not well investigated. In this study, we constructed a chromosome-level genome assembly of Lindenbergia philippensis (Orobanchaceae) and conducted comparative genomic analyses with 14 other Lamiales species. L. philippensis is positioned closest to the parasitic lineage within Orobanchaceae and has a conserved karyotype. Through a combination of Ks analysis and syntenic depth analysis, we reconstructed and validated polyploidization histories of Lamiales species. Our results indicated that Primulina huaijiensis underwent three rounds of diploidization events following the γ-WGT event, rather than two rounds as reported. Besides, we reconfirmed that most Lamiales species shared a common diploidization event (L-WGD). Subsequently, we constructed the Lamiales Ancestral Karyotype (LAK), comprising 11 proto-chromosomes, and elucidated its evolutionary trajectory, highlighting the highly flexible reshuffling of the Lamiales paleogenome. We identified biased fractionation of subgenomes following the L-WGD event across eight species, and highlighted the positive impacts of non-WGD genes on gene family expansion. This study provides novel genomic resources and insights into polyploidy and karyotype remodeling of Lamiales species, essential for advancing our understanding of species diversification and genome evolution.
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Affiliation(s)
- Bao-Zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Da-Wei Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Kai-Yong Luo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Song-Tao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wei-Bin Wang
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xu-Zhen Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ting-Ting Hao
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ya-Hui Lei
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Da-Zhong Guo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xu-Tao Liu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sheng-Chang Duan
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yi-Fan Zhu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wei Chen
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yang Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wen-Bin Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, China
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4
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Feng K, Walker JF, Marx HE, Yang Y, Brockington SF, Moore MJ, Rabeler RK, Smith SA. The link between ancient whole-genome duplications and cold adaptations in the Caryophyllaceae. AMERICAN JOURNAL OF BOTANY 2024; 111:e16350. [PMID: 38825760 DOI: 10.1002/ajb2.16350] [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: 01/26/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024]
Abstract
PREMISE The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation, indicating that they may provide a natural system for cold adaptation research. Previous research has suggested that putative ancient whole-genome duplications (WGDs) are correlated with niche shifts into colder climates across the Caryophyllales. Here, we explored the genomic changes potentially involved in one of these discovered shifts in the Caryophyllaceae. METHODS We constructed a data set combining 26 newly generated transcriptomes with 45 published transcriptomes, including 11 cushion plant species across seven genera. With this data set, we inferred a dated phylogeny for the Caryophyllaceae and mapped ancient WGDs and gene duplications onto the phylogeny. We also examined functional groups enriched for gene duplications related to the climatic shift. RESULTS The ASTRAL topology was mostly congruent with the current consensus of relationships within the family. We inferred 15 putative ancient WGDs in the family, including eight that have not been previously published. The oldest ancient WGD (ca. 64.4-56.7 million years ago), WGD1, was found to be associated with a shift into colder climates by previous research. Gene regions associated with ubiquitination were overrepresented in gene duplications retained after WGD1 and those convergently retained by cushion plants in Colobanthus and Eremogone, along with other functional annotations. CONCLUSIONS Gene family expansions induced by ancient WGDs may have contributed to the shifts to cold climatic niches in the Caryophyllaceae. Transcriptomic data are crucial resources that help unravel heterogeneity in deep-time evolutionary patterns in plants.
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Affiliation(s)
- Keyi Feng
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Joseph F Walker
- Department of Biological Sciences, University of Illinois Chicago, Chicago, 60607, IL, USA
| | - Hannah E Marx
- Department of Biology, University of New Mexico, Albuquerque, 87131, NM, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, 55108, MN, USA
| | | | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, 44074, OH, USA
| | - Richard K Rabeler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
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5
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Hagen ER, Vasconcelos T, Boyko JD, Beaulieu JM. Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multiclade perspective. AMERICAN JOURNAL OF BOTANY 2024; 111:e16356. [PMID: 38867412 DOI: 10.1002/ajb2.16356] [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: 05/06/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
PREMISE The proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aimed to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assessed whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization). METHODS We reconstructed the ploidy states and ancestral niches of 1032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We used ancestral niche reconstruction models alongside a customized discrete character evolution model to allow reconstruction of states at specific time slices. Patterns of latitudinal movement were reconstructed and compared in relation to inferred ploidy shifts. RESULTS No single hypothesis applied equally well across all analyzed clades. While significant differences in median latitudinal occurrence were detected in the largest clade, Poaceae, no significant differences were detected in latitudinal movement in any clade. CONCLUSIONS Our preliminary study is the first to attempt to connect ploidy changes to continuous latitudinal movement, but we cannot favor one hypothesis over another. Given that patterns seem to be clade-specific, more clades must be analyzed in future studies for generalities to be drawn.
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Affiliation(s)
- Eric R Hagen
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, ON, Canada
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - James D Boyko
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
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6
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Jeon D, Kim C. Polyploids of Brassicaceae: Genomic Insights and Assembly Strategies. PLANTS (BASEL, SWITZERLAND) 2024; 13:2087. [PMID: 39124204 PMCID: PMC11314605 DOI: 10.3390/plants13152087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Abstract
The Brassicaceae family is distinguished by its inclusion of high-value crops such as cabbage, broccoli, mustard, and wasabi, all noted for their glucosinolates. In this family, many polyploidy species are distributed and shaped by numerous whole-genome duplications, independent genome doublings, and hybridization events. The evolutionary trajectory of the family is marked by enhanced diversification and lineage splitting after paleo- and meso-polyploidization, with discernible remnants of whole-genome duplications within their genomes. The recent neopolyploidization events notably increased the proportion of polyploid species within the family. Although sequencing efforts for the Brassicaceae genome have been robust, accurately distinguishing sub-genomes remains a significant challenge, frequently complicating the assembly process. Assembly strategies include comparative analyses with ancestral species and examining k-mers, long terminal repeat retrotransposons, and pollen sequencing. This review comprehensively explores the unique genomic characteristics of the Brassicaceae family, with a particular emphasis on polyploidization events and the latest strategies for sequencing and assembly. This review will significantly improve our understanding of polyploidy in the Brassicaceae family and assist in future genome assembly methods.
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Affiliation(s)
- Donghyun Jeon
- Department of Science in Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Changsoo Kim
- Department of Science in Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea;
- Department of Crop Science, Chungnam National University, Daejeon 34134, Republic of Korea
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Beránková D, Čížková J, Majzlíková G, Doležalová A, Mduma H, Brown A, Swennen R, Hřibová E. Striking variation in chromosome structure within Musa acuminata subspecies, diploid cultivars, and F1 diploid hybrids. FRONTIERS IN PLANT SCIENCE 2024; 15:1387055. [PMID: 39027673 PMCID: PMC11255410 DOI: 10.3389/fpls.2024.1387055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024]
Abstract
The majority of cultivated bananas originated from inter- and intra(sub)specific crosses between two wild diploid species, Musa acuminata and Musa balbisiana. Hybridization and polyploidization events during the evolution of bananas led to the formation of clonally propagated cultivars characterized by a high level of genome heterozygosity and reduced fertility. The combination of low fertility in edible clones and differences in the chromosome structure among M. acuminata subspecies greatly hampers the breeding of improved banana cultivars. Using comparative oligo-painting, we investigated large chromosomal rearrangements in a set of wild M. acuminata subspecies and cultivars that originated from natural and human-made crosses. Additionally, we analyzed the chromosome structure of F1 progeny that resulted from crosses between Mchare bananas and the wild M. acuminata 'Calcutta 4' genotype. Analysis of chromosome structure within M. acuminata revealed the presence of a large number of chromosomal rearrangements showing a correlation with banana speciation. Chromosome painting of F1 hybrids was complemented by Illumina resequencing to identify the contribution of parental subgenomes to the diploid hybrid clones. The balanced presence of both parental genomes was revealed in all F1 hybrids, with the exception of one clone, which contained only Mchare-specific SNPs and thus most probably originated from an unreduced diploid gamete of Mchare.
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Affiliation(s)
- Denisa Beránková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Gabriela Majzlíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Alžběta Doležalová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Hassan Mduma
- International Institute of Tropical Agriculture, Banana Breeding, Arusha, Tanzania
| | - Allan Brown
- International Institute of Tropical Agriculture, Banana Breeding, Arusha, Tanzania
| | - Rony Swennen
- International Institute of Tropical Agriculture, Kampala, Uganda
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
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8
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Mandáková T, Krumpolcová A, Matyášek R, Volkov R, Lysak MA, Kovařík A. Uniparental silencing of 5S rRNA genes in plant allopolyploids - insights from Cardamine (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38838061 DOI: 10.1111/tpj.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/30/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
While the phenomenon of uniparental silencing of 35S rDNA in interspecific hybrids and allopolyploids is well documented, there is a notable absence of information regarding whether such silencing extends to the 5S RNA component of ribosomes. To address this gap in knowledge, we analyzed the 5S and 35S rDNA expression in Cardamine (Brassicaceae) allopolyploids, namely C. × insueta (2n = 3x = 24, genome composition RRA), C. flexuosa (2n = 4x = 32, AAHH), and C. scutata (2n = 4x = 32, PPAA) which share a common diploid ancestor (AA). We employed high-throughput sequencing of transcriptomes and genomes and phylogenetic analyses of 5S rRNA variants. The genomic organization of rDNA was further scrutinized through clustering and fluorescence in situ hybridization. In the C. × insueta allotriploid, we observed uniparental dominant expression of 5S and 35S rDNA loci. In the C. flexuosa and C. scutata allotetraploids, the expression pattern differed, with the 35S rDNA being expressed from the A subgenome, whereas the 5S rDNA was expressed from the partner subgenome. Both C. flexuosa and C. scutata but not C. × insueta showed copy and locus number changes. We conclude that in stabilized allopolyploids, transcription of ribosomal RNA components occurs from different subgenomes. This phenomenon appears to result in the formation of chimeric ribosomes comprising rRNA molecules derived from distinct parental origins. We speculate that the interplay of epigenetic silencing and rDNA rearrangements introduces an additional layer of variation in multimolecule ribosomal complexes, potentially contributing to the evolutionary success of allopolyploids.
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Affiliation(s)
- Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Alice Krumpolcová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
| | - Roman Matyášek
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
| | - Roman Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, 58012, Chernivtsi, Ukraine
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Ales Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
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9
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Reis Soares N, Costa ZP, Marques JPR, Garsmeur O, Sampaio Carneiro M, Monteiro Vitorello CB, D'Hont A, Vieira MLC. First investigation into the genetic control of meiosis in sugarcane. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2094-2107. [PMID: 38523577 DOI: 10.1111/tpj.16731] [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: 11/15/2023] [Revised: 01/28/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024]
Abstract
The sugarcane (Saccharum spp.) genome is one of the most complex of all. Modern varieties are highly polyploid and aneuploid as a result of hybridization between Saccharum officinarum and S. spontaneum. Little research has been done on meiotic control in polyploid species, with the exception of the wheat Ph1 locus harboring the ZIP4 gene (TaZIP4-B2) which promotes pairing between homologous chromosomes while suppressing crossover between homeologs. In sugarcane, despite its interspecific origin, bivalent association is favored, and multivalents, if any, are resolved at the end of prophase I. Thus, our aim herein was to investigate the purported genetic control of meiosis in the parental species and in sugarcane itself. We investigated the ZIP4 gene and immunolocalized meiotic proteins, namely synaptonemal complex proteins Zyp1 and Asy1. The sugarcane ZIP4 gene is located on chromosome 2 and expressed more abundantly in flowers, a similar profile to that found for TaZIP4-B2. ZIP4 expression is higher in S. spontaneum a neoautopolyploid, with lower expression in S. officinarum, a stable octoploid species. The sugarcane Zip4 protein contains a TPR domain, essential for scaffolding. Its 3D structure was also predicted, and it was found to be very similar to that of TaZIP4-B2, reflecting their functional relatedness. Immunolocalization of the Asy1 and Zyp1 proteins revealed that S. officinarum completes synapsis. However, in S. spontaneum and SP80-3280 (a modern variety), no nuclei with complete synapsis were observed. Importantly, our results have implications for sugarcane cytogenetics, genetic mapping, and genomics.
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Affiliation(s)
- Nina Reis Soares
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, São Paulo, Brazil
| | - Zirlane Portugal Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, São Paulo, Brazil
| | - João Paulo Rodrigues Marques
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, SP, 13635-900, Pirassununga, São Paulo, Brazil
| | - Olivier Garsmeur
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, 13604-900, Araras, São Paulo, Brazil
| | - Cláudia Barros Monteiro Vitorello
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, São Paulo, Brazil
| | - Angélique D'Hont
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, São Paulo, Brazil
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10
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Nicol DA, Saldivia P, Summerfield TC, Heads M, Lord JM, Khaing EP, Larcombe MJ. Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications. Mol Phylogenet Evol 2024; 195:108064. [PMID: 38508479 DOI: 10.1016/j.ympev.2024.108064] [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: 01/22/2024] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
The tribe Astereae (Asteraceae) includes 36 subtribes and 252 genera, and is distributed worldwide in temperate and tropical regions. One of the subtribes, Celmisiinae Saldivia, has been recently circumscribed to include six genera and ca. 160 species, and is restricted to eastern Australia, New Zealand, and New Guinea. The species show an impressive range of growth habit, from small herbs and ericoid subshrubs to medium-sized trees. They live in a wide range of habitats and are often dominant in subalpine and alpine vegetation. Despite the well-supported circumscription of Celmisiinae, uncertainties have remained about their internal relationships and classification at genus and species levels. This study exploited recent advances in high-throughput sequencing to build a robust multi-gene phylogeny for the subtribe Celmisiinae. The target enrichment Angiosperms353 bait set and the hybpiper-nf and paragone-nf pipelines were used to retrieve, infer, and assemble orthologous loci from 75 taxa representing all the main putative clades within the subtribe. Because of the diploidised ploidy level in Celmisiinae, as well as missing data in the assemblies, uncertainty remains surrounding the inference of orthology detection. However, based on a variety of gene-family sets, coalescent and concatenation-based phylogenetic reconstructions recovered similar topologies. Paralogy and missing data in the gene-families caused some problems, but the estimated phylogenies were well-supported and well-resolved. The phylogenomic evidence supported Celmisiinae and three main clades: the Pleurophyllum clade (Pleurophyllum, Macrolearia and Damnamenia), mostly in the New Zealand Subantarctic Islands, Celmisia of mainland New Zealand and Australia, and Shawia (including 'Olearia pro parte' and Pachystegia) of New Zealand, Australia and New Guinea. The results presented here add to the accumulating support for the Angiosperms353 bait set as an efficient method for documenting plant diversity.
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Affiliation(s)
- Duncan A Nicol
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand.
| | - Patricio Saldivia
- Biota Ltda. Av. Miguel Claro 1224, Providencia, Santiago, Chile; Museo Regional de Aysén, Km 3 Camino a Coyhaique Alto, Coyhaique, Chile
| | - Tina C Summerfield
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Michael Heads
- Buffalo Museum of Science, Buffalo, NY 14211-1293, USA
| | - Janice M Lord
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Ei P Khaing
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand
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11
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Puchta H. Regulation of gene-edited plants in Europe: from the valley of tears into the shining sun? ABIOTECH 2024; 5:231-238. [PMID: 38974871 PMCID: PMC11224193 DOI: 10.1007/s42994-023-00130-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 07/09/2024]
Abstract
Some 20 years ago, the EU introduced complex regulatory rules for the growth of transgenic crops, which resulted in a de facto ban to grow these plants in fields within most European countries. With the rise of novel genome editing technologies, it has become possible to improve crops genetically in a directed way without the need for incorporation of foreign genes. Unfortunately, in 2018, the European Court of Justice ruled that such gene-edited plants are to be regulated like transgenic plants. Since then, European scientists and breeders have challenged this decision and requested a revision of this outdated law. Finally, after 5 years, the European Commission has now published a proposal on how, in the future, to regulate crops produced by new breeding technologies. The proposal tries to find a balance between the different interest groups in Europe. On one side, genetically modified plants, which cannot be discerned from their natural counterparts, will exclusively be used for food and feed and are-besides a registration step-not to be regulated at all. On the other side, plants expressing herbicide resistance are to be excluded from this regulation, a concession to the strong environmental associations and NGOs in Europe. Moreover, edited crops are to be excluded from organic farming to protect the business interests of the strong organic sector in Europe. Nevertheless, if this law passes European parliament and council, unchanged, it will present a big step forward toward establishing a more sustainable European agricultural system. Thus, it might soon be possible to develop and grow crops that are more adapted to global warming and whose cultivation will require lower amounts of pesticides. However, there is still a long way to go until the law is passed. Too often, the storm of arguments raised by the opponents, based on irrational fears of mutations and a naive understanding of nature, has fallen on fruitful ground in Europe.
