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Li W, Chen X, Yu J, Zhu Y. Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution, lignin biosynthesis regulation, and stress tolerance. Sci China Life Sci 2024:10.1007/s11427-024-2580-3. [PMID: 38763999 DOI: 10.1007/s11427-024-2580-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/26/2024] [Indexed: 05/21/2024]
Abstract
Durian (Durio zibethinus) is a tropical fruit that has a unique flavor and aroma. It occupies a significant phylogenetic position within the Malvaceae family. Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling, resulting in an abundant genomic diversity. However, the ancestral karyotypes of the Malvaceae family, as well as the evolution trajectory leading to the 28 chromosomes in durian, remain poorly understood. Here, we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses. By analyzing the collinear blocks between cacao and durian, we inferred 11 Malvaceae ancestral karyotypes. These blocks were present in a single-copy form in cacao and mainly in triplicates in durian, possibly resulting from a recent whole genome triplication (WGT) event that led to hexaploidization of the durian genome around 20 (17-24) million years ago. A large proportion of the duplicated genes in durian, such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis, are derived directly from whole genome duplication, which makes it an important force in reshaping its genomic architecture. Transcriptome studies have revealed that genes involved in feruloyl-CoA formations were highly preferentially expressed in fruit peels, indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins. Among all the analyzed transcription factors (TFs), members of the heat shock factor family (HSF) were the most significantly upregulated under heat stress. All subfamilies of genes encoding heat shock proteins (HSPs) in the durian genome appear to have undergone expansion. The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified. Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome. We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.
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Affiliation(s)
- Wanwan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xin Chen
- The State Key Laboratory of Protein and Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
| | - Yuxian Zhu
- The Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
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Shahbazi M, Majka J, Kubíková D, Zwierzykowski Z, Glombik M, Wendel JF, Sharbrough J, Hartmann S, Szecówka M, Doležel J, Bartoš J, Kopecký D, Kneřová J. Cytonuclear interplay in auto- and allopolyploids: a multifaceted perspective from the Festuca-Lolium complex. Plant J 2024; 118:1102-1118. [PMID: 38323852 DOI: 10.1111/tpj.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/15/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon in auto- and allopolyploids of the Festuca-Lolium complex providing insights into the mechanisms governing cytonuclear interactions in early polyploid and hybrid generations. Our study examined the main processes potentially involved in restoring the cytonuclear balance after WGD comparing diploids and new and well-established autopolyploids. We uncovered that both the number of chloroplasts and the number of chloroplast genome copies were significantly higher in the newly established autopolyploids and grew further in more established autopolyploids. The increase in the copy number of the chloroplast genome exceeded the rise in the number of chloroplasts and fully compensated for the doubling of the nuclear genome. In addition, changes in nuclear and organelle gene expression were insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts in parental protein variants within the cytonuclear complexes. While biased maternal allele expression has been observed in numerous hybrids, our results suggest that its role in cytonuclear stabilization in the Festuca × Lolium hybrids is limited. This study provides insights into the restoration of the cytonuclear stoichiometry, yet it emphasizes the need for future research to explore post-transcriptional regulation and its impact on cytonuclear gene expression stoichiometry. Our findings may enhance the understanding of polyploid plant evolution, with broader implications for the study of cytonuclear interactions in diverse biological contexts.
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Affiliation(s)
- Mehrdad Shahbazi
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Joanna Majka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Denisa Kubíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Marek Glombik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, Iowa, USA
| | - Joel Sharbrough
- New Mexico Institute of Mining and Technology, Biology Department, Socorro, New Mexico, 87801, USA
| | - Stephan Hartmann
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 4, 85354, Freising, Germany
| | - Marek Szecówka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Kneