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Katayama N, Yamamoto T, Aiuchi S, Watano Y, Fujiwara T. Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales). FRONTIERS IN PLANT SCIENCE 2024; 14:1286320. [PMID: 38264021 PMCID: PMC10803465 DOI: 10.3389/fpls.2023.1286320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern-Phegopteris decursivepinnata-and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.
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Affiliation(s)
- Natsu Katayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Takuya Yamamoto
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Sakura Aiuchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Tao Fujiwara
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
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2
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Yu Q, Yang FS, Chen YX, Wu H, Ickert-Bond SM, Wang XQ. Diploid species phylogeny and evolutionary reticulation indicate early radiation of Ephedra in the Tethys coast. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2619-2630. [PMID: 37837251 DOI: 10.1111/jipb.13573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
Reconstructing a robust species phylogeny and disentangling the evolutionary and biogeographic history of the gymnosperm genus Ephedra, which has a large genome and rich polyploids, remain a big challenge. Here we reconstructed a transcriptome-based phylogeny of 19 diploid Ephedra species, and explored evolutionary reticulations in this genus represented by 50 diploid and polyploid species, using four low-copy nuclear and nine plastid genes. The diploid species phylogeny indicates that the Mediterranean species diverged first, and the remaining species split into three clades, including the American species (Clade A), E. rhytidosperma, and all other Asian species (Clade B). The single-gene trees placed E. rhytidosperma sister to Clade A, Clade B, or Clades A + B in similar proportions, suggesting that radiation and gene flow likely occurred in the early evolution of Ephedra. In addition, reticulate evolution occurred not only among the deep nodes, but also in the recently evolved South American species, which further caused difficulty in phylogenetic reconstruction. Moreover, we found that allopolyploid speciation was pervasive in Ephedra. Our study also suggests that Ephedra very likely originated in the Tethys coast during the late Cretaceous, and the South American Ephedra species have a single origin by dispersal from Mexico or North America.
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Affiliation(s)
- Qiong Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fu-Sheng Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Xing Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Stefanie M Ickert-Bond
- Department of Biology and Wildlife & UA Museum of the North, University of Alaska Fairbanks (UAF), Fairbanks, AK, 99775, USA
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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3
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Xing L, Wang M, He Q, Zhang H, Liang H, Zhou Q, Liu Y, Liu Z, Wang Y, Du C, Xiao Y, Liu J, Li W, Liu G, Du H. Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum. BMC Biol 2023; 21:161. [PMID: 37480118 PMCID: PMC10362693 DOI: 10.1186/s12915-023-01643-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/06/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. RESULTS Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. CONCLUSIONS Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.
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Affiliation(s)
- Longsheng Xing
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Meijia Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qiang He
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Hongyu Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Hanfei Liang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qinghong Zhou
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Ze Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Cailian Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yao Xiao
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Jianan Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Wei Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Guixia Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
| | - Huilong Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
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4
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Farhat P, Siljak-Yakovlev S, Takvorian N, Bou Dagher Kharrat M, Robert T. Allopolyploidy: An Underestimated Driver in Juniperus Evolution. Life (Basel) 2023; 13:1479. [PMID: 37511854 PMCID: PMC10381917 DOI: 10.3390/life13071479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Allopolyploidy is considered as a principal driver that shaped angiosperms' evolution in terms of diversification and speciation. Despite the unexpected high frequency of polyploidy that was recently discovered in the coniferous genus Juniperus, little is known about the origin of these polyploid taxa. Here, we conducted the first study devoted to deciphering the origin of the only hexaploid taxon in Juniperus along with four of its closely related tetraploid taxa using AFLP markers with four primers combinations. Phylogenetic analysis revealed that the 10 studied species belong to 2 major clusters. J. foetidissima appeared to be more related to J. thurifera, J. sabina, and J. chinensis. The Bayesian clustering analysis showing a slight variation in genetic admixture between the studied populations of J. foetidissima, suggesting an allopolyploid origin of this species involving J. thurifera and J. sabina lineages, although a purely autopolyploidy origin of both J. thurifera and J. foetidissima cannot be ruled out. The admixed genetic pattern revealed for J. seravschanica showed that the tetraploid cytotypes of this species originated from allopolyploidy, whereas no clear evidence of hybridization in the origin of the tetraploid J. thurifera and J. chinensis was detected. This study provides first insights into the polyploidy origin of the Sabina section and highlights the potential implication of allopolyploidy in the evolution of the genus Juniperus. Further analyses are needed for a more in-depth understanding of the evolutionary scenarios that produced the observed genetic patterns.