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Affiliation(s)
- Holger Puchta
- Department of Molecular Biology, Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
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12
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Gao M, Hua T, Niu G, Masabni J, Dewalt W. A locus-dependent mixed inheritance in the segmental allohexaploid sweetpotato ( Ipomoea batatas [L.] Lam). FRONTIERS IN PLANT SCIENCE 2024; 15:1398081. [PMID: 38863536 PMCID: PMC11165125 DOI: 10.3389/fpls.2024.1398081] [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: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024]
Abstract
Two interrelated aspects of the sweetpotato genome, its polyploid origin and inheritance type, remain uncertain. We recently proposed a segmental allohexaploid sweetpotato and thus sought to clarify its inheritance type by direct analyses of homoeolog segregations at selected single-copy loci. For such analyses, we developed a digital quantitative PCR genotyping method using one nondiscriminatory and three discriminatory probes for each selected locus to discriminate and quantify three homoeolog-differentiating variation types (homoeolog-types) in genomic DNA samples for genotype fitting and constructed a F2 population for segregation analyses. We confirmed inter-subgenomic distinctions of three identified homoeolog-types at each of five selected loci by their interspecific differentiations among 14 species in Ipomoea section batatas and genotyped the loci in 549 F2 lines, selected F1 progenies, and their founding parents. Segregation and genotype analyses revealed a locus-dependent mixed inheritance (disomic, polysomic, and intermediate types) of the homoeolog-types at 4 loci in the F2 population, displaying estimated disomic-inheritance frequencies of 0, 2.72%, 14.52%, and 36.92%, and probably in the F1 population too. There were also low-frequency non-hexaploid F1 and F2 genotypes that were probably derived from double-reduction recombination or partially unreduced gametes, and F2 genotypes of apparent aneuploids/dysploids with neopolyploid-like frequencies. Additional analyses of homoeolog-type genotypes at the 5 loci in 46 lines from various regions revealed locus-dependent selection biases, favoring genotypes having more of one homoeolog-type, i.e. more of di- or homogenized homoeolog-type composition, and one-direction ploidy trending among apparent aneuploids/dysploids. These inheritance features pointed to an evolving segmental allohexaploid sweetpotato impacted by selection biases.
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Affiliation(s)
- Ming Gao
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| | - Tien Hua
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| | - Genhua Niu
- AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States
| | - Joe Masabni
- AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States
| | - Willie Dewalt
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
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13
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Rurik I, Melichárková A, Gbúrová Štubová E, Kučera J, Kochjarová J, Paun O, Vďačný P, Slovák M. Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus Soldanella (Primulaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:753-765. [PMID: 38217489 DOI: 10.1111/tpj.16630] [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: 09/08/2023] [Revised: 12/02/2023] [Accepted: 12/27/2023] [Indexed: 01/15/2024]
Abstract
Specific ecological conditions in the high mountain environment exert a selective pressure that often leads to convergent trait evolution. Reticulations induced by incomplete lineage sorting and introgression can lead to discordant trait patterns among gene and species trees (hemiplasy/xenoplasy), providing a false illusion that the traits under study are homoplastic. Using phylogenetic species networks, we explored the effect of gene exchange on trait evolution in Soldanella, a genus profoundly influenced by historical introgression. At least three features evolved independently multiple times: the single-flowered dwarf phenotype, dysploid cytotype, and ecological generalism. The present analyses also indicated that the recurring occurrence of stoloniferous growth might have been prompted by an introgression event between an ancestral lineage and a still extant species, although its emergence via convergent evolution cannot be completely ruled out. Phylogenetic regression suggested that the independent evolution of larger genomes in snowbells is most likely a result of the interplay between hybridization events of dysploid and euploid taxa and hostile environments at the range margins of the genus. The emergence of key intrinsic and extrinsic traits in snowbells has been significantly impacted not only by convergent evolution but also by historical and recent introgression events.
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Affiliation(s)
- Ivan Rurik
- Department of Zoology, Comenius University Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Andrea Melichárková
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
| | - Eliška Gbúrová Štubová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
- Slovak National Museum, Natural History Museum, Vajanského nábrežie 2, 810 06, Bratislava, Slovak Republic
| | - Jaromír Kučera
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
| | - Judita Kochjarová
- Department of Phytology, Faculty of Forestry, Technical University Zvolen, Masarykova 24, 960 53, Zvolen, Slovak Republic
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Peter Vďačný
- Department of Zoology, Comenius University Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Marek Slovák
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
- Department of Botany, Charles University, Benátská 2, 128 01, Prague, Czech Republic
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14
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Booker WW, Schrider DR. The genetic consequences of range expansion and its influence on diploidization in polyploids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.18.562992. [PMID: 37905020 PMCID: PMC10614938 DOI: 10.1101/2023.10.18.562992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Despite newly formed polyploids being subjected to myriad fitness consequences, the relative prevalence of polyploidy both contemporarily and in ancestral branches of the tree of life suggests alternative advantages that outweigh these consequences. One proposed advantage is that polyploids may more easily colonize novel habitats such as deglaciated areas. However, previous research conducted in diploids suggests that range expansion comes with a fitness cost as deleterious mutations may fix rapidly on the expansion front. Here, we interrogate the potential consequences of expansion in polyploids by conducting spatially explicit forward-in-time simulations to investigate how ploidy and inheritance patterns impact the relative ability of polyploids to expand their range. We show that under realistic dominance models, autopolyploids suffer greater fitness reductions than diploids as a result of range expansion due to the fixation of increased mutational load that is masked in the range core. Alternatively, the disomic inheritance of allopolyploids provides a shield to this fixation resulting in minimal fitness consequences. In light of this advantage provided by disomy, we investigate how range expansion may influence cytogenetic diploidization through the reversion to disomy in autotetraploids. We show that under a wide range of parameters investigated for two models of diploidization, disomy frequently evolves more rapidly on the expansion front than in the range core, and that this dynamic inheritance model has additional effects on fitness. Together our results point to a complex interaction between dominance, ploidy, inheritance, and recombination on fitness as a population spreads across a geographic range.
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Affiliation(s)
- William W. Booker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27514-2916, United States of America
| | - Daniel R. Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27514-2916, United States of America
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15
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Bureš P, Elliott TL, Veselý P, Šmarda P, Forest F, Leitch IJ, Nic Lughadha E, Soto Gomez M, Pironon S, Brown MJM, Šmerda J, Zedek F. The global distribution of angiosperm genome size is shaped by climate. THE NEW PHYTOLOGIST 2024; 242:744-759. [PMID: 38264772 DOI: 10.1111/nph.19544] [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: 11/30/2022] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.
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Affiliation(s)
- Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | | | | | | | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, CB3 0DL, UK
| | | | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
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16
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Nieuwenhuis R, Hesselink T, van den Broeck HC, Cordewener J, Schijlen E, Bakker L, Diaz Trivino S, Struss D, de Hoop SJ, de Jong H, Peters SA. Genome architecture and genetic diversity of allopolyploid okra (Abelmoschus esculentus). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:225-241. [PMID: 38133904 DOI: 10.1111/tpj.16602] [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: 06/21/2023] [Revised: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The allopolyploid okra (Abelmoschus esculentus) unveiled telomeric repeats flanking distal gene-rich regions and short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation. Ribosomal RNA (rRNA) genes organize into 5S clusters, distinct from the 18S-5.8S-28S units, indicating an S-type rRNA gene arrangement. The assembly, in line with cytogenetic and cytometry observations, identifies 65 chromosomes and a 1.45 Gb genome size estimate in a haploid sibling. The lack of aberrant meiotic configurations implies limited to no recombination among sub-genomes. k-mer distribution analysis reveals 75% has a diploid nature and 15% heterozygosity. The configurations of Benchmarking Universal Single-Copy Ortholog (BUSCO), k-mer, and repeat clustering point to the presence of at least two sub-genomes one with 30 and the other with 35 chromosomes, indicating the allopolyploid nature of the okra genome. Over 130 000 putative genes, derived from mapped IsoSeq data and transcriptome data from public okra accessions, exhibit a low genetic diversity of one single nucleotide polymorphisms per 2.1 kbp. The genes are predominantly located at the distal chromosome ends, declining toward central scaffold domains. Long terminal repeat retrotransposons prevail in central domains, consistent with the observed pericentromeric heterochromatin and distal euchromatin. Disparities in paralogous gene counts suggest potential sub-genome differentiation implying possible sub-genome dominance. Amino acid query sequences of putative genes facilitated phenol biosynthesis pathway annotation. Comparison with manually curated reference KEGG pathways from related Malvaceae species reveals the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra.
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Affiliation(s)
- Ronald Nieuwenhuis
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Thamara Hesselink
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Hetty C van den Broeck
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan Cordewener
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Linda Bakker
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sara Diaz Trivino
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Darush Struss
- East-West International B.V., Heiligeweg 18, 1601 PN, Enkhuizen, The Netherlands
| | - Simon-Jan de Hoop
- East-West International B.V., Heiligeweg 18, 1601 PN, Enkhuizen, The Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sander A Peters
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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17
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Feng X, Chen Q, Wu W, Wang J, Li G, Xu S, Shao S, Liu M, Zhong C, Wu CI, Shi S, He Z. Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication. Nat Commun 2024; 15:1635. [PMID: 38388712 PMCID: PMC10884412 DOI: 10.1038/s41467-024-46080-7] [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: 08/01/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. To elucidate the role of ploidy changes in genome evolution, we improve a model of the polyploidization-rediploidization process based on genomic evidence, contributing to the understanding of adaptive evolution during climate change.
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Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Jiexin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Guohong Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), 571100, Haikou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
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18
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Katayama N, Yamamoto T, Aiuchi S, Watano Y, Fujiwara T. Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales). FRONTIERS IN PLANT SCIENCE 2024; 14:1286320. [PMID: 38264021 PMCID: PMC10803465 DOI: 10.3389/fpls.2023.1286320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern-Phegopteris decursivepinnata-and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.
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Affiliation(s)
- Natsu Katayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Takuya Yamamoto
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Sakura Aiuchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Tao Fujiwara
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
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Puchta H, Houben A. Plant chromosome engineering - past, present and future. THE NEW PHYTOLOGIST 2024; 241:541-552. [PMID: 37984056 DOI: 10.1111/nph.19414] [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: 09/06/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
Spontaneous chromosomal rearrangements (CRs) play an essential role in speciation, genome evolution and crop domestication. To be able to use the potential of CRs for breeding, plant chromosome engineering was initiated by fragmenting chromosomes by X-ray irradiation. With the rise of the CRISPR/Cas system, it became possible to induce double-strand breaks (DSBs) in a highly efficient manner at will at any chromosomal position. This has enabled a completely new level of predesigned chromosome engineering. The genetic linkage between specific genes can be broken by inducing chromosomal translocations. Natural inversions, which suppress genetic exchange, can be reverted for breeding. In addition, various approaches for constructing minichromosomes by downsizing regular standard A or supernumerary B chromosomes, which could serve as future vectors in plant biotechnology, have been developed. Recently, a functional synthetic centromere could be constructed. Also, different ways of genome haploidization have been set up, some based on centromere manipulations. In the future, we expect to see even more complex rearrangements, which can be combined with previously developed engineering technologies such as recombinases. Chromosome engineering might help to redefine genetic linkage groups, change the number of chromosomes, stack beneficial genes on mini cargo chromosomes, or set up genetic isolation to avoid outcrossing.
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Affiliation(s)
- Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP) - Molecular Biology, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
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20
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Zhang J, Fan C, Liu Y, Shi Q, Sun Y, Huang Y, Yuan J, Han F. Cytological analysis of the diploid-like inheritance of newly synthesized allotetraploid wheat. Chromosome Res 2023; 32:1. [PMID: 38108925 DOI: 10.1007/s10577-023-09745-5] [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: 06/07/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
Polyploidization is a process which is related to species hybridization and whole genome duplication. It is widespread among angiosperm evolution and is essential for speciation and diversification. Allopolyploidization is mainly derived from interspecific hybridization and is believed to pose chromosome imbalances and genome instability caused by meiotic irregularity. However, the self-compatible allopolyploid in wild nature is cytogenetically and genetically stable. Whether this stabilization form was achieved in initial generation or a consequence of long term of evolution was largely unknown. Here, we synthesized a series of nascent allotetraploid wheat derived from three diploid genomes of A, S*, and D. The chromosome numbers of the majority of the progeny derived from these newly formed allotetraploid wheat plants were found to be relatively consistent, with each genome containing 14 chromosomes. In meiosis, bivalent was the majority of the chromosome configuration in metaphase I which supports the stable chromosome number inheritance in the nascent allotetraploid. These findings suggest that diploidization occurred in the newly formed synthetic allotetraploid wheat. However, we still detected aneuploids in a proportion of newly formed allotetraploid wheat, and meiosis of these materials present more irregular chromosome behavior than the euploid. We found that centromere pairing and centromere clustering in meiosis was affected in the aneuploids, which suggest that aneuploidy may trigger the irregular interactions of centromere in early meiosis which may take participate in promoting meiosis stabilization in newly formed allotetraploid wheat.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaolan Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qinghua Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yishuang Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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21
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Nguyen TH, Kang BY, Kim HH. Chromosomal dynamics in Senna: comparative PLOP-FISH analysis of tandem repeats and flow cytometric nuclear genome size estimations. FRONTIERS IN PLANT SCIENCE 2023; 14:1288220. [PMID: 38173930 PMCID: PMC10762312 DOI: 10.3389/fpls.2023.1288220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024]
Abstract
Introduction Tandem repeats (TRs) occur abundantly in plant genomes. They play essential roles that affect genome organization and evolution by inducing or generating chromosomal rearrangements such as duplications, deletions, inversions, and translocations. These impact gene expression and chromosome structure and even contribute to the emergence of new species. Method We investigated the effects of TRs on speciation in Senna genus by performing a comparative analysis using fluorescence in situ hybridization (FISH) with S. tora-specific TR probes. We examined the chromosomal distribution of these TRs and compared the genome sizes of seven Senna species (estimated using flow cytometry) to better understand their evolutionary relationships. Results Two (StoTR03_159 and StoTR04_55) of the nine studied TRs were not detected in any of the seven Senna species, whereas the remaining seven were found in all or some species with patterns that were similar to or contrasted with those of S. tora. Of these studies species, only S. angulata showed significant genome rearrangements and dysploid karyotypes resembling those of S. tora. The genome sizes varied among these species and did not positively correlate with chromosome number. Notably, S. angulata had the fewest chromosomes (2n = 22) but a relatively large genome size. Discussion These findings reveal the dynamics of TRs and provide a cytogenetic depiction of chromosomal rearrangements during speciation in Senna. To further elucidate the dynamics of repeat sequences in Senna, future studies must include related species and extensive repeatomic studies, including those on transposable elements.
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Affiliation(s)
| | | | - Hyun Hee Kim
- Chromosome Research Institute, Department of Chemistry & Life Science, Sahmyook University, Seoul, Republic of Korea
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22
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Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution. Cold Spring Harb Perspect Biol 2023; 15:a041447. [PMID: 37604585 PMCID: PMC10626258 DOI: 10.1101/cshperspect.a041447] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.
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Affiliation(s)
- Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier, France
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Nora Walden
- Centre for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany
| | - Anja Marie Westram
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado;
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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23
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Hendriks KP, Kiefer C, Al-Shehbaz IA, Bailey CD, Hooft van Huysduynen A, Nikolov LA, Nauheimer L, Zuntini AR, German DA, Franzke A, Koch MA, Lysak MA, Toro-Núñez Ó, Özüdoğru B, Invernón VR, Walden N, Maurin O, Hay NM, Shushkov P, Mandáková T, Schranz ME, Thulin M, Windham MD, Rešetnik I, Španiel S, Ly E, Pires JC, Harkess A, Neuffer B, Vogt R, Bräuchler C, Rainer H, Janssens SB, Schmull M, Forrest A, Guggisberg A, Zmarzty S, Lepschi BJ, Scarlett N, Stauffer FW, Schönberger I, Heenan P, Baker WJ, Forest F, Mummenhoff K, Lens F. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol 2023; 33:4052-4068.e6. [PMID: 37659415 DOI: 10.1016/j.cub.2023.08.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 09/04/2023]
Abstract
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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Affiliation(s)
- Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany; Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands.
| | - Christiane Kiefer
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM 88003, USA
| | - Alex Hooft van Huysduynen
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lachezar A Nikolov
- Department of Molecular, Cell and Developmental Biology, University of California, 610 Charles E. Young Dr. S., Los Angeles, CA 90095, USA
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | | | - Dmitry A German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Lesosechnaya Ulitsa, 25, Barnaul, Altai Krai, Russia
| | - Andreas Franzke
- Heidelberg Botanic Garden, Heidelberg University, Im Neuenheimer Feld 361, 69120 Heidelberg, Germany
| | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Óscar Toro-Núñez
- Departamento de Botánica, Universidad de Concepción, Barrio Universitario, Concepción, Chile
| | - Barış Özüdoğru
- Department of Biology, Hacettepe University, Beytepe, Ankara 06800, Türkiye
| | - Vanessa R Invernón
- Sorbonne Université, Muséum National d'Histoire Naturelle, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP 39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Nora Walden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Nikolai M Hay
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip Shushkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mats Thulin
- Department of Organismal Biology, Uppsala University, Norbyvägen 18, 752 36 Uppsala, Sweden
| | | | - Ivana Rešetnik
- Department of Biology, University of Zagreb, Marulićev trg 20/II, 10000 Zagreb, Croatia
| | - Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Dúbravská cesta 9, 845 23 Bratislava, Slovakia
| | - Elfy Ly
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, 307 University Ave., Fort Collins, CO 80523-1170, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Barbara Neuffer
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Robert Vogt
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Christian Bräuchler
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Heimo Rainer
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Steven B Janssens
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31 - box 2435, 3001 Leuven, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Michaela Schmull
- Harvard University Herbaria, 22 Divinity Ave., Cambridge, MA 02138, USA
| | - Alan Forrest
- Centre for Middle Eastern Plants, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Alessia Guggisberg
- ETH Zürich, Institut für Integrative Biologie, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Sue Zmarzty
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Brendan J Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, Clunies Ross St, Acton, ACT 2601, Australia
| | - Neville Scarlett
- La Trobe University, Plenty Road and Kingsbury Dr., Bundoora, VIC 3086, Australia
| | - Fred W Stauffer
- Conservatory and Botanic Gardens of Geneva, CP 60, Chambésy, 1292 Geneva, Switzerland
| | - Ines Schönberger
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | - Peter Heenan
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Frederic Lens
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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24
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Márquez-Corro JI, Martín-Bravo S, Blanco-Pastor JL, Luceño M, Escudero M. The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients. Mol Ecol 2023. [PMID: 37795678 DOI: 10.1111/mec.17156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023]
Abstract
Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.
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Affiliation(s)
- José Ignacio Márquez-Corro
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
- Jodrell Laboratory, Department of Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, UK
| | - Santiago Martín-Bravo
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - José Luis Blanco-Pastor
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
- Departamento de Biología, IVAGRO, Universidad de Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Cádiz, Spain
| | - Modesto Luceño
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
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25
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Huang Y, Guo X, Zhang K, Mandáková T, Cheng F, Lysak MA. The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:446-466. [PMID: 37428465 DOI: 10.1111/tpj.16383] [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: 02/17/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Although the South African Cape flora is one of the most remarkable biodiversity hotspots, its high diversity has not been associated with polyploidy. Here, we report the chromosome-scale genome assembly of an ephemeral cruciferous species Heliophila variabilis (~334 Mb, n = 11) adapted to South African semiarid biomes. Two pairs of differently fractionated subgenomes suggest an allo-octoploid origin of the genome at least 12 million years ago. The ancestral octoploid Heliophila genome (2n = 8x = ~60) has probably originated through hybridization between two allotetraploids (2n = 4x = ~30) formed by distant, intertribal, hybridization. Rediploidization of the ancestral genome was marked by extensive reorganization of parental subgenomes, genome downsizing, and speciation events in the genus Heliophila. We found evidence for loss-of-function changes in genes associated with leaf development and early flowering, and over-retention and sub/neofunctionalization of genes involved in pathogen response and chemical defense. The genomic resources of H. variabilis will help elucidate the role of polyploidization and genome diploidization in plant adaptation to hot arid environments and origin of the Cape flora. The sequenced H. variabilis represents the first chromosome-scale genome assembly of a meso-octoploid representative of the mustard family.
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Affiliation(s)
- Yile Huang
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Xinyi Guo
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
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Nascimento T, Pedrosa-Harand A. High rates of structural rearrangements have shaped the chromosome evolution in dysploid Phaseolus beans. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:215. [PMID: 37751069 DOI: 10.1007/s00122-023-04462-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
KEY MESSAGE Karyotypes evolve through numerical and structural chromosome rearrangements. We show that Phaseolus leptostachyus, a wild bean, underwent a rapid genome reshuffling associated with the reduction from 11 to 10 chromosome pairs, but without whole genome duplication, the highest chromosome evolution rate known for plants. Plant karyotypes evolve through structural rearrangements often associated with polyploidy or dysploidy. The genus Phaseolus comprises ~ 90 species, five of them domesticated due to their nutritional relevance. Most of the species have 2n = 22 karyotypes and are highly syntenic, except for three dysploid karyotypes of species from the Leptostachyus group (2n = 20) that have accumulated several rearrangements. Here, we investigated the degrees of structural rearrangements among Leptostachyus and other Phaseolus groups by estimating their chromosomal evolution rates (CER). For this, we combined our oligo-FISH barcode system for beans and chromosome-specific painting probes for chromosomes 2 and 3, with rDNA and a centromeric probe to establish chromosome orthologies and identify structural rearrangements across nine Phaseolus species. We also integrated the detected rearrangements with a phylogenomic approach to estimate the CERs for each Phaseolus lineage. Our data allowed us to identify translocations, inversions, duplications and deletions, mostly in species belonging to the Leptostachyus group. Phaseolus leptostachyus showed the highest CER (12.31 rearrangements/My), a tenfold increase in contrast to the 2n = 22 species analysed. This is the highest rate known yet for plants, making it a model species for investigating the mechanisms behind rapid genome reshuffling in early species diversification.
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Affiliation(s)
- Thiago Nascimento
- Laboratory of Plants Cytogenetics and Evolution, Department of Botany, Biosciences Center, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plants Cytogenetics and Evolution, Department of Botany, Biosciences Center, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil.
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27
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Blume RY, Kalendar R, Guo L, Cahoon EB, Blume YB. Overcoming genetic paucity of Camelina sativa: possibilities for interspecific hybridization conditioned by the genus evolution pathway. FRONTIERS IN PLANT SCIENCE 2023; 14:1259431. [PMID: 37818316 PMCID: PMC10561096 DOI: 10.3389/fpls.2023.1259431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023]
Abstract
Camelina or false flax (Camelina sativa) is an emerging oilseed crop and a feedstock for biofuel production. This species is believed to originate from Western Asian and Eastern European regions, where the center of diversity of the Camelina genus is located. Cultivated Camelina species arose via a series of polyploidization events, serving as bottlenecks narrowing genetic diversity of the species. The genetic paucity of C. sativa is foreseen as the most crucial limitation for successful breeding and improvement of this crop. A potential solution to this challenge could be gene introgression from Camelina wild species or from resynthesized allohexaploid C. sativa. However, both approaches would require a complete comprehension of the evolutionary trajectories that led to the C. sativa origin. Although there are some studies discussing the origin and evolution of Camelina hexaploid species, final conclusions have not been made yet. Here, we propose the most complete integrated evolutionary model for the Camelina genus based on the most recently described findings, which enables efficient improvement of C. sativa via the interspecific hybridization with its wild relatives. We also discuss issues of interspecific and intergeneric hybridization, aimed on improving C. sativa and overcoming the genetic paucity of this crop. The proposed comprehensive evolutionary model of Camelina species indicates that a newly described species Camelina neglecta has a key role in origin of tetra- and hexaploids, all of which have two C. neglecta-based subgenomes. Understanding of species evolution within the Camelina genus provides insights into further research on C. sativa improvements via gene introgression from wild species, and a potential resynthesis of this emerging oilseed crop.
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Affiliation(s)
- Rostyslav Y. Blume
- Institute of Food Biotechnology and Genomics of National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Ruslan Kalendar
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Edgar B. Cahoon
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Yaroslav B. Blume
- Institute of Food Biotechnology and Genomics of National Academy of Science of Ukraine, Kyiv, Ukraine
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28
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Yan X, Chen X, Li Y, Li Y, Wang F, Zhang J, Ning G, Bao M. The Abundant and Unique Transcripts and Alternative Splicing of the Artificially Autododecaploid London Plane ( Platanus × acerifolia). Int J Mol Sci 2023; 24:14486. [PMID: 37833935 PMCID: PMC10572260 DOI: 10.3390/ijms241914486] [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: 08/24/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Transcription and alternative splicing (AS) are now appreciated in plants, but few studies have examined the effects of changing ploidy on transcription and AS. In this study, we showed that artificially autododecaploid plants of London plane (Platanus × acerifolia (Aiton) Willd) had few flowers relative to their hexaploid progenitors. Transcriptome analysis based on full-length Oxford Nanopore Technologies (ONTs) and next-generation sequencing (NGS) revealed that the increased ploidy level in P. × acerifolia led to more transcribed isoforms, accompanied by an increase in the number of isoforms per gene. The functional enrichment of genes indicated that novel genes transcribed specifically in the dodecaploids may have been highly correlated with the ability to maintain genome stability. The dodecaploids showed a higher number of genes with upregulated differentially expressed genes (DEGs) compared with the hexaploid counterpart. The genome duplication of P. × acerifolia resulted mainly in the DEGs involved in basic biological pathways. It was noted that there was a greater abundance of alternative splicing (AS) events and AS genes in the dodecaploids compared with the hexaploids in P. × acerifolia. In addition, a significant difference between the structure and expression of AS events between the hexaploids and dodecaploids of Platanus was found. Of note, some DEGs and differentially spliced genes (DSGs) related to floral transition and flower development were consistent with the few flower traits in the dodecaploids of P. × acerifolia. Collectively, our findings explored the difference in transcription and AS regulation between the hexaploids and dodecaploids of P. × acerifolia and gained new insight into the molecular mechanisms underlying the few-flower phenotype of P. × acerifolia. These results contribute to uncovering the regulatory role of transcription and AS in polyploids and breeding few-flower germplasms.
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Affiliation(s)
| | | | | | | | | | | | | | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (X.Y.); (J.Z.)
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29
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Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [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: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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30
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Slovák M, Melichárková A, Štubňová EG, Kučera J, Mandáková T, Smyčka J, Lavergne S, Passalacqua NG, Vďačný P, Paun O. Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae). Syst Biol 2023; 72:491-504. [PMID: 36331548 PMCID: PMC10276626 DOI: 10.1093/sysbio/syac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
Hybridization is a key mechanism involved in lineage diversification and speciation, especially in ecosystems that experienced repeated environmental oscillations. Recently radiated plant groups, which have evolved in mountain ecosystems impacted by historical climate change provide an excellent model system for studying the impact of gene flow on speciation. We combined organellar (whole-plastome) and nuclear genomic data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the effects of hybridization and introgression on evolution and speciation in the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has already occurred among ancestral lineages of snowbells and has persisted throughout the entire evolutionary history of the genus, regardless of the ecology, cytotype, or distribution range size of the affected species. The highest extent of introgression has been detected in the Carpathian species, which is also reflected in their extensive karyotype variation. Introgression occurred even between species with dysploid and euploid cytotypes, which were considered to be reproductively isolated. The magnitude of introgression detected in snowbells is unprecedented in other mountain genera of the European Alpine System investigated hitherto. Our study stresses the prominent evolutionary role of hybridization in facilitating speciation and diversification on the one hand, but also enriching previously isolated genetic pools. [chloroplast capture; diversification; dysploidy; European Alpine system; introgression; nuclear-cytoplasmic discordance; ribosomal DNA.].
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Affiliation(s)
- Marek Slovák
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czech Republic
| | - Andrea Melichárková
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Eliška Gbúrová Štubňová
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | - Jaromír Kučera
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Terezie Mandáková
- Central European Institute of Technology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Jan Smyčka
- Department of Botany, Charles University, Prague, Czech Republic
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, Jilská 1, 110 00 Praha, Czech Republic
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | - Sébastien Lavergne
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | | | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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31
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Cao Y, Almeida-Silva F, Zhang WP, Ding YM, Bai D, Bai WN, Zhang BW, Van de Peer Y, Zhang DY. Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae). Mol Biol Evol 2023; 40:msad121. [PMID: 37216901 PMCID: PMC10257982 DOI: 10.1093/molbev/msad121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023] Open
Abstract
When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes and its only congeneric species, Platycarya strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole-genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics and the driving forces underneath the incipient speciation of the two Platycarya lineages.
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Affiliation(s)
- Yu Cao
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ya-Mei Ding
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Dan Bai
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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32
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Deb SK, Edger PP, Pires JC, McKain MR. Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective. THE NEW PHYTOLOGIST 2023; 238:2284-2304. [PMID: 37010081 DOI: 10.1111/nph.18927] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.
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Affiliation(s)
- Sontosh K Deb
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48823, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
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33
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Redmond AK, Casey D, Gundappa MK, Macqueen DJ, McLysaght A. Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor. Nat Commun 2023; 14:2879. [PMID: 37208359 DOI: 10.1038/s41467-023-38714-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/12/2023] [Indexed: 05/21/2023] Open
Abstract
Whole genome duplication (WGD) is a dramatic evolutionary event generating many new genes and which may play a role in survival through mass extinctions. Paddlefish and sturgeon are sister lineages that both show genomic evidence for ancient WGD. Until now this has been interpreted as two independent WGD events due to a preponderance of duplicate genes with independent histories. Here we show that although there is indeed a plurality of apparently independent gene duplications, these derive from a shared genome duplication event occurring well over 200 million years ago, likely close to the Permian-Triassic mass extinction period. This was followed by a prolonged process of reversion to stable diploid inheritance (rediploidization), that may have promoted survival during the Triassic-Jurassic mass extinction. We show that the sharing of this WGD is masked by the fact that paddlefish and sturgeon lineage divergence occurred before rediploidization had proceeded even half-way. Thus, for most genes the resolution to diploidy was lineage-specific. Because genes are only truly duplicated once diploid inheritance is established, the paddlefish and sturgeon genomes are thus a mosaic of shared and non-shared gene duplications resulting from a shared genome duplication event.
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Affiliation(s)
- Anthony K Redmond
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Dearbhaile Casey
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
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34
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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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35
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Peng F, Zhou L, Lu W, Gan R, Lu M, Li Z, Zhang X, Wang Y, Gui J. Genomic and Transcriptional Profiles of Kelch-like ( klhl) Gene Family in Polyploid Carassius Complex. Int J Mol Sci 2023; 24:8367. [PMID: 37176071 PMCID: PMC10179623 DOI: 10.3390/ijms24098367] [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: 12/14/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select Kelch-like (klhl) genes to study the evolution of the duplicated genes in the polyploid Carassius complex, including amphidiploid C. auratus and amphitriploid C. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most of Carassius klhl genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during Carassius evolution. The lineage-specific expansion and biased retention/loss of klhl genes are also found in Carassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of klhls in response to Carassius herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three C. gibelio gynogenetic clones. Finally, we find that most C. gibelio klhl genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for Cgklhl genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.
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Affiliation(s)
- Fang Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijia Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruihai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaojuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Shafir A, Halabi K, Escudero M, Mayrose I. A non-homogeneous model of chromosome-number evolution to reveal shifts in the transition patterns across the phylogeny. THE NEW PHYTOLOGIST 2023; 238:1733-1744. [PMID: 36759331 DOI: 10.1111/nph.18805] [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: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Changes in chromosome numbers, including polyploidy and dysploidy events, play a key role in eukaryote evolution as they could expediate reproductive isolation and have the potential to foster phenotypic diversification. Deciphering the pattern of chromosome-number change within a phylogeny currently relies on probabilistic evolutionary models. All currently available models assume time homogeneity, such that the transition rates are identical throughout the phylogeny. Here, we develop heterogeneous models of chromosome-number evolution that allow multiple transition regimes to operate in distinct parts of the phylogeny. The partition of the phylogeny to distinct transition regimes may be specified by the researcher or, alternatively, identified using a sequential testing approach. Once the number and locations of shifts in the transition pattern are determined, a second search phase identifies regimes with similar transition dynamics, which could indicate on convergent evolution. Using simulations, we study the performance of the developed model to detect shifts in patterns of chromosome-number evolution and demonstrate its applicability by analyzing the evolution of chromosome numbers within the Cyperaceae plant family. The developed model extends the capabilities of probabilistic models of chromosome-number evolution and should be particularly helpful for the analyses of large phylogenies that include multiple distinct subclades.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Keren Halabi
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Reina Mercedes, ES-41012, Seville, Spain
| | - Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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Windham MD, Picard KT, Pryer KM. An in-depth investigation of cryptic taxonomic diversity in the rare endemic mustard Draba maguirei. AMERICAN JOURNAL OF BOTANY 2023; 110:1-22. [PMID: 36779544 DOI: 10.1002/ajb2.16138] [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: 10/30/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Previously published evidence suggests that Draba maguirei, a mustard endemic to a few localities in the Bear River, Wellsville, and Wasatch Mountains of northern Utah, may represent a cryptic species complex rather than a single species. Conservation concerns prompted an in-depth systematic study of this taxon and its putative relatives. METHODS Sampling most known populations of D. maguirei s.l. (D. maguirei var. maguirei and D. maguirei var. burkei), we integrate data from geography, ecology, morphology, cytogenetics and pollen, enzyme electrophoresis, and the phylogenetic analysis of nuclear internal transcribed spacer sequences to explore potential taxonomic diversity in the species complex. RESULTS Draba maguirei var. burkei is shown here to be a distinct species (D. burkei) most closely related to D. globosa, rather than to D. maguirei. Within D. maguirei s.s., the northern (high elevation) and southern (low elevation) population clusters are genetically isolated and morphologically distinguishable, leading to the recognition here of the southern taxon as D. maguirei subsp. stonei. CONCLUSIONS Our study reveals that plants traditionally assigned to D. maguirei comprise three genetically divergent lineages (D. burkei and two newly recognized subspecies of D. maguirei), each exhibiting a different chromosome number and occupying a discrete portion of the geographic range. Although previously overlooked and underappreciated taxonomically, the three taxa are morphologically recognizable based on the distribution and types of trichomes present on the leaves, stems, and fruit. Our clarification of the diversity and distribution of these taxa provides an improved framework for conservation efforts.
