151
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Yu F, Wang H, Zhao Y, Liu R, Dou Q, Dong J, Wang T. Karyotypic evolution of the Medicago complex: sativa-caerulea-falcata inferred from comparative cytogenetic analysis. BMC Evol Biol 2017; 17:104. [PMID: 28427346 PMCID: PMC5399346 DOI: 10.1186/s12862-017-0951-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 04/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyploidy plays an important role in the adaptation and speciation of plants. The alteration of karyotype is a significant event during polyploidy formation. The Medicago sativa complex includes both diploid (2n = 2× = 16) and tetraploid (2n = 2× = 32) subspecies. The tetraploid M. ssp. sativa was regarded as having a simple autopolyploid origin from diploid ssp. caerulea, whereas the autopolyploid origin of tetraploid ssp. falcata from diploid form ssp. falcata is still in doubt. In this study, detailed comparative cytogenetic analysis between diploid to tetraploid species, as well as genomic affinity across different species in the M. sativa complex, were conducted based on comparative mapping of 11 repeated DNA sequences and two rDNA sequences by a fluorescence in situ hybridization (FISH) technique. RESULTS FISH patterns of the repeats in diploid subspecies caerulea were highly similar to those in tetraploid subspecies sativa. Distinctly different FISH patterns were first observed in diploid ssp. falcata, with only centromeric hybridizations using centromeric and multiple region repeats and a few subtelomeric hybridizations using subtelomeric repeats. Tetraploid subspecies falcata was unexpectedly found to possess a highly variable karyotype, which agreed with neither diploid ssp. falcata nor ssp. sativa. Reconstruction of chromosome-doubling process of diploid ssp. caerulea showed that chromosome changes have occurred during polyploidization process. CONCLUSIONS The comparative cytogenetic results provide reliable evidence that diploid subspecies caerulea is the direct progenitor of tetraploid subspecies sativa. And autotetraploid ssp. sativa has been suggested to undergo a partial diploidization by the progressive accumulation of chromosome structural rearrangements during evolution. However, the tetraploid subspecies falcata is far from a simple autopolyploid from diploid subspecies falcata although no obvious morphological change was observed between these two subspecies.
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Affiliation(s)
- Feng Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiqing Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Yanyan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruijuan Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quanwen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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152
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Chromosomal structural changes and microsatellite variations in newly synthesized hexaploid wheat mediated by unreduced gametes. J Genet 2017; 95:819-830. [PMID: 27994180 DOI: 10.1007/s12041-016-0704-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Allohexaploid wheat was derived from interspecific hybridization, followed by spontaneous chromosome doubling. Newly synthesized hexaploid wheat by crossing Triticum turgidum and Aegilops tauschii provides a classical model to understand the mechanisms of allohexaploidization in wheat. However, immediate chromosome level variation and microsatellite level variation of newly synthesized hexaploid wheat have been rarely reported. Here, unreduced gametes were applied to develop synthesized hexaploid wheat, NA0928, population by crossing T. turgidum ssp. dicoccum MY3478 and Ae. tauschii SY41, and further S0-S3 generations of NA0928 were assayed by sequential cytological and microsatellite techniques. We demonstrated that plentiful chromosomal structural changes and microsatellite variations emerged in the early generations of newly synthesized hexaploid wheat population NA0928, including aneuploidy with whole-chromosome loss or gain, aneuploidy with telosome formation, chromosome-specific repeated sequence elimination (indicated by fluorescence in situ hybridization) and microsatellite sequence elimination (indicated by sequencing), and many kinds of variations have not been previously reported. Additionally, we reported a new germplasm, T. turgidum accession MY3478 with excellent unreduced gametes trait, and then succeeded to transfer powdery mildew resistance from Ae. tauschii SY41 to synthesized allohexaploid wheat population NA0928, which would be valuable resistance resources for wheat improvement.
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153
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de Carvalho RF, Amaral-Silva PM, Spadeto MS, Nunes ACP, Carrijo TT, Carvalho CR, Clarindo WR. First karyotype description and nuclear 2C value for Myrsine (Primulaceae): comparing three species. COMPARATIVE CYTOGENETICS 2017; 11:163-177. [PMID: 28919956 PMCID: PMC5599700 DOI: 10.3897/compcytogen] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 01/21/2017] [Indexed: 06/07/2023]
Abstract
Cytogenetic studies in Primulaceae are mostly available for herbaceous species, and are focused on the chromosome number determination. An accurate karyotype characterization represents a starting point to know the morphometry and class of the chromosomes. Comparison among species within Myrsine, associating these data with the nuclear 2C value, can show changes that led the karyotype evolution. Here, we studied three Myrsine species [Myrsine coriacea (Swartz, 1788) Brown ex Roemer et Schultes, 1819, Myrsine umbellata Martius, 1841 and Myrsine parvifolia Candolle, 1841] that show different abilities to occupy the varied types of vegetation within the Brazilian Atlantic Forest. Cytogenetic characterization showed some individuals with 2n = 45 chromosomes for Myrsine parvifolia and Myrsine coriacea, with most individuals of the three species having 2n = 46. The first karyograms for Myrsine were assembled and presented morphologically identical and distinct chromosome pairs. In addition, differences in the mean 2C nuclear value and chromosome morphometry were found. Therefore, the first description of the Myrsine karyotype has been presented, as well as the nuclear 2C value. The procedures can be applied to other Myrsine species for future investigations in order to better understand its effects on the differential spatial occupation abilities shown by the species in Brazilian Atlantic Forest.
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Affiliation(s)
- Renata Flávia de Carvalho
- Laboratório de Citogenética, Departamento de Biologia, Centro de Ciências
Agrárias, Universidade Federal do Espírito Santo, 29.500-000 Alegre (ES),
Brazil
| | - Paulo Marcos Amaral-Silva
- Laboratório de Citogenética, Departamento de Biologia, Centro de Ciências
Agrárias, Universidade Federal do Espírito Santo, 29.500-000 Alegre (ES),
Brazil
| | - Micheli Sossai Spadeto
- Laboratório de Citogenética, Departamento de Biologia, Centro de Ciências
Agrárias, Universidade Federal do Espírito Santo, 29.500-000 Alegre (ES),
Brazil
| | - Andrei Caíque Pires Nunes
- Laboratório de Biometria, Departamento de Biologia Geral, Universidade Federal de
Viçosa, 36.570-000 Viçosa (MG), Brazil
| | - Tatiana Tavares Carrijo
- Laboratório de Botânica, Departamento de Biologia, Centro de Ciências Agrárias,
Universidade Federal do Espírito Santo, 29.500-000 Alegre (ES), Brazil
| | - Carlos Roberto Carvalho
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro
de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, 36.570-000 Viçosa (MG),
Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética, Departamento de Biologia, Centro de Ciências
Agrárias, Universidade Federal do Espírito Santo, 29.500-000 Alegre (ES),
Brazil
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154
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Gompert Z, Mock KE. Detection of individual ploidy levels with genotyping‐by‐sequencing (GBS) analysis. Mol Ecol Resour 2017; 17:1156-1167. [DOI: 10.1111/1755-0998.12657] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Zachariah Gompert
- Department of Biology and the Ecology Center Utah State University 5305 Old Main Hill Logan UT 84322‐5305 USA
| | - Karen E. Mock
- Wildland Resources Department and the Ecology Center Utah State University Logan UT 84322 USA
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155
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Hao M, Li A, Shi T, Luo J, Zhang L, Zhang X, Ning S, Yuan Z, Zeng D, Kong X, Li X, Zheng H, Lan X, Zhang H, Zheng Y, Mao L, Liu D. The abundance of homoeologue transcripts is disrupted by hybridization and is partially restored by genome doubling in synthetic hexaploid wheat. BMC Genomics 2017; 18:149. [PMID: 28187716 PMCID: PMC5303294 DOI: 10.1186/s12864-017-3558-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 02/07/2017] [Indexed: 11/10/2022] Open
Abstract
Background The formation of an allopolyploid is a two step process, comprising an initial wide hybridization event, which is later followed by a whole genome doubling. Both processes can affect the transcription of homoeologues. Here, RNA-Seq was used to obtain the genome-wide leaf transcriptome of two independent Triticum turgidum × Aegilops tauschii allotriploids (F1), along with their spontaneous allohexaploids (S1) and their parental lines. The resulting sequence data were then used to characterize variation in homoeologue transcript abundance. Results The hybridization event strongly down-regulated D-subgenome homoeologues, but this effect was in many cases reversed by whole genome doubling. The suppression of D-subgenome homoeologue transcription resulted in a marked frequency of parental transcription level dominance, especially with respect to genes encoding proteins involved in photosynthesis. Singletons (genes where no homoeologues were present) were frequently transcribed at both the allotriploid and allohexaploid plants. Conclusions The implication is that whole genome doubling helps to overcome the phenotypic weakness of the allotriploid, restoring a more favourable gene dosage in genes experiencing transcription level dominance in hexaploid wheat. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3558-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tongwei Shi
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Jiangtao Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xuechuan Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Deying Zeng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xingchen Kong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiaolong Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Huaigang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China. .,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
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156
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Braynen J, Yang Y, Wei F, Cao G, Shi G, Tian B, Zhang X, Jia H, Wei X, Wei Z. Transcriptome Analysis of Floral Buds Deciphered an Irregular Course of Meiosis in Polyploid Brassica rapa. FRONTIERS IN PLANT SCIENCE 2017; 8:768. [PMID: 28553302 PMCID: PMC5427127 DOI: 10.3389/fpls.2017.00768] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/24/2017] [Indexed: 05/21/2023]
Abstract
Polyploidy is a fundamental process in plant evolution. Understanding the polyploidy-associated effects on plant reproduction is essential for polyploid breeding program. In the present study, our cytological analysis firstly demonstrated that an overall course of meiosis was apparently distorted in the synthetic polyploid Brassica rapa in comparison with its diploid progenitor. To elucidate genetic basis of this irregular meiosis at a molecular level, the comparative RNA-seq analysis was further used to investigate differential genetic regulation of developing floral buds identified at meiosis between autotetraploid and diploid B. rapa. In total, compared to its diploid counterparts, among all 40,927 expressed genes revealed, 4,601 differentially expressed genes (DEGs) were identified in the floral buds of autotetraploid B. rapa, among which 288 DEGs annotated were involved in meiosis. Notably, DMC1 identified as one previously known meiosis-specific gene involved in inter-homologous chromosome dependent repair of DNA double stranded breaks (DSBs), was significantly down-regulated in autotetraploid B. rapa, which presumably contributed to abnormal progression during meiosis I. Although certain DEGs associated with RNA helicase, cell cycling, and somatic DNA repair were up-regulated after genome duplication, genes associated with meiotic DSB repair were significantly down-regulated. Furthermore, the expression of randomly selected DEGs by RNA-seq analysis was confirmed by quantitative real-time PCR analysis in both B. rapa and Arabidopsis thaliana. Our results firstly account for adverse effects of polyploidy on an entire course of meiosis at both cytological and transcriptomic levels, and allow for a comprehensive understanding of the uniformity and differences in the transcriptome of floral buds at meiosis between diploid and polyploid B. rapa as well.