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Affiliation(s)
- Perla Farhat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP, 1514 Riad el Solh, Beirut 1107 2050, Lebanon
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Najat Takvorian
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Faculté des Sciences et Ingénierie, Sorbonne Université, UFR 927, 4 Place Jussieu, 75252 Paris, France
| | - Magda Bou Dagher Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP, 1514 Riad el Solh, Beirut 1107 2050, Lebanon
- European Forest Institute, Mediterranean, Sant Pau Art Nouveau Site, St. Antoni M. Claret, 167, 08025 Barcelona, Spain
| | - Thierry Robert
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Faculté des Sciences et Ingénierie, Sorbonne Université, UFR 927, 4 Place Jussieu, 75252 Paris, France
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5
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Premachandra T, Cauret CMS, Conradie W, Measey J, Evans BJ. Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa. G3 (BETHESDA, MD.) 2022; 13:6916838. [PMID: 36524354 PMCID: PMC9911082 DOI: 10.1093/g3journal/jkac325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
Abstract
Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog-the African clawed frog (Xenopus laevis)-over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa.
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Affiliation(s)
- Tharindu Premachandra
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, ON L8S4K1, Canada
| | - Caroline M S Cauret
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, ON L8S4K1, Canada,Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Gqeberha 6013, South Africa,Department of Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, Nelson Mandela University, George Campus, George 6019, South Africa
| | - John Measey
- Corresponding author: Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa.
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6
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Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton. Proc Natl Acad Sci U S A 2022; 119:e2209743119. [PMID: 36279429 PMCID: PMC9636936 DOI: 10.1073/pnas.2209743119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton (
Gossypium hirsutum
and
Gossypium barbadense
, AADD) and its extant AA (
Gossypium arboreum
) and DD (
Gossypium raimondii
) progenitors. We observed distinct DHS distributions between
G. arboreum
and
G. raimondii
. In contrast, the DHSs of the two subgenomes of
G. hirsutum
and
G. barbadense
showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids
Gossypium darwinii
and
G. hirsutum
var.
yucatanense
, but absent from a resynthesized hybrid of
G. arboreum
and
G. raimondii
, suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative
cis
-regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.
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7
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Scarlett VT, Lovell JT, Shao M, Phillips J, Shu S, Lusinska J, Goodstein DM, Jenkins J, Grimwood J, Barry K, Chalhoub B, Schmutz J, Hasterok R, Catalán P, Vogel JP. Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium. Genetics 2022; 223:6758249. [PMID: 36218464 PMCID: PMC9910409 DOI: 10.1093/genetics/iyac146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
The "genomic shock" hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession "Bhyb26." We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species' similarity in transposable element load may account for the subtlety of the observed genome dominance.
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Affiliation(s)
- Virginia T Scarlett
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mingqin Shao
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Jeremy Phillips
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Shengqiang Shu
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - David M Goodstein
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kerrie Barry
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Jeremy Schmutz
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA,Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - John P Vogel
- Corresponding author: U.S. Dept. of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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8
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Zumajo-Cardona C, Ambrose BA. Fleshy or dry: transcriptome analyses reveal the genetic mechanisms underlying bract development in Ephedra. EvoDevo 2022; 13:10. [PMID: 35477429 PMCID: PMC9047513 DOI: 10.1186/s13227-022-00195-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gnetales have a key phylogenetic position in the evolution of seed plants. Among the Gnetales, there is an extraordinary morphological diversity of seeds, the genus Ephedra, in particular, exhibits fleshy, coriaceous or winged (dry) seeds. Despite this striking diversity, its underlying genetic mechanisms remain poorly understood due to the limited studies in gymnosperms. Expanding the genomic and developmental data from gymnosperms contributes to a better understanding of seed evolution and development. RESULTS We performed transcriptome analyses on different plant tissues of two Ephedra species with different seed morphologies. Anatomical observations in early developing ovules, show that differences in the seed morphologies are established early in their development. The transcriptomic analyses in dry-seeded Ephedra californica and fleshy-seeded Ephedra antisyphilitica, allowed us to identify the major differences between the differentially expressed genes in these species. We detected several genes known to be involved in fruit ripening as upregulated in the fleshy seed of Ephedra antisyphilitica. CONCLUSIONS This study allowed us to determine the differentially expressed genes involved in seed development of two Ephedra species. Furthermore, the results of this study of seeds with the enigmatic morphology in Ephedra californica and Ephedra antisyphilitica, allowed us to corroborate the hypothesis which suggest that the extra envelopes covering the seeds of Gnetales are not genetically similar to integument. Our results highlight the importance of carrying out studies on less explored species such as gymnosperms, to gain a better understanding of the evolutionary history of plants.