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Affiliation(s)
- Michael D Windham
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Kathryn T Picard
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, 20560, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
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Disentangling Crocus Series Verni and Its Polyploids. BIOLOGY 2023; 12:biology12020303. [PMID: 36829579 PMCID: PMC9953621 DOI: 10.3390/biology12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023]
Abstract
Spring crocuses, the eleven species within Crocus series Verni (Iridaceae), consist of di- and tetraploid cytotypes. Among them is a group of polyploids from southeastern Europe with yet-unclear taxonomic affiliation. Crocuses are generally characterized by complex dysploid chromosome number changes, preventing a clear correlation between these numbers and ploidy levels. To reconstruct the evolutionary history of series Verni and particularly its polyploid lineages associated with C. heuffelianus, we used an approach combining phylogenetic analyses of two chloroplast regions, 14 nuclear single-copy genes plus rDNA spacers, genome-wide genotyping-by-sequencing (GBS) data, and morphometry with ploidy estimations through genome size measurements, analysis of genomic heterozygosity frequencies and co-ancestry, and chromosome number counts. Chromosome numbers varied widely in diploids with 2n = 8, 10, 12, 14, 16, and 28 and tetraploid species or cytotypes with 2n = 16, 18, 20, and 22 chromosomes. Crocus longiflorus, the diploid with the highest chromosome number, possesses the smallest genome (2C = 3.21 pg), while the largest diploid genomes are in a range of 2C = 7-8 pg. Tetraploid genomes have 2C values between 10.88 pg and 12.84 pg. Heterozygosity distribution correlates strongly with genome size classes and allows discernment of di- and tetraploid cytotypes. Our phylogenetic analyses showed that polyploids in the C. heuffelianus group are allotetraploids derived from multiple and partly reciprocal crosses involving different genotypes of diploid C. heuffelianus (2n = 10) and C. vernus (2n = 8). Dysploid karyotype changes after polyploidization resulted in the tetraploid cytotypes with 20 and 22 chromosomes. The multi-data approach we used here for series Verni, combining evidence from nuclear and chloroplast phylogenies, genome sizes, chromosome numbers, and genomic heterozygosity for ploidy estimations, provides a way to disentangle the evolution of plant taxa with complex karyotype changes that can be used for the analysis of other groups within Crocus and beyond. Comparing these results with morphometric analysis results in characters that can discern the different taxa currently subsumed under C. heuffelianus.
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Joshi P, Ansari H, Dickson R, Ellison NW, Skema C, Tate JA. Polyploidy on islands - concerted evolution and gene loss amid chromosomal stasis. ANNALS OF BOTANY 2023; 131:33-44. [PMID: 35390127 PMCID: PMC9904340 DOI: 10.1093/aob/mcac051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/04/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Polyploidy is an important process that often generates genomic diversity within lineages, but it can also cause changes that result in loss of genomic material. Island lineages, while often polyploid, typically show chromosomal stasis but have not been investigated in detail regarding smaller-scale gene loss. Our aim was to investigate post-polyploidization genome dynamics in a chromosomally stable lineage of Malvaceae endemic to New Zealand. METHODS We determined chromosome numbers and used fluorescence in situ hybridization to localize 18S and 5S rDNA. Gene sequencing of 18S rDNA, the internal transcribed spacers (ITS) with intervening 5.8S rDNA, and a low-copy nuclear gene, GBSSI-1, was undertaken to determine if gene loss occurred in the New Zealand lineage following polyploidy. KEY RESULTS The chromosome number for all species investigated was 2n = 42, with the first published report for the monotypic Australian genus Asterotrichion. The five species investigated all had two 5S rDNA signals localized interstitially on the long arm of one of the largest chromosome pairs. All species, except Plagianthus regius, had two 18S rDNA signals localized proximally on the short arm of one of the smallest chromosome pairs. Plagianthus regius had two additional 18S rDNA signals on a separate chromosome, giving a total of four. Sequencing of nuclear ribosomal 18S rDNA and the ITS cistron indicated loss of historical ribosomal repeats. Phylogenetic analysis of a low-copy nuclear gene, GBSSI-1, indicated that some lineages maintained three copies of the locus, while others have lost one or two copies. CONCLUSIONS Although island endemic lineages show chromosomal stasis, with no additional changes in chromosome number, they may undergo smaller-scale processes of gene loss and concerted evolution ultimately leading to further genome restructuring and downsizing.
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Affiliation(s)
- Prashant Joshi
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Helal Ansari
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Rowan Dickson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Cynthia Skema
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Morris Arboretum of the University of Pennsylvania, Philadelphia, PA, USA
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Zhao L, Yang YY, Qu XJ, Ma H, Hu Y, Li HT, Yi TS, Li DZ. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. ANNALS OF BOTANY 2023; 131:199-214. [PMID: 35671385 PMCID: PMC9904356 DOI: 10.1093/aob/mcac062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of 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, Ji’nan, Shandong 250014, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Guo W, Comai L, Henry IM. Chromoanagenesis in plants: triggers, mechanisms, and potential impact. Trends Genet 2023; 39:34-45. [PMID: 36055901 DOI: 10.1016/j.tig.2022.08.003] [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: 05/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
Abstract
Chromoanagenesis is a single catastrophic event that involves, in most cases, localized chromosomal shattering and reorganization, resulting in a dramatically restructured chromosome. First discovered in cancer cells, it has since been observed in various other systems, including plants. In this review, we discuss the origin, characteristics, and potential mechanisms underlying chromoanagenesis in plants. We report that multiple processes, including mutagenesis and genetic engineering, can trigger chromoanagenesis via a variety of mechanisms such as micronucleation, breakage-fusion-bridge (BFB) cycles, or chain-like translocations. The resulting rearranged chromosomes can be preserved during subsequent plant growth, and sometimes inherited to the next generation. Because of their high tolerance to genome restructuring, plants offer a unique system for investigating the evolutionary consequences and potential practical applications of chromoanagenesis.
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Affiliation(s)
- Weier Guo
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Luca Comai
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
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Dong C, Wang S, Zhang H, Liu J, Li M. Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae. DNA Res 2022; 30:6912218. [PMID: 36521020 PMCID: PMC9835862 DOI: 10.1093/dnares/dsac051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available for this family. Here, we reported a chromosome-level genome for Cornus controversa. This was generated using high-fidelity plus Hi-C sequencing, and totally ~771.80 Mb assembled sequences and 39,886 protein-coding genes were obtained. We provided evidence for a whole-genome duplication event (WGD) unique to C. controversa. The evolutionary features of this genome indicated that the expanded and unique genes might have contributed to response to stress, stimulus and defense. By using chromosome-level syntenic blocks shared between eight living genomes, we found high degrees of genomic diversification from the ancestral core-eudicot genome to the present-day genomes, suggesting an important role of WGD in genomic plasticity that leads to speciation and diversification. These results provide foundational insights on the evolutionary history of Cornaceae, as well as on the Asterids diversification.
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Affiliation(s)
| | | | - Han Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China,Key Laboratory of BioResource and EcoEnvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minjie Li
- To whom correspondence should be addressed. (M.L.)
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Garassino F, Wijfjes RY, Boesten R, Reyes Marquez F, Becker FFM, Clapero V, van den Hatert I, Holmer R, Schranz ME, Harbinson J, de Ridder D, Smit S, Aarts MGM. The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1298-1315. [PMID: 36239071 PMCID: PMC10100226 DOI: 10.1111/tpj.16005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C3 plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C3 species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.
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Affiliation(s)
| | - Raúl Y. Wijfjes
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
- Present address:
Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
| | - René Boesten
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
| | | | - Frank F. M. Becker
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
| | - Vittoria Clapero
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
- Present address:
Max Planck Institute for Molecular Plant PhysiologyGolmGermany
| | | | - Rens Holmer
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - M. Eric Schranz
- Biosystematics GroupWageningen University & ResearchWageningenNetherlands
| | - Jeremy Harbinson
- Laboratory of BiophysicsWageningen University & ResearchWageningenNetherlands
| | - Dick de Ridder
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - Sandra Smit
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
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Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae. Chromosome Res 2022; 30:477-492. [PMID: 35715657 DOI: 10.1007/s10577-022-09702-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 01/25/2023]
Abstract
The tribe Phaseoleae includes several legume crops with assembled genomes. Comparative genomic studies have evidenced the preservation of large genomic blocks among legumes, although chromosome dynamics during Phaseoleae evolution has not been investigated. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We identified GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata and searched for GBs in different genomes of the Phaseolinae (P. lunatus) and Glycininae (Amphicarpaea edgeworthii) subtribes and Spatholobus suberectus (sister to Phaseolinae and Glycininae), using Medicago truncatula as the outgroup. We also used oligo-FISH probes of two P. vulgaris chromosomes to paint the orthologous chromosomes of two non-sequenced Phaseolinae species. We inferred the APK as having n = 11 and 19 GBs (A to S), hypothesizing five chromosome fusions that reduced the ancestral legume karyotype to n = 11. We identified the rearrangements among the APK and the subtribes and species, with extensive centromere repositioning in Phaseolus. We also reconstructed the chromosome number reduction in S. suberectus. The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.