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Affiliation(s)
- Janeen Braynen
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Yan Yang
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
| | - Fang Wei
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- *Correspondence: Fang Wei
| | - Gangqiang Cao
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
| | - Gongyao Shi
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
| | - Baoming Tian
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- Baoming Tian
| | - Xiaowei Zhang
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Hao Jia
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xiaochun Wei
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
- Xiaochun Wei
| | - Zhenzhen Wei
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
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157
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Dodsworth S, Jang TS, Struebig M, Chase MW, Weiss-Schneeweiss H, Leitch AR. Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae). PLANT SYSTEMATICS AND EVOLUTION = ENTWICKLUNGSGESCHICHTE UND SYSTEMATIK DER PFLANZEN 2017; 303:1013-1020. [PMID: 32009724 PMCID: PMC6961477 DOI: 10.1007/s00606-016-1356-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/23/2016] [Indexed: 05/02/2023]
Abstract
Nicotiana sect. Repandae is a group of four allotetraploid species originating from a single allopolyploidisation event approximately 5 million years ago. Previous phylogenetic analyses support the hypothesis of N. nudicaulis as sister to the other three species. This is concordant with changes in genome size, separating those with genome downsizing (N. nudicaulis) from those with genome upsizing (N. repanda, N. nesophila, N. stocktonii). However, a recent analysis reflecting genome dynamics of different transposable element families reconstructed greater similarity between N. nudicaulis and the Revillagigedo Island taxa (N. nesophila and N. stocktonii), thereby placing N. repanda as sister to the rest of the group. This could reflect a different phylogenetic hypothesis or the unique evolutionary history of these particular elements. Here we re-examine relationships in this group and investigate genome-wide patterns in repetitive DNA, utilising high-throughput sequencing and a genome skimming approach. Repetitive DNA clusters provide support for N. nudicaulis as sister to the rest of the section, with N. repanda sister to the two Revillagigedo Island species. Clade-specific patterns in the occurrence and abundance of particular repeats confirm the original (N. nudicaulis (N. repanda (N. nesophila + N. stocktonii))) hypothesis. Furthermore, overall repeat dynamics in the island species N. nesophila and N. stocktonii confirm their similarity to N. repanda and the distinctive patterns between these three species and N. nudicaulis. Together these results suggest that broad-scale repeat dynamics do in fact reflect evolutionary history and could be predicted based on phylogenetic distance.
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Affiliation(s)
- Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS UK
| | - Tae-Soo Jang
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| | - Mark W. Chase
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Hanna Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
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158
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Mason AS, Snowdon RJ. Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:883-892. [PMID: 27063780 DOI: 10.1111/plb.12462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/06/2016] [Indexed: 05/18/2023]
Abstract
Oilseed rape (Brassica napus) is one of our youngest crop species, arising several times under cultivation in the last few thousand years and completely unknown in the wild. Oilseed rape originated from hybridisation events between progenitor diploid species B. rapa and B. oleracea, both important vegetable species. The diploid progenitors are also ancient polyploids, with remnants of two previous polyploidisation events evident in the triplicated genome structure. This history of polyploid evolution and human agricultural selection makes B. napus an excellent model with which to investigate processes of genomic evolution and selection in polyploid crops. The ease of de novo interspecific hybridisation, responsiveness to tissue culture, and the close relationship of oilseed rape to the model plant Arabidopsis thaliana, coupled with the recent availability of reference genome sequences and suites of molecular cytogenetic and high-throughput genotyping tools, allow detailed dissection of genetic, genomic and phenotypic interactions in this crop. In this review we discuss the past and present uses of B. napus as a model for polyploid speciation and evolution in crop species, along with current and developing analysis tools and resources. We further outline unanswered questions that may now be tractable to investigation.
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Affiliation(s)
- A S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
| | - R J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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159
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Dou Q, Liu R, Yu F. Chromosomal organization of repetitive DNAs in Hordeum bogdanii and H. brevisubulatum (Poaceae). COMPARATIVE CYTOGENETICS 2016; 10:465-481. [PMID: 28123672 PMCID: PMC5240503 DOI: 10.3897/compcytogen.v10i4.9666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/12/2016] [Indexed: 05/29/2023]
Abstract
Molecular karyotypes of Hordeum bogdanii Wilensky, 1918 (2n = 14), and Hordeum brevisubulatum Link, 1844 ssp. brevisubulatum (2n = 28), were characterized by physical mapping of several repetitive sequences. A total of 18 repeats, including all possible di- or trinucleotide SSR (simple sequence repeat) motifs and satellite DNAs, such as pAs1, 5S rDNA, 45S rDNA, and pSc119.2, were used as probes for fluorescence in situ hybridization on root-tip metaphase chromosomes. Except for the SSR motifs AG, AT and GC, all the repeats we examined produced detectable hybridization signals on chromosomes of both species. A detailed molecular karyotype of the I genome of Hordeum bogdanii is described for the first time, and each repetitive sequence is physically mapped. A high degree of chromosome variation, including aneuploidy and structural changes, was observed in Hordeum brevisubulatum. Although the distribution of repeats in the chromosomes of Hordeum brevisubulatum is different from that of Hordeum bogdanii, similar patterns between the two species imply that the autopolyploid origin of Hordeum brevisubulatum is from a Hordeum species with an I genome. A comparison of the I genome and the other Hordeum genomes, H, Xa and Xu, shows that colocalization of motifs AAC, ACT and CAT and colocalization of motifs AAG and AGG are characteristic of the I genome. In addition, we discuss the evolutionary significance of repeats in the genome during genome differentiation.
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Affiliation(s)
- Quanwen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Ruijuan Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Feng Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810001, China
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160
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Xu Z, Xie B, Wu T, Xin X, Man L, Tan G, Xiong Z. Karyotyping and identifying all of the chromosomes of allopolyploid Brassica juncea using multicolor FISH. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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161
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Aleza P, Cuenca J, Juárez J, Navarro L, Ollitrault P. Inheritance in doubled-diploid clementine and comparative study with SDR unreduced gametes of diploid clementine. PLANT CELL REPORTS 2016; 35:1573-86. [PMID: 27038940 DOI: 10.1007/s00299-016-1972-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/21/2016] [Indexed: 05/23/2023]
Abstract
Tetraploid clementine displays mainly tetrasomic inheritance. Genetic structures of 2n SDR and 2 × gametes from DD clementine are complementary and will guides triploids citrus breeding strategies. Triploid breeding is developed worldwide to create new seedless cultivars. Citrus triploid hybrids can be recovered from 2x × 2x sexual hybridizations as a consequence of the formation of unreduced gametes (2n), or from 4x × 2x interploid hybridizations in which tetraploid parents used are most often doubled-diploid (DD). Here we have analyzed the inheritance in doubled-diploid clementine and compared the genetic structures of gametes of DD clementine with SDR unreduced gametes of diploid clementine. Parental heterozygosity restitution (PHR) with DD parents depends on the rate of preferential chromosome pairing and thus the proportion of disomic versus tetrasomic segregations. Doubled-diploid clementine largely exhibited tetrasomic segregation. However, three linkage groups had intermediate segregation and one had a tendency for disomy. Significant doubled reduction rates (DR) rates were observed in six of the nine LGs. Differences of PHR between 2n SDR and 2x DD gametes were highest in the centromeric region and progressively decreased toward the distal regions where they were not significant. Over all markers, PHR was lower (two-thirds) in SDR 2n gametes than in DD-derived diploid gametes. The two strategies appear complementary in terms of genotypic variability. Interploid 4x × 2x hybridization is potentially more efficient for developing new cultivars that are phenotypically closer to the diploid parent of the DD than sexual hybridization through SDR 2n gametes. Conversely, 2x × 2x triploidisation has the potential to produce novel products with characteristics for market segmentation strategies.
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Affiliation(s)
- P Aleza
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - J Cuenca
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - J Juárez
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - L Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain.
| | - P Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain.
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Station de Roujol, 97170, Petit-Bourg, Guadeloupe.
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162
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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163
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Zhou J, Tan C, Cui C, Ge X, Li Z. Distinct subgenome stabilities in synthesized Brassica allohexaploids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1257-1271. [PMID: 26971112 DOI: 10.1007/s00122-016-2701-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/27/2016] [Indexed: 05/10/2023]
Abstract
Trigenomic Brassica allohexaploids synthesized from three crossing strategies showed diploidized and non-diploidized meiotic behaviors and produced both euploid and aneuploid progenies during successive generations, revealing the distinct subgenome stabilities (B > A> C). Three cultivated allotetraploid Brassica species (Brassica napus, B. juncea, B. carinata) represent the model system of speciation through interspecific hybridization and allopolyploidization, but no Brassica species at higher ploidy level exists in nature. In this study, Brassica allohexaploids (2n = 54, AABBCC) were artificially synthesized using three crossing strategies, and had combinations of the genomes from the extant allotetraploids and diploids (B. rapa, B. oleracea and B. nigra). The chromosome numbers and complements of these allohexaploids and the self-pollinated progenies of successive generations (S0-S7) were determined using multicolor fluorescent in situ hybridization that distinguished the chromosomes of three constituent genomes from each other. Both euploid and aneuploid progenies were identified. The most aneuploids maintained all B- and A-genome chromosomes and variable number of C-genome chromosomes, suggesting that genome stability was B > A > C. In the extreme case, loss of whole set of C-genome chromosomes led to the production of B. juncea-type progeny. Some aneuploid progenies had the same number of chromosomes (2n = 54) as the euploid, but the simultaneous loss and gain of A- and C-genome chromosomes. The diploidized and non-diploidized meiotic behaviors co-occurred in all allohexaploid individuals of consecutive generations. The aberrant chromosome pairing and segregation mainly involved the chromosomes of A and C genomes, which resulted in aneuploidy in self-pollinated progenies. The mechanisms for the differential stability of three genomes and the stabilization of the new allohexaploids are discussed.
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Affiliation(s)
- Jiannan Zhou
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chen Tan
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China
| | - Xianhong Ge
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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164
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Mandáková T, Gloss AD, Whiteman NK, Lysak MA. How diploidization turned a tetraploid into a pseudotriploid. AMERICAN JOURNAL OF BOTANY 2016; 103:1187-96. [PMID: 27206460 DOI: 10.3732/ajb.1500452] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/10/2016] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Despite being highly fertile and occupying a large geographic region, the North American heartleaf bittercress (Cardamine cordifolia; Brassicaceae) has a puzzling triploid-like chromosome number (2n = 3x = 24). As most triploids are sterile, we embarked on a detailed analysis of the C. cordifolia genome to elucidate its origin and structure. METHODS Mitotic and meiotic chromosome complement of C. cordifolia was analyzed by comparative chromosome painting using chromosome-specific BAC contigs of Arabidopsis thaliana. Resulting chromosome patterns were documented by multicolor fluorescence microscopy and compared with known ancestral and extant Brassicaceae genomes. KEY RESULTS We discovered that C. cordifolia is not a triploid hybrid but a diploidized tetraploid with the prevalence of regular, diploid-like meiotic pairing. The ancestral tetraploid chromosome number (2n = 32) was reduced to a triploid-like number (2n = 24) through four terminal chromosome translocations. CONCLUSIONS The structure of the pseudotriploid C. cordifolia genome results from a stepwise diploidization process after whole-genome duplication. We showed that translocation-based descending dysploidy (from n = 16 to n = 12) was mediated by the formation of five new chromosomes. The genome of C. cordifolia represents the diploidization process in statu nascendi and provides valuable insights into mechanisms of postpolyploidy rediploidization in land plants. Our data further suggest that chromosome number alone does not need to be a reliable proxy of species' evolutionary past and that the same chromosome number may originate either by polyploidization (hybridization) or due to descending dysploidy.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Noah K Whiteman
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Martin A Lysak
- Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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165
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Tonosaki K, Osabe K, Kawanabe T, Fujimoto R. The importance of reproductive barriers and the effect of allopolyploidization on crop breeding. BREEDING SCIENCE 2016; 66:333-49. [PMID: 27436943 PMCID: PMC4902455 DOI: 10.1270/jsbbs.15114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/25/2016] [Indexed: 05/04/2023]
Abstract
Inter-specific hybrids are a useful source for increasing genetic diversity. Some reproductive barriers before and/or after fertilization prevent production of hybrid plants by inter-specific crossing. Therefore, techniques to overcome the reproductive barrier have been developed, and have contributed to hybridization breeding. In recent studies, identification of molecules involved in plant reproduction has been studied to understand the mechanisms of reproductive barriers. Revealing the molecular mechanisms of reproductive barriers may allow us to overcome reproductive barriers in inter-specific crossing, and to efficiently produce inter-specific hybrids in cross-combinations that cannot be produced through artificial techniques. Inter-specific hybrid plants can potentially serve as an elite material for plant breeding, produced through the merging of genomes of parental species by allopolyploidization. Allopolyploidization provides some benefits, such as heterosis, increased genetic diversity and phenotypic variability, which are caused by dynamic changes of the genome and epigenome. Understanding of allopolyploidization mechanisms is important for practical utilization of inter-specific hybrids as a breeding material. This review discusses the importance of reproductive barriers and the effect of allopolyploidization in crop breeding programs.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University,
641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813,
Japan
- Corresponding author (e-mail: )
| | - Kenji Osabe
- Okinawa Institute of Science and Technology,
1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495,
Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
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166
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Gallagher JP, Grover CE, Hu G, Wendel JF. Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis. Mol Ecol 2016; 25:2644-60. [PMID: 27027619 DOI: 10.1111/mec.13626] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/09/2016] [Accepted: 03/22/2016] [Indexed: 12/18/2022]
Abstract
Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a better understanding of the complex 'omic' underpinnings of phenotypic and ecological traits common to polyploidy, but also to provide novel insight into the interaction among duplicated genes and genomes. This adds perspective to the global patterns of expression (and other 'omic') change that accompany polyploidy and to the patterns of recruitment and/or loss of genes following polyploidization. While network analysis in polyploid species faces challenges common to other analyses of duplicated genomes, present technologies combined with thoughtful experimental design provide a powerful system to explore polyploid evolution. Here, we demonstrate the utility and potential of network analysis to questions pertaining to polyploidy with an example involving evolution of the transgressively superior cotton fibres found in polyploid Gossypium hirsutum. By combining network analysis with prior knowledge, we provide further insights into the role of profilins in fibre domestication and exemplify the potential for network analysis in polyploid species.
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Affiliation(s)
- Joseph P Gallagher
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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167
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Fulneček J, Matyášek R. The origin of exon 3 skipping of paternal GLOBOSA pre-mRNA in some Nicotiana tabacum lines correlates with a point mutation of the very last nucleotide of the exon. Mol Genet Genomics 2016; 291:801-18. [PMID: 26603606 DOI: 10.1007/s00438-015-1149-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
In plants, genome duplication followed by genome diversification and selection is recognized as a major evolutionary process. Rapid epigenetic and genetic changes that affect the transcription of parental genes are frequently observed after polyploidization. The pattern of alternative splicing is also frequently altered, yet the related molecular processes remain largely unresolved. Here, we study the inheritance and expression of parental variants of three floral organ identity genes in allotetraploid tobacco. DEFICIENS and GLOBOSA are B-class genes, and AGAMOUS is a C-class gene. Parental variants of these genes were found to be maintained in the tobacco genome, and the respective mRNAs were present in flower buds in comparable amounts. However, among five tobacco cultivars, we identified two in which the majority of paternal GLOBOSA pre-mRNA transcripts undergo exon 3 skipping, producing an mRNA with a premature termination codon. At the DNA level, we identified a G-A transition at the very last position of exon 3 in both cultivars. Although alternative splicing resulted in a dramatic decrease in full-length paternal GLOBOSA mRNA, no phenotypic effect was observed. Our finding likely serves as an example of the initiation of homoeolog diversification in a relatively young polyploid genome.
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Affiliation(s)
- Jaroslav Fulneček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265, Brno, Czech Republic.
| | - Roman Matyášek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265, Brno, Czech Republic
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168
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Balao F, Tannhäuser M, Lorenzo MT, Hedrén M, Paun O. Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex. Heredity (Edinb) 2016; 116:351-61. [PMID: 26604189 PMCID: PMC4787024 DOI: 10.1038/hdy.2015.98] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 10/17/2015] [Accepted: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.
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Affiliation(s)
- F Balao
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Tannhäuser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M T Lorenzo
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Hedrén
- Department of Biology, Lund University, Lund, Sweden
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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169
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Soltis PS, Soltis DE. Ancient WGD events as drivers of key innovations in angiosperms. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:159-65. [PMID: 27064530 DOI: 10.1016/j.pbi.2016.03.015] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 05/18/2023]
Abstract
Polyploidy, or whole-genome duplication (WGD), is a ubiquitous feature of plant genomes, contributing to variation in both genome size and gene content. Although polyploidy has occurred in all major clades of land plants, it is most frequent in angiosperms. Following a WGD in the common ancestor of all extant angiosperms, a complex pattern of both ancient and recent polyploidy is evident across angiosperm phylogeny. In several cases, ancient WGDs are associated with increased rates of species diversification. For example, a WGD in the common ancestor of Asteraceae, the largest family of angiosperms with ∼25000 species, is statistically linked to a shift in species diversification; several other old WGDs are followed by increased diversification after a 'lag' of up to three nodes. WGD may thus lead to a genomic combination that generates evolutionary novelty and may serve as a catalyst for diversification. In this paper, we explore possible links between WGD, the origin of novelty, and key innovations and propose a research path forward.
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Affiliation(s)
- Pamela S Soltis
- University of Florida, Florida Museum of Natural History, USA; University of Florida, Genetics Institute, USA.
| | - Douglas E Soltis
- University of Florida, Florida Museum of Natural History, USA; University of Florida, Genetics Institute, USA; Department of Biology, University of Florida, Gainesville, FL, USA
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170
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Soltis DE, Misra BB, Shan S, Chen S, Soltis PS. Polyploidy and the proteome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:896-907. [PMID: 26993527 DOI: 10.1016/j.bbapap.2016.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 03/06/2016] [Accepted: 03/11/2016] [Indexed: 12/23/2022]
Abstract
Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.
| | - Biswapriya B Misra
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Shengchen Shan
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.
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171
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Volis S, Ormanbekova D, Yermekbayev K, Abugalieva S, Turuspekov Y, Shulgina I. Genetic architecture of adaptation to novel environmental conditions in a predominantly selfing allopolyploid plant. Heredity (Edinb) 2016; 116:485-90. [PMID: 26837272 DOI: 10.1038/hdy.2016.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 12/09/2015] [Accepted: 12/18/2015] [Indexed: 11/09/2022] Open
Abstract
Genetic architecture of adaptation is traditionally studied in the context of local adaptation, viz. spatially varying conditions experienced by the species. However, anthropogenic changes in the natural environment pose a new context to this issue, that is, adaptation to an environment that is new for the species. In this study, we used crossbreeding to analyze genetic architecture of adaptation to conditions not currently experienced by the species but with high probability of encounter in the near future due to global climate change. We performed targeted interpopulation crossing using genotypes from two core and two peripheral Triticum dicoccoides populations and raised the parents and three generations of hybrids in a greenhouse under simulated desert conditions to analyze the genetic architecture of adaptation to these conditions and an effect of gene flow from plants having different origin. The hybrid (F1) fitness did not differ from that of the parents in crosses where both plants originated from the species core, but in crosses involving one parent from the species core and another one from the species periphery the fitness of F1 was consistently higher than that of the periphery-originated parent. Plant fitness in the next two generations (F2 and F3) did not differ from the F1, suggesting that effects of epistatic interactions between recombining and segregating alleles of genes contributing to fitness were minor or absent. The observed low importance of epistatic gene interactions in allopolyploid T. dicoccoides and low probability of hybrid breakdown appear to be the result of permanent fixation of heterozygosity and lack of intergenomic recombination in this species. At the same time, predominant but not complete selfing combined with an advantage of bivalent pairing of homologous chromosomes appears to maintain high genetic variability in T. dicoccoides, greatly enhancing its adaptive ability.
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Affiliation(s)
- S Volis
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - D Ormanbekova
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - K Yermekbayev
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - S Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Y Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - I Shulgina
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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172
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Matyášek R, Dobešová E, Húska D, Ježková I, Soltis PS, Soltis DE, Kovařík A. Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:362-377. [PMID: 26711705 DOI: 10.1111/tpj.13110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
Uniparental silencing of 35S rRNA genes (rDNA), known as nucleolar dominance (ND), is common in interspecific hybrids. Allotetraploid Tragopogon mirus composed of Tragopogon dubius (d) and Tragopogon porrifolius (p) genomes shows highly variable ND. To examine the molecular basis of such variation, we studied the genetic and epigenetic features of rDNA homeologs in several lines derived from recently and independently formed natural populations. Inbred lines derived from T. mirus with a dominant d-rDNA homeolog transmitted this expression pattern over generations, which may explain why it is prevalent among natural populations. In contrast, lines derived from the p-rDNA dominant progenitor were meiotically unstable, frequently switching to co-dominance. Interpopulation crosses between progenitors displaying reciprocal ND resulted in d-rDNA dominance, indicating immediate suppression of p-homeologs in F1 hybrids. Original p-rDNA dominance was not restored in later generations, even in those segregants that inherited the corresponding parental rDNA genotype, thus indicating the generation of additional p-rDNA and d-rDNA epigenetic variants. Despite preserved intergenic spacer (IGS) structure, they showed altered cytosine methylation and chromatin condensation patterns, and a correlation between expression, hypomethylation of RNA Pol I promoters and chromatin decondensation was apparent. Reversion of such epigenetic variants occurred rarely, resulting in co-dominance maintained in individuals with distinct genotypes. Generally, interpopulation crosses may generate epialleles that are not present in natural populations, underlying epigenetic dynamics in young allopolyploids. We hypothesize that highly expressed variants with distinct IGS features may induce heritable epigenetic reprogramming of the partner rDNA arrays, harmonizing the expression of thousands of genes in allopolyploids.
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Affiliation(s)
- Roman Matyášek
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Eva Dobešová
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Dalibor Húska
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Ivana Ježková
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Pamela S Soltis
- Florida Museum of National History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of National History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
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173
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Carmona A, de Bustos A, Jouve N, Cuadrado Á. Allopolyploidy and the complex phylogenetic relationships within the Hordeum brachyantherum taxon. Mol Phylogenet Evol 2016; 97:107-119. [PMID: 26790585 DOI: 10.1016/j.ympev.2016.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 12/12/2015] [Accepted: 01/05/2016] [Indexed: 12/30/2022]
Abstract
Hordeum brachyantherum Nevski includes two subspecies: the diploid (2×) subsp. californicum, and subsp. brachyantherum, which itself includes a tetraploid (4×) and a hexaploid (6×) cytotype. The phylogenetic relationships between these taxa and the origin of the polyploids remain controversial. To provide additional information to the many molecular phylogenetic analyses conducted within Hordeum, FISH-based karyotypes were produced for all subspecies/cytotypes within H. brachyantherum. Chromosomes of H. roshevitzii and H. marinum subsp. gussoneanum were also analysed since these species are potentially involved in the origin of the polyploids. For karyotyping, ten repetitive DNA sequences were screened to indentify repeats showing sufficient diversity in terms of copy number and localisation that they might serve as physical markers for distinguishing between each mitotic chromosome pair in all accessions. Genomic in situ hybridisation (GISH) was used to distinguish between subgenomes in polyploids. The karyotype maps allowed the assessment of the chromosomal diversity within species/cytotypes and the identification of possibly homoeologous chromosomes. The results show a wide divergence between the chromosomes of subsp. californicum and H. roshevitzii, and with their supposed derivatives in subsp. brachyantherum 4×. One of the three subgenomes of subsp. brachyantherum 6× is derived from subsp. gussoneanum with no genomic reorganisation (i.e., neither amplification nor loss of the repetitive DNA sequences analysed). It is generally accepted that subsp. brachyantherum 4× is the other progenitor of subsp. brachyantherum 6×, but the present results suggest this to be unlikely. The present findings thus show the cytogenetic diversity and genomic structure of H. brachyantherum, and reveal its complex evolutionary history, in which chromosomal diversification and allopolyploidy have played important roles.
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Affiliation(s)
- Alejandro Carmona
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Alfredo de Bustos
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Nicolás Jouve
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Ángeles Cuadrado
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain.
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174
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Lafon-Placette C, Vallejo-Marín M, Parisod C, Abbott RJ, Köhler C. Current plant speciation research: unravelling the processes and mechanisms behind the evolution of reproductive isolation barriers. THE NEW PHYTOLOGIST 2016; 209:29-33. [PMID: 26625345 DOI: 10.1111/nph.13756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Clément Lafon-Placette
- Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala BioCenter, Uppsala, SE-75007, Sweden
| | - Mario Vallejo-Marín
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, CH-2000, Switzerland
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Claudia Köhler
- Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala BioCenter, Uppsala, SE-75007, Sweden
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175
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Gao L, Diarso M, Zhang A, Zhang H, Dong Y, Liu L, Lv Z, Liu B. Heritable alteration of DNA methylation induced by whole-chromosome aneuploidy in wheat. THE NEW PHYTOLOGIST 2016; 209:364-75. [PMID: 26295562 DOI: 10.1111/nph.13595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/03/2015] [Indexed: 05/05/2023]
Abstract
Aneuploidy causes changes in gene expression and phenotypes in all organisms studied. A previous study in the model plant Arabidopsis thaliana showed that aneuploidy-generated phenotypic changes can be inherited to euploid progenies and implicated an epigenetic underpinning of the heritable variations. Based on an analysis by amplified fragment length polymorphism and methylation-sensitive amplified fragment length polymorphism markers, we found that although genetic changes at the nucleotide sequence level were negligible, extensive changes in cytosine DNA methylation patterns occurred in all studied homeologous group 1 whole-chromosome aneuploid lines of common wheat (Triticum aestivum), with monosomic 1A showing the greatest amount of methylation changes. The changed methylation patterns were inherited by euploid progenies derived from the aneuploid parents. The aneuploidy-induced DNA methylation alterations and their heritability were verified at selected loci by bisulfite sequencing. Our data have provided empirical evidence supporting earlier suggestions that heritability of aneuploidy-generated, but aneuploidy-independent, phenotypic variations may have an epigenetic basis. That at least one type of aneuploidy - monosomic 1A - was able to cause significant epigenetic divergence of the aneuploid plants and their euploid progenies also lends support to recent suggestions that aneuploidy may have played an important and protracted role in polyploid genome evolution.
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Affiliation(s)
- Lihong Gao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- School of Life Science, Changchun Normal University, Changchun, 130032, China
| | - Moussa Diarso
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yuzhu Dong
- School of Life Science, Changchun Normal University, Changchun, 130032, China
| | - Lixia Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhenling Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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176
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Cytonuclear Coordination Is Not Immediate upon Allopolyploid Formation in Tragopogon miscellus (Asteraceae) Allopolyploids. PLoS One 2015; 10:e0144339. [PMID: 26646761 PMCID: PMC4673006 DOI: 10.1371/journal.pone.0144339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/17/2015] [Indexed: 11/19/2022] Open
Abstract
Allopolyploids, formed by hybridization and chromosome doubling, face the immediate challenge of having duplicated nuclear genomes that interact with the haploid and maternally inherited cytoplasmic (plastid and mitochondrial) genomes. Most of our knowledge of the genomic consequences of allopolyploidy has focused on the fate of the duplicated nuclear genes without regard to their potential interactions with cytoplasmic genomes. As a step toward understanding the fates of nuclear-encoded subunits that are plastid-targeted, here we examine the retention and expression of the gene encoding the small subunit of Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco; rbcS) in multiple populations of allotetraploid Tragopogon miscellus (Asteraceae). These polyploids formed recently (~80 years ago) and repeatedly from T. dubius and T. pratensis in the northwestern United States. Examination of 79 T. miscellus individuals from 10 natural populations, as well as 25 synthetic allotetraploids, including reciprocally formed plants, revealed a low percentage of naturally occurring individuals that show a bias in either gene (homeolog) loss (12%) or expression (16%), usually toward maintaining the maternal nuclear copy of rbcS. For individuals showing loss, seven retained the maternally derived rbcS homeolog only, while three had the paternally derived copy. All of the synthetic polyploid individuals examined (S0 and S1 generations) retained and expressed both parental homeologs. These results demonstrate that cytonuclear coordination does not happen immediately upon polyploid formation in Tragopogon miscellus.
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177
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Polyploidy and genome evolution in plants. Curr Opin Genet Dev 2015; 35:119-25. [PMID: 26656231 DOI: 10.1016/j.gde.2015.11.003] [Citation(s) in RCA: 358] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 11/20/2022]
Abstract
Plant genomes vary in size and complexity, fueled in part by processes of whole-genome duplication (WGD; polyploidy) and subsequent genome evolution. Despite repeated episodes of WGD throughout the evolutionary history of angiosperms in particular, the genomes are not uniformly large, and even plants with very small genomes carry the signatures of ancient duplication events. The processes governing the evolution of plant genomes following these ancient events are largely unknown. Here, we consider mechanisms of diploidization, evidence of genome reorganization in recently formed polyploid species, and macroevolutionary patterns of WGD in plant genomes and propose that the ongoing genomic changes observed in recent polyploids may illustrate the diploidization processes that result in ancient signatures of WGD over geological timescales.
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178
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Liu HJ, Tang ZX, Han XM, Yang ZL, Zhang FM, Yang HL, Liu YJ, Zeng QY. Divergence in Enzymatic Activities in the Soybean GST Supergene Family Provides New Insight into the Evolutionary Dynamics of Whole-Genome Duplicates. Mol Biol Evol 2015; 32:2844-59. [PMID: 26219583 PMCID: PMC4651234 DOI: 10.1093/molbev/msv156] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Whole-genome duplication (WGD), or polyploidy, is a major force in plant genome evolution. A duplicate of all genes is present in the genome immediately following a WGD event. However, the evolutionary mechanisms responsible for the loss of, or retention and subsequent functional divergence of polyploidy-derived duplicates remain largely unknown. In this study we reconstructed the evolutionary history of the glutathione S-transferase (GST) gene family from the soybean genome, and identified 72 GST duplicated gene pairs formed by a recent Glycine-specific WGD event occurring approximately 13 Ma. We found that 72% of duplicated GST gene pairs experienced gene losses or pseudogenization, whereas 28% of GST gene pairs have been retained in the soybean genome. The GST pseudogenes were under relaxed selective constraints, whereas functional GSTs were subject to strong purifying selection. Plant GST genes play important roles in stress tolerance and detoxification metabolism. By examining the gene expression responses to abiotic stresses and enzymatic properties of the ancestral and current proteins, we found that polyploidy-derived GST duplicates show the divergence in enzymatic activities. Through site-directed mutagenesis of ancestral proteins, this study revealed that nonsynonymous substitutions of key amino acid sites play an important role in the divergence of enzymatic functions of polyploidy-derived GST duplicates. These findings provide new insights into the evolutionary and functional dynamics of polyploidy-derived duplicate genes.
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Affiliation(s)
- Hai-Jing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Zhen-Xin Tang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xue-Min Han
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Zhi-Ling Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hai-Ling Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yan-Jing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qing-Yin Zeng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
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179
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Jang TS, Weiss-Schneeweiss H. Formamide-Free Genomic in situ Hybridization Allows Unambiguous Discrimination of Highly Similar Parental Genomes in Diploid Hybrids and Allopolyploids. Cytogenet Genome Res 2015; 146:325-31. [PMID: 26492445 DOI: 10.1159/000441210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2015] [Indexed: 11/19/2022] Open
Abstract
Polyploidy and hybridization play an important role in plant diversification and speciation. The application of genomic in situ hybridization (GISH) allows the identification of parental genomes in hybrids, thus elucidating their origins and allowing for analysis of their genomic evolution. The performance of GISH depends on the similarity of the parental genomes and on the age of hybrids. Here, we present the formamide-free GISH (ff-GISH) protocol applied to diploid and polyploid hybrids of monocots (Prospero, Hyacinthaceae) and dicots (Melampodium, Asteraceae) differing in similarity of the parental genomes and in chromosome and genome sizes. The efficiency of the new protocol is compared to the standard GISH protocol. As a result, ff-GISH allowed efficient labeling and discrimination of the parental chromosome sets in diploid and allopolyploid hybrids in Prospero autumnale species complex. In contrast, the standard GISH protocol failed to differentiate the parental genomes due to high levels of similar repetitive DNA. Likewise, an unambiguous identification of parental genomes in allotetraploid Melampodium nayaritense (Asteraceae) was possible after ff-GISH, whereas the standard GISH hybridization performance was suboptimal. The modified method is simple and non-toxic and allows the discrimination of very similar parental genomes in hybrids. This method lends itself to modifications and improvements and can also be used for FISH.
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Affiliation(s)
- Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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180
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Matthews A, Emelianova K, Hatimy AA, Chester M, Pellicer J, Ahmad KS, Guignard MS, Rouhan G, Soltis DE, Soltis PS, Leitch IJ, Leitch AR, Mavrodiev EV, Buggs RJA. 250 years of hybridization between two biennial herb species without speciation. AOB PLANTS 2015; 7:plv081. [PMID: 26187604 PMCID: PMC4571729 DOI: 10.1093/aobpla/plv081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/04/2015] [Indexed: 05/23/2023]
Abstract
Hybridization between plant species can generate novel morphological diversity and lead to speciation at homoploid or polyploid levels. Hybrids between biennial herbs Tragopogon pratensis and T. porrifolius have been studied in experimental and natural populations for over 250 years. Here we examine their current status in natural populations in southeast England. All hybrids found were diploid; they tended to grow taller and with more buds than their parental species; many showed partial fertility; a few showed evidence of backcrossing. However, we found no evidence to suggest that the hybrids are establishing as a new species, nor can we find literature documenting speciation of these hybrids elsewhere. This lack of speciation despite at least 250 years of hybridization contrasts with the fact that both parental species have formed new allopolyploid species through hybridization with another diploid, T. dubius. Understanding why hybrids often do not speciate, despite repeated opportunities, would enhance our understanding of both the evolutionary process and risk assessments of invasive species.
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Affiliation(s)
- Andrew Matthews
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK Present address: Division of Ecology and Evolution, Imperial College London, Silwood Park Campus, Ascot, UK
| | - Katie Emelianova
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Abubakar A Hatimy
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Michael Chester
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Department of Plant Science, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Khawaja Shafique Ahmad
- Lab of Plant Taxonomy, Department of Botany, University of Agriculture, Faisalabad 38040, Pakistan
| | - Maité S Guignard
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Germinal Rouhan
- Museum national d'Histoire naturelle, UMR CNRS 7205, Herbier National, CP3916 rue Buffon, F-75231 Paris, France
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Evgeny V Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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181
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Abstract
Allopolyploidy involves hybridization and duplication of divergent parental genomes and provides new avenues for gene expression. The expression levels of duplicated genes in polyploids can show deviation from parental additivity (the arithmetic average of the parental expression levels). Nonadditive expression has been widely observed in diverse polyploids and comprises at least three possible scenarios: (a) The total gene expression level in a polyploid is similar to that of one of its parents (expression-level dominance); (b) total gene expression is lower or higher than in both parents (transgressive expression); and (c) the relative contribution of the parental copies (homeologs) to the total gene expression is unequal (homeolog expression bias). Several factors may result in expression nonadditivity in polyploids, including maternal-paternal influence, gene dosage balance, cis- and/or trans-regulatory networks, and epigenetic regulation. As our understanding of nonadditive gene expression in polyploids remains limited, a new generation of investigators should explore additional phenomena (i.e., alternative splicing) and use other high-throughput "omics" technologies to measure the impact of nonadditive expression on phenotype, proteome, and metabolome.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525; , ,
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182
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Li AL, Geng SF, Zhang LQ, Liu DC, Mao L. Making the Bread: Insights from Newly Synthesized Allohexaploid Wheat. MOLECULAR PLANT 2015; 8:847-59. [PMID: 25747845 DOI: 10.1016/j.molp.2015.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/13/2015] [Accepted: 02/25/2015] [Indexed: 05/27/2023]
Abstract
Bread wheat (or common wheat, Triticum aestivum) is an allohexaploid (AABBDD, 2n = 6x = 42) that arose by hybridization between a cultivated tetraploid wheat T. turgidum (AABB, 2n = 4x = 28) and the wild goatgrass Aegilops tauschii (DD, 2n = 2x = 14). Polyploidization provided niches for rigorous genome modification at cytogenetic, genetic, and epigenetic levels, rendering a broader spread than its progenitors. This review summarizes the latest advances in understanding gene regulation mechanisms in newly synthesized allohexaploid wheat and possible correlation with polyploid growth vigor and adaptation. Cytogenetic studies reveal persistent association of whole-chromosome aneuploidy with nascent allopolyploids, in contrast to the genetic stability in common wheat. Transcriptome analysis of the euploid wheat shows that small RNAs are driving forces for homoeo-allele expression regulation via genetic and epigenetic mechanisms. The ensuing non-additively expressed genes and those with expression level dominance to the respective progenitor may play distinct functions in growth vigor and adaptation in nascent allohexaploid wheat. Further genetic diploidization of allohexaploid wheat is not random. Regional asymmetrical gene distribution, rather than subgenome dominance, is observed in both synthetic and natural allohexaploid wheats. The combinatorial effects of diverged genomes, subsequent selection of specific gene categories, and subgenome-specific traits are essential for the successful establishment of common wheat.
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Affiliation(s)
- Ai-li Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai-Feng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lian-quan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Deng-cai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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183
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Vallejo-Marín M, Buggs RJA, Cooley AM, Puzey JR. Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus. Evolution 2015; 69:1487-1500. [PMID: 25929999 PMCID: PMC5033005 DOI: 10.1111/evo.12678] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Abstract
Whole genome duplication (polyploidization) is a mechanism of “instantaneous” species formation that has played a major role in the evolutionary history of plants. Much of what we know about the early evolution of polyploids is based upon studies of a handful of recently formed species. A new polyploid hybrid (allopolyploid) species Mimulus peregrinus, formed within the last 140 years, was recently discovered on the Scottish mainland and corroborated by chromosome counts. Here, using targeted, high‐depth sequencing of 1200 genic regions, we confirm the parental origins of this new species from M. x robertsii, a sterile triploid hybrid between the two introduced species M. guttatus and M. luteus that are naturalized and widespread in the United Kingdom. We also report a new population of M. peregrinus on the Orkney Islands and demonstrate that populations on the Scottish mainland and Orkney Islands arose independently via genome duplication from local populations of M. x robertsii. Our data raise the possibility that some alleles are already being lost in the evolving M. peregrinus genomes. The recent origins of a new species of the ecological model genus Mimulus via allopolyploidization provide a powerful opportunity to explore the early stages of hybridization and genome duplication in naturally evolved lineages.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington, 99362
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, 23185
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184
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Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides. Genetics 2015; 200:771-9. [PMID: 25971668 DOI: 10.1534/genetics.115.177642] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022] Open
Abstract
Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a single chromosome of cucumber were identified using a newly developed bioinformatic pipeline and then massively synthesized de novo in parallel. The synthesized oligos were amplified and labeled with biotin or digoxigenin for use in fluorescence in situ hybridization (FISH). We developed three different probes with each containing 23,000-27,000 oligos. These probes spanned 8.3-17 Mb of DNA on targeted cucumber chromosomes and had the densities of 1.5-3.2 oligos per kilobases. These probes produced FISH signals on a single cucumber chromosome and were used to paint homeologous chromosomes in other Cucumis species diverged from cucumber for up to 12 million years. The bulked oligo probes allowed us to track a single chromosome in early stages during meiosis. We were able to precisely map the pairing between cucumber chromosome 7 and chromosome 1 of Cucumis hystrix in a F1 hybrid. These two homeologous chromosomes paired in 71% of prophase I cells but only 25% of metaphase I cells, which may provide an explanation of the higher recombination rates compared to the chiasma frequencies between homeologous chromosomes reported in plant hybrids.
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185
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Mavrodiev EV, Chester M, Suárez-Santiago VN, Visger CJ, Rodriguez R, Susanna A, Baldini RM, Soltis PS, Soltis DE. Multiple origins and chromosomal novelty in the allotetraploid Tragopogon castellanus (Asteraceae). THE NEW PHYTOLOGIST 2015; 206:1172-1183. [PMID: 25557021 DOI: 10.1111/nph.13227] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
Tragopogon includes two classic examples of recently formed allopolyploid species in North America: T. mirus and T. miscellus. Older Tragopogon allotetraploids from Eurasia offer ideal taxa for comparing the longer term outcomes of allopolyploidy. To help resolve the ancestry of one of these older polyploids, phylogenetic analyses of multiple populations of the allotetraploid T. castellanus (2n = 24) and its putative diploid parents, T. crocifolius and T. lamottei, were conducted using sequences from nuclear (internal transcribed spacer, ITS; and alcohol dehydrogenase 1A, Adh) and plastid (trnT-trnL spacer, trnL intron, trnL-trnF spacer and rpl16 intron) loci. Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used to investigate the chromosomal constitution of T. castellanus. Our data confirm that the widely distributed T. crocifolius and the Iberian endemic, T. lamottei, are the diploid parents of T. castellanus, and that this polyploid formed at least three times. One group of populations of T. castellanus is distinct in exhibiting two pairs of rearranged chromosomes. These data suggest that some of the chromosomal variants that originate in young polyploids (here, an intergenomic translocation) may become fixed in populations, contributing to novelty in older polyploid lineages. The geographical distributions of the allopolyploids and parents are also complex, with allotetraploid populations being disjunct from one or both of the most closely related diploid parental populations.
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Affiliation(s)
- Evgeny V Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Michael Chester
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Roseana Rodriguez
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB-CSIC-ICUB), Pg. del Migdia, s.n., ES-08038, Barcelona, Spain
| | - Riccardo M Baldini
- Dipartimento di Biologia & Centro Studi Erbario Tropicale, Università degli Studi, Via G. La Pira 4, I-50121, Firenze, Italy
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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186
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Gene-expression novelty in allopolyploid cotton: a proteomic perspective. Genetics 2015; 200:91-104. [PMID: 25735302 DOI: 10.1534/genetics.115.174367] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/28/2015] [Indexed: 01/20/2023] Open
Abstract
Allopolyploidization is accompanied by changes in gene expression that are thought to contribute to phenotypic diversification. Here we describe global changes in the single-celled cotton fiber proteome of two natural allopolyploid species (Gossypium hirsutum and G. barbadense) and living models of their diploid parents using two different proteomic approaches. In total, 1323 two-dimensional gel electrophoresis spots and 1652 identified proteins by isobaric tags for relative and absolute quantitation were quantitatively profiled during fiber elongation. Between allopolyploids and their diploid A- and D-genome progenitors, amounts of differential expression ranged from 4.4 to 12.8%. Over 80% of the allopolyploid proteome was additively expressed with respect to progenitor diploids. Interestingly, the fiber proteome of G. hirsutum resembles the parental A-genome more closely, where long, spinable fiber first evolved, than does the fiber proteome of G. barbadense. More protein expression patterns were A-dominant than D-dominant in G. hirsutum, but in G. barbadense, the direction of expression-level dominance switched from the D-genome to the A-genome during fiber development. Comparison of developmental changes between the two allopolyploid species revealed a high level of proteomic differentiation despite their shared ancestry, relatively recent evolutionary divergence, and similar gross morphology. These results suggest that the two allopolyploid species have achieved superficially similar modern fiber phenotypes through different evolutionary routes at the proteome level. We also detected homeolog-specific expression for 1001 proteins and present a novel approach to infer the relationship between homeolog-specific and duplicate expression patterns. Our study provides a proteomic perspective on understanding evolutionary consequences of allopolyploidization, showing how protein expression has been altered by polyploidization and subsequently has diversified among species.
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187
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Chester M, Riley RK, Soltis PS, Soltis DE. Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae). Heredity (Edinb) 2015; 114:309-17. [PMID: 25370212 PMCID: PMC4815575 DOI: 10.1038/hdy.2014.101] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 09/04/2014] [Accepted: 09/09/2014] [Indexed: 12/16/2022] Open
Abstract
Cytological studies have shown many newly formed allopolyploids (neoallopolyploids) exhibit chromosomal variation as a result of meiotic irregularities, but few naturally occurring neoallopolyploids have been examined. Little is known about how long chromosomal variation may persist and how it might influence the establishment and evolution of allopolyploids in nature. In this study we assess chromosomal composition in a natural neoallotetraploid, Tragopogon mirus, and compare it with T. miscellus, which is an allotetraploid of similar age (~40 generations old). We also assess whether parental gene losses in T. mirus correlate with entire or partial chromosome losses. Of 37 T. mirus individuals that were karyotyped, 23 (62%) were chromosomally additive of the parents, whereas the remaining 14 individuals (38%) had aneuploid compositions. The proportion of additive versus aneuploid individuals differed from that found previously in T. miscellus, in which aneuploidy was more common (69%; Fisher's exact test, P=0.0033). Deviations from parental chromosome additivity within T. mirus individuals also did not reach the levels observed in T. miscellus, but similar compensated changes were observed. The loss of T. dubius-derived genes in two T. mirus individuals did not correlate with any chromosomal changes, indicating a role for smaller-scale genetic alterations. Overall, these data for T. mirus provide a second example of prolonged chromosomal instability in natural neoallopolyploid populations.
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Affiliation(s)
- M Chester
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - R K Riley
- Department of Biology, University of Florida, Gainesville, FL, USA
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - P S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - D E Soltis
- Department of Biology, University of Florida, Gainesville, FL, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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188
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Zhu B, Shao Y, Pan Q, Ge X, Li Z. Genome-wide gene expression perturbation induced by loss of C2 chromosome in allotetraploid Brassica napus L. FRONTIERS IN PLANT SCIENCE 2015; 6:763. [PMID: 26442076 PMCID: PMC4585227 DOI: 10.3389/fpls.2015.00763] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/05/2015] [Indexed: 05/05/2023]
Abstract
Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and nullisomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the nullisomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than nullisomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.
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Affiliation(s)
- Bin Zhu
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Bin Zhu and Zaiyun Li, College of Plant Science and Technology, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan 430070, China ;
| | - Yujiao Shao
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- College of Chemistry and Life Science, Hubei University of EducationWuhan, China
| | - Qi Pan
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xianhong Ge
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Bin Zhu and Zaiyun Li, College of Plant Science and Technology, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan 430070, China ;
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189
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Renny-Byfield S, Wendel JF. Doubling down on genomes: polyploidy and crop plants. AMERICAN JOURNAL OF BOTANY 2014; 101:1711-25. [PMID: 25090999 DOI: 10.3732/ajb.1400119] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidy, or whole genome multiplication, is ubiquitous among angiosperms. Many crop species are relatively recent allopolyploids, resulting from interspecific hybridization and polyploidy. Thus, an appreciation of the evolutionary consequences of (allo)polyploidy is central to our understanding of crop plant domestication, agricultural improvement, and the evolution of angiosperms in general. Indeed, many recent insights into plant biology have been gleaned from polyploid crops, including, but not limited to wheat, tobacco, sugarcane, apple, and cotton. A multitude of evolutionary processes affect polyploid genomes, including rapid and substantial genome reorganization, transgressive gene expression alterations, gene fractionation, gene conversion, genome downsizing, and sub- and neofunctionalization of duplicate genes. Often these genomic changes are accompanied by heterosis, robustness, and the improvement of crop yield, relative to closely related diploids. Historically, however, the genome-wide analysis of polyploid crops has lagged behind those of diploid crops and other model organisms. This lag is partly due to the difficulties in genome assembly, resulting from the genomic complexities induced by combining two or more evolutionarily diverged genomes into a single nucleus and by the significant size of polyploid genomes. In this review, we explore the role of polyploidy in angiosperm evolution, the domestication process and crop improvement. We focus on the potential of modern technologies, particularly next-generation sequencing, to inform us on the patterns and processes governing polyploid crop improvement and phenotypic change subsequent to domestication.
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Affiliation(s)
- Simon Renny-Byfield
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
| | - Jonathan F Wendel
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
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190
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Sherman-Broyles S, Bombarely A, Powell AF, Doyle JL, Egan AN, Coate JE, Doyle JJ. The wild side of a major crop: soybean's perennial cousins from Down Under. AMERICAN JOURNAL OF BOTANY 2014; 101:1651-65. [PMID: 25326613 DOI: 10.3732/ajb.1400121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The accumulation of over 30 years of basic research on the biology, genetic variation, and evolution of the wild perennial relatives of soybean (Glycine max) provides a foundation to improve cultivated soybean. The cultivated soybean and its wild progenitor, G. soja, have a center of origin in eastern Asia and are the only two species in the annual subgenus Soja. Systematic and evolutionary studies of the ca. 30 perennial species of subgenus Glycine, native to Australia, have benefited from the availability of the G. max genomic sequence. The perennial species harbor many traits of interest to soybean breeders, among them resistance to major soybean pathogens such as cyst nematode and leaf rust. New species in the Australian subgenus continue to be described, due to the collection of new material and to insights gleaned through systematic studies of accessions in germplasm collections. Ongoing studies in perennial species focus on genomic regions that contain genes for key traits relevant to soybean breeding. These comparisons also include the homoeologous regions that are the result of polyploidy in the common ancestor of all Glycine species. Subgenus Glycine includes a complex of recently formed allopolyploids that are the focus of studies aimed at elucidating genomic, transcriptomic, physiological, taxonomic, morphological, developmental, and ecological processes related to polyploid evolution. Here we review what has been learned over the past 30 years and outline ongoing work on photosynthesis, nitrogen fixation, and floral biology, much of it drawing on new technologies and resources.
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Affiliation(s)
| | | | - Adrian F Powell
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Jane L Doyle
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Ashley N Egan
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington D.C. 20013-7012 USA
| | - Jeremy E Coate
- Reed College, Department of Biology, 3203 SE Woodstock Blvd., Portland, Oregon 97202 USA
| | - Jeff J Doyle
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
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191
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Martin KJ, Holland PWH. Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication. Mol Biol Evol 2014; 31:2592-611. [PMID: 24974377 PMCID: PMC4166920 DOI: 10.1093/molbev/msu202] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2014] [Indexed: 12/13/2022] Open
Abstract
Numerous ancient whole-genome duplications (WGD) have occurred during eukaryote evolution. In vertebrates, duplicated developmental genes and their functional divergence have had important consequences for morphological evolution. Although two vertebrate WGD events (1R/2R) occurred over 525 Ma, we have focused on the more recent 3R or TGD (teleost genome duplication) event which occurred approximately 350 Ma in a common ancestor of over 26,000 species of teleost fishes. Through a combination of whole genome and bacterial artificial chromosome clone sequencing we characterized all Hox gene clusters of Pantodon buchholzi, a member of the early branching teleost subdivision Osteoglossomorpha. We find 45 Hox genes organized in only five clusters indicating that Pantodon has suffered more Hox cluster loss than other known species. Despite strong evidence for homology of the five Pantodon clusters to the four canonical pre-TGD vertebrate clusters (one HoxA, two HoxB, one HoxC, and one HoxD), we were unable to confidently resolve 1:1 orthology relationships between four of the Pantodon clusters and the eight post-TGD clusters of other teleosts. Phylogenetic analysis revealed that many Pantodon genes segregate outside the conventional "a" and "b" post-TGD orthology groups, that extensive topological incongruence exists between genes physically linked on a single cluster, and that signal divergence causes ambivalence in assigning 1:1 orthology in concatenated Hox cluster analyses. Out of several possible explanations for this phenomenon we favor a model which keeps with the prevailing view of a single TGD prior to teleost radiation, but which also considers the timing of diploidization after duplication, relative to speciation events. We suggest that although the duplicated hoxa clusters diploidized prior to divergence of osteoglossomorphs, the duplicated hoxb, hoxc, and hoxd clusters concluded diploidization independently in osteoglossomorphs and other teleosts. We use the term "tetralogy" to describe the homology relationship which exists between duplicated sequences which originate through a shared WGD, but which diploidize into distinct paralogs from a common allelic pool independently in two lineages following speciation.
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Affiliation(s)
- Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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192
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Sehrish T, Symonds VV, Soltis DE, Soltis PS, Tate JA. Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids. BMC Genomics 2014; 15:701. [PMID: 25145399 PMCID: PMC4148530 DOI: 10.1186/1471-2164-15-701] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/18/2014] [Indexed: 01/03/2023] Open
Abstract
Background Hybridization coupled with whole-genome duplication (allopolyploidy) leads to a variety of genetic and epigenetic modifications in the resultant merged genomes. In particular, gene loss and gene silencing are commonly observed post-polyploidization. Here, we investigated DNA methylation as a potential mechanism for gene silencing in Tragopogon miscellus (Asteraceae), a recent and recurrently formed allopolyploid. This species, which also exhibits extensive gene loss, was formed from the diploids T. dubius and T. pratensis. Results Comparative bisulfite sequencing revealed CG methylation of parental homeologs for three loci (S2, S18 and TDF-44) that were previously identified as silenced in T. miscellus individuals relative to the diploid progenitors. One other locus (S3) examined did not show methylation, indicating that other transcriptional and post-transcriptional mechanisms are likely responsible for silencing that homeologous locus. Conclusions These results indicate that Tragopogon miscellus allopolyploids employ diverse mechanisms, including DNA methylation, to respond to the potential shock of genome merger and doubling. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-701) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Jennifer A Tate
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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193
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Soltis PS, Liu X, Marchant DB, Visger CJ, Soltis DE. Polyploidy and novelty: Gottlieb's legacy. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130351. [PMID: 24958924 PMCID: PMC4071524 DOI: 10.1098/rstb.2013.0351] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30, 818-830. (doi:10.2307/2407821)) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents (T. dubius and T. porrifolius, and T. dubius and T. pratensis, respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity-the production of novel enzyme forms in the allopolyploids-can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes-with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity-may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.