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Affiliation(s)
- Cecilia Zumajo-Cardona
- New York Botanical Garden, Bronx, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Barbara A Ambrose
- New York Botanical Garden, Bronx, NY, USA. .,The Graduate Center, City University of New York, New York, NY, USA.
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9
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Roy SW. Dual Fertilization, Intragenomic Conflict, Genome Downsizing, and Angiosperm Dominance. TRENDS IN PLANT SCIENCE 2021; 26:767-769. [PMID: 34108106 DOI: 10.1016/j.tplants.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
New work suggests 'subgenome dominance' in polyploids may only occur in angiosperms. Subgenome dominance could explain angiosperm-specific genome reduction, with potential implications for angiosperms' global dominance. I suggest that evolution of the endosperm could have selected for the evolution of subgenome dominance, due to increased hybrid/polyploid incompatibilities and/or through direct reciprocal suppression of maternally- and paternally-inherited genomes.
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10
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Wang X, Morton JA, Pellicer J, Leitch IJ, Leitch AR. Genome downsizing after polyploidy: mechanisms, rates and selection pressures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1003-1015. [PMID: 34077584 DOI: 10.1111/tpj.15363] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 05/20/2023]
Abstract
An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70 Mb/million years, 4-482 bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO2 uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales.
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Affiliation(s)
- Xiaotong Wang
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Joseph A Morton
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia sn, Barcelona, 08038, Spain
| | | | - Andrew R Leitch
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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Boatwright JL, Yeh CT, Hu HC, Susanna A, Soltis DE, Soltis PS, Schnable PS, Barbazuk WB. Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins. FRONTIERS IN PLANT SCIENCE 2021; 12:679047. [PMID: 34249049 PMCID: PMC8261302 DOI: 10.3389/fpls.2021.679047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.
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Affiliation(s)
- J. Lucas Boatwright
- Advanced Plant Technology Program, Clemson University, Clemson, SC, United States
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Heng-Cheng Hu
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Covance Inc., Indianapolis, IN, United States
| | - Alfonso Susanna
- Botanic Institute of Barcelona, Consejo Superior de Investigaciones Científicas, ICUB, Barcelona, Spain
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Biodiversity Institute, University of Florida, Gainesville, FL, United States
| | - Pamela S. Soltis
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Biodiversity Institute, University of Florida, Gainesville, FL, United States
| | | | - William B. Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
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Di Stilio VS, Ickert-Bond SM. Ephedra as a gymnosperm evo-devo model lineage. Evol Dev 2021; 23:256-266. [PMID: 33503333 DOI: 10.1111/ede.12370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/29/2020] [Accepted: 01/02/2021] [Indexed: 11/28/2022]
Abstract
Established model systems in the flowering plants have greatly advanced our understanding of plant developmental biology, facilitating in turn its investigation across diverse land plants. The reliance on a limited number of model organisms, however, constitutes a barrier for future progress in evolutionary developmental biology (evo-devo). In particular, a more thorough understanding of seed plant character evolution and of its genetic and developmental basis has been hampered in part by a lack of gymnosperm model systems, since most are trees with decades-long generation times. Guided by the premise that future model organisms should be selected based on their character diversity, rather than simply phylogenetic "position," we highlight biological questions of potential interest that can be addressed via comparative studies in Ephedra (Gnetales). In addition to having relatively small genomes and shorter generation times in comparison to most other gymnosperms, Ephedra are amenable to investigations on the evolution of the key reproductive seed plant innovations of pollination and seed dispersal, as well as on polyploidy, and adaptation to extreme environments.
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13
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Burns R, Mandáková T, Gunis J, Soto-Jiménez LM, Liu C, Lysak MA, Novikova PY, Nordborg M. Gradual evolution of allopolyploidy in Arabidopsis suecica. Nat Ecol Evol 2021; 5:1367-1381. [PMID: 34413506 PMCID: PMC8484011 DOI: 10.1038/s41559-021-01525-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.
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Affiliation(s)
- Robin Burns
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Terezie Mandáková
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Joanna Gunis
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Luz Mayela Soto-Jiménez
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Chang Liu
- grid.9464.f0000 0001 2290 1502Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Martin A. Lysak
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Polina Yu. Novikova
- grid.511033.5VIB-UGent Center for Plant Systems Biology, Ghent, Belgium ,grid.419498.90000 0001 0660 6765Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Magnus Nordborg
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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