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Nie S, Tian XC, Kong L, Zhao SW, Chen ZY, Jiao SQ, El-Kassaby YA, Porth I, Yang FS, Zhao W, Mao JF. Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation. FRONTIERS IN PLANT SCIENCE 2022; 13:1006904. [PMID: 36457535 PMCID: PMC9706204 DOI: 10.3389/fpls.2022.1006904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/27/2022] [Indexed: 05/31/2023]
Abstract
Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.
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Affiliation(s)
- Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Chan Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Kong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhao-Yang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, Canada
| | - Fu-Sheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Parey E, Louis A, Montfort J, Guiguen Y, Crollius HR, Berthelot C. An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication. Genome Res 2022; 32:1685-1697. [PMID: 35961774 PMCID: PMC9528989 DOI: 10.1101/gr.276953.122] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
Abstract
Teleost fishes are ancient tetraploids descended from an ancestral whole-genome duplication that may have contributed to the impressive diversification of this clade. Whole-genome duplications can occur via self-doubling (autopolyploidy) or via hybridization between different species (allopolyploidy). The mode of tetraploidization conditions evolutionary processes by which duplicated genomes return to diploid meiotic pairing, and subsequent genetic divergence of duplicated genes (cytological and genetic rediploidization). How teleosts became tetraploid remains unresolved, leaving a fundamental gap in the interpretation of their functional evolution. As a result of the whole-genome duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering genome-wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes. We then leverage this atlas to investigate how rediploidization occurred in teleosts at the genome-wide level. We uncover that some duplicated regions maintained tetraploidy for more than 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families. This evidence suggests that the teleost ancestor was an autopolyploid. Further, we find evidence for biased gene retention along several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into genome evolutionary dynamics following ancient polyploidizations in vertebrates.
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Affiliation(s)
- Elise Parey
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- INRAE, LPGP, 35000, Rennes, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | | | | | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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47
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Yucel G, Betekhtin A, Cabi E, Tuna M, Hasterok R, Kolano B. The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae). Int J Mol Sci 2022; 23:ijms231911033. [PMID: 36232345 PMCID: PMC9570107 DOI: 10.3390/ijms231911033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 02/02/2023] Open
Abstract
The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus.
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Affiliation(s)
- Gulru Yucel
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55200, Turkey
- Department of Biology, Institute of Natural and Applied Sciences, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Alexander Betekhtin
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Evren Cabi
- Department of Biology, Faculty of Arts and Sciences, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Metin Tuna
- Department of Field Crops, Faculty of Agriculture, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Bozena Kolano
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
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48
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Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of Allotetraploid Iris koreana and Its Putative Diploid Parental Species ( Iris Series Chinenses, Iridaceae). Int J Mol Sci 2022; 23:ijms231810929. [PMID: 36142840 PMCID: PMC9504294 DOI: 10.3390/ijms231810929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 12/16/2022] Open
Abstract
The Iris series Chinenses in Korea comprises four species (I. minutoaurea, I. odaesanensis, I. koreana, and I. rossii), and the group includes some endangered species, owing to their high ornamental, economic, and conservation values. Among them, the putative allotetraploid, Iris koreana (2n = 4x = 50), is hypothesized to have originated from the hybridization of the diploids I. minutoaurea (2n = 2x = 22) and I. odaesanensis (2n = 2x = 28) based on morphological characters, chromosome numbers, and genome size additivity. Despite extensive morphological and molecular phylogenetical studies on the genus Iris, little is known about Korean irises in terms of their complete chloroplast (cp) genomes and molecular cytogenetics that involve rDNA loci evolution based on fluorescence in situ hybridization (FISH). This study reports comparative analyses of the karyotypes of the three Iris species (I. koreana, I. odaesanensis, and I. minutoaurea), with an emphasis on the 5S and 35S rDNA loci number and localization using FISH together with the genome size and chromosome number. Moreover, the cp genomes of the same individuals were sequenced and assembled for comparative analysis. The rDNA loci numbers, which were localized consistently at the same position in all species, and the chromosome numbers and genome size values of tetraploid Iris koreana (four 5S and 35S loci; 2n = 50; 1C = 7.35 pg) were additively compared to its putative diploid progenitors, I. minutoaurea (two 5S and 35S loci; 2n = 22; 1C = 3.71 pg) and I. odaesanensis (two 5S and 35S loci; 2n = 28; 1C = 3.68 pg). The chloroplast genomes were 152,259–155,145 bp in length, and exhibited a conserved quadripartite structure. The Iris cp genomes were highly conserved and similar to other Iridaceae cp genomes. Nucleotide diversity analysis indicated that all three species had similar levels of genetic variation, but the cp genomes of I. koreana and I. minutoaurea were more similar to each other than to I. odaesanensis. Positive selection was inferred for psbK and ycf2 genes of the three Iris species. Phylogenetic analyses consistently recovered I. odaesanensis as a sister to a clade containing I. koreana and I. minutoaurea. Although the phylogenetic relationship, rDNA loci number, and localization, together with the genome size and chromosome number of the three species, allowed for the inference of I. minutoaurea as a putative maternal taxon and I. odaesanensis as a paternal taxon, further analyses involving species-specific molecular cytogenetic markers and genomic in situ hybridization are required to interpret the mechanisms involved in the origin of the chromosomal variation in Iris series Chinenses. This study contributes towards the genomic and chromosomal evolution of the genus Iris.
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Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, Rössner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Theißen G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, Chen ZH. Dynamic genome evolution in a model fern. NATURE PLANTS 2022; 8:1038-1051. [PMID: 36050461 PMCID: PMC9477723 DOI: 10.1038/s41477-022-01226-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/15/2022] [Indexed: 05/31/2023]
Abstract
The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.
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Affiliation(s)
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Shengguan Cai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Fei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | | | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Rijan R Dhakal
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Clemens Rössner
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Annette Becker
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuhuan Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Tao Tong
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yuanyuan Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shengchun Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Honglang Duan
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | | | | | | | | | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
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Schilbert HM, Glover BJ. Analysis of flavonol regulator evolution in the Brassicaceae reveals MYB12, MYB111 and MYB21 duplications and MYB11 and MYB24 gene loss. BMC Genomics 2022; 23:604. [PMID: 35986242 PMCID: PMC9392221 DOI: 10.1186/s12864-022-08819-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flavonols are the largest subgroup of flavonoids, possessing multiple functions in plants including protection against ultraviolet radiation, antimicrobial activities, and flower pigmentation together with anthocyanins. They are of agronomical and economical importance because the major off-taste component in rapeseed protein isolates is a flavonol derivative, which limits rapeseed protein use for human consumption. Flavonol production in Arabidopsis thaliana is mainly regulated by the subgroup 7 (SG7) R2R3-MYB transcription factors MYB11, MYB12, and MYB111. Recently, the SG19 MYBs MYB21, MYB24, and MYB57 were shown to regulate flavonol accumulation in pollen and stamens. The members of each subgroup are closely related, showing gene redundancy and tissue-specific expression in A. thaliana. However, the evolution of these flavonol regulators inside the Brassicaceae, especially inside the Brassiceae, which include the rapeseed crop species, is not fully understood. RESULTS We studied the SG7 and SG19 MYBs in 44 species, including 31 species of the Brassicaceae, by phylogenetic analyses followed by synteny and gene expression analyses. Thereby we identified a deep MYB12 and MYB111 duplication inside the Brassicaceae, which likely occurred before the divergence of Brassiceae and Thelypodieae. These duplications of SG7 members were followed by the loss of MYB11 after the divergence of Eruca vesicaria from the remaining Brassiceae species. Similarly, MYB21 experienced duplication before the emergence of the Brassiceae tribe, where the gene loss of MYB24 is also proposed to have happened. The members of each subgroup revealed frequent overlapping spatio-temporal expression patterns in the Brassiceae member B. napus, which are assumed to compensate for the loss of MYB11 and MYB24 in the analysed tissues. CONCLUSIONS We identified a duplication of MYB12, MYB111, and MYB21 inside the Brassicaceae and MYB11 and MYB24 gene loss inside the tribe Brassiceae. We propose that polyploidization events have shaped the evolution of the flavonol regulators in the Brassicaceae, especially in the Brassiceae.
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Affiliation(s)
- Hanna M Schilbert
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Bielefeld, Germany.
| | - Beverley J Glover
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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