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Affiliation(s)
- Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Xiaoxian Liu
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
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194
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Parasexuality and mosaic aneuploidy in Leishmania: alternative genetics. Trends Parasitol 2014; 30:429-35. [PMID: 25073852 DOI: 10.1016/j.pt.2014.07.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 12/25/2022]
Abstract
Reproduction as identical or similar organisms in most biological systems depends on the extreme accuracy of the mitotic (and meiotic) mechanisms involved in the transmission of the genetic material to the two daughter cells. Character recombination and genotype diversification are ensured by the alternation between haploidy and diploidy, which corresponds to the most predominant model in sexually reproducing organisms. In Leishmania, the unique association of high levels of automixis and of constitutive 'mosaic aneuploidy' unexpectedly does not lead to loss of heterozygosity but constitutes an alternative for genotype recombination, hence a source of adaptability.
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195
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Fuentes I, Stegemann S, Golczyk H, Karcher D, Bock R. Horizontal genome transfer as an asexual path to the formation of new species. Nature 2014; 511:232-5. [PMID: 24909992 DOI: 10.1038/nature13291] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/31/2014] [Indexed: 11/08/2022]
Abstract
Allopolyploidization, the combination of the genomes from two different species, has been a major source of evolutionary innovation and a driver of speciation and environmental adaptation. In plants, it has also contributed greatly to crop domestication, as the superior properties of many modern crop plants were conferred by ancient allopolyploidization events. It is generally thought that allopolyploidization occurred through hybridization events between species, accompanied or followed by genome duplication. Although many allopolyploids arose from closely related species (congeners), there are also allopolyploid species that were formed from more distantly related progenitor species belonging to different genera or even different tribes. Here we have examined the possibility that allopolyploidization can also occur by asexual mechanisms. We show that upon grafting--a mechanism of plant-plant interaction that is widespread in nature--entire nuclear genomes can be transferred between plant cells. We provide direct evidence for this process resulting in speciation by creating a new allopolyploid plant species from a herbaceous species and a woody species in the nightshade family. The new species is fertile and produces fertile progeny. Our data highlight natural grafting as a potential asexual mechanism of speciation and also provide a method for the generation of novel allopolyploid crop species.
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Affiliation(s)
- Ignacia Fuentes
- 1] Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany [2]
| | - Sandra Stegemann
- 1] Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany [2]
| | - Hieronim Golczyk
- Department of Molecular Biology, Institute of Biotechnology, John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708 Lublin, Poland
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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196
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Zhang H, Zhu B, Qi B, Gou X, Dong Y, Xu C, Zhang B, Huang W, Liu C, Wang X, Yang C, Zhou H, Kashkush K, Feldman M, Wendel JF, Liu B. Evolution of the BBAA component of bread wheat during its history at the allohexaploid level. THE PLANT CELL 2014; 26:2761-76. [PMID: 24989045 PMCID: PMC4145112 DOI: 10.1105/tpc.114.128439] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Subgenome integrity in bread wheat (Triticum aestivum; BBAADD) makes possible the extraction of its BBAA component to restitute a novel plant type. The availability of such a ploidy-reversed wheat (extracted tetraploid wheat [ETW]) provides a unique opportunity to address whether and to what extent the BBAA component of bread wheat has been modified in phenotype, karyotype, and gene expression during its evolutionary history at the allohexaploid level. We report here that ETW was anomalous in multiple phenotypic traits but maintained a stable karyotype. Microarray-based transcriptome profiling identified a large number of differentially expressed genes between ETW and natural tetraploid wheat (Triticum turgidum), and the ETW-downregulated genes were enriched for distinct Gene Ontology categories. Quantitative RT-PCR analysis showed that gene expression differences between ETW and a set of diverse durum wheat (T. turgidum subsp durum) cultivars were distinct from those characterizing tetraploid cultivars per se. Pyrosequencing revealed that the expression alterations may occur to either only one or both of the B and A homoeolog transcripts in ETW. A majority of the genes showed additive expression in a resynthesized allohexaploid wheat. Analysis of a synthetic allohexaploid wheat and diverse bread wheat cultivars revealed the rapid occurrence of expression changes to the BBAA subgenomes subsequent to allohexaploidization and their evolutionary persistence.
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Affiliation(s)
- Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bo Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bao Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Yuzhu Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011
| | - Bangjiao Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Wei Huang
- Key Laboratory for Applied Statistics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Chang Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Hao Zhou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Moshe Feldman
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
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197
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An Z, Tang Z, Ma B, Mason AS, Guo Y, Yin J, Gao C, Wei L, Li J, Fu D. Transposon variation by order during allopolyploidisation between Brassica oleracea and Brassica rapa. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:825-35. [PMID: 24176077 DOI: 10.1111/plb.12121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 09/23/2013] [Indexed: 05/02/2023]
Abstract
Although many studies have shown that transposable element (TE) activation is induced by hybridisation and polyploidisation in plants, much less is known on how different types of TE respond to hybridisation, and the impact of TE-associated sequences on gene function. We investigated the frequency and regularity of putative transposon activation for different types of TE, and determined the impact of TE-associated sequence variation on the genome during allopolyploidisation. We designed different types of TE primers and adopted the Inter-Retrotransposon Amplified Polymorphism (IRAP) method to detect variation in TE-associated sequences during the process of allopolyploidisation between Brassica rapa (AA) and Brassica oleracea (CC), and in successive generations of self-pollinated progeny. In addition, fragments with TE insertions were used to perform Blast2GO analysis to characterise the putative functions of the fragments with TE insertions. Ninety-two primers amplifying 548 loci were used to detect variation in sequences associated with four different orders of TE sequences. TEs could be classed in ascending frequency into LTR-REs, TIRs, LINEs, SINEs and unknown TEs. The frequency of novel variation (putative activation) detected for the four orders of TEs was highest from the F1 to F2 generations, and lowest from the F2 to F3 generations. Functional annotation of sequences with TE insertions showed that genes with TE insertions were mainly involved in metabolic processes and binding, and preferentially functioned in organelles. TE variation in our study severely disturbed the genetic compositions of the different generations, resulting in inconsistencies in genetic clustering. Different types of TE showed different patterns of variation during the process of allopolyploidisation.
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Affiliation(s)
- Z An
- Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
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198
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Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton). Genetics 2014; 197:1153-63. [PMID: 24907262 DOI: 10.1534/genetics.114.166124] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Genome duplication is thought to be central to the evolution of morphological complexity, and some polyploids enjoy a variety of capabilities that transgress those of their diploid progenitors. Comparison of genomic sequences from several tetraploid (AtDt) Gossypium species and genotypes with putative diploid A- and D-genome progenitor species revealed that unidirectional DNA exchanges between homeologous chromosomes were the predominant mechanism responsible for allelic differences between the Gossypium tetraploids and their diploid progenitors. Homeologous gene conversion events (HeGCEs) gradually subsided, declining to rates similar to random mutation during radiation of the polyploid into multiple clades and species. Despite occurring in a common nucleus, preservation of HeGCE is asymmetric in the two tetraploid subgenomes. At-to-Dt conversion is far more abundant than the reciprocal, is enriched in heterochromatin, is highly correlated with GC content and transposon distribution, and may silence abundant A-genome-derived retrotransposons. Dt-to-At conversion is abundant in euchromatin and genes, frequently reversing losses of gene function. The long-standing observation that the nonspinnable-fibered D-genome contributes to the superior yield and quality of tetraploid cotton fibers may be explained by accelerated Dt to At conversion during cotton domestication and improvement, increasing dosage of alleles from the spinnable-fibered A-genome. HeGCE may provide an alternative to (rare) reciprocal DNA exchanges between chromosomes in heterochromatin, where genes have approximately five times greater abundance of Dt-to-At conversion than does adjacent intergenic DNA. Spanning exon-to-gene-sized regions, HeGCE is a natural noninvasive means of gene transfer with the precision of transformation, potentially important in genetic improvement of many crop plants.
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Moghe GD, Shiu SH. The causes and molecular consequences of polyploidy in flowering plants. Ann N Y Acad Sci 2014; 1320:16-34. [PMID: 24903334 DOI: 10.1111/nyas.12466] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polyploidy is an important force shaping plant genomes. All flowering plants are descendants of an ancestral polyploid species, and up to 70% of extant vascular plant species are believed to be recent polyploids. Over the past century, a significant body of knowledge has accumulated regarding the prevalence and ecology of polyploid plants. In this review, we summarize our current understanding of the causes and molecular consequences of polyploidization in angiosperms. We also provide a discussion on the relationships between polyploidy and adaptation and suggest areas where further research may provide a better understanding of polyploidy.
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Soltis DE, Segovia-Salcedo MC, Jordon-Thaden I, Majure L, Miles NM, Mavrodiev EV, Mei W, Cortez MB, Soltis PS, Gitzendanner MA. Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al. (). THE NEW PHYTOLOGIST 2014; 202:1105-1117. [PMID: 24754325 DOI: 10.1111/nph.12756] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - María Claudia Segovia-Salcedo
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Grupo de Investigacíon Conservación de Bosques de Polylepis, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de la Fuerzas Armadas - ESPE, Sangolquí, Ecuador
| | - Ingrid Jordon-Thaden
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- University and Jepson Herbaria, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Lucas Majure
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Nicolas M Miles
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Evgeny V Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Wenbin Mei
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | | | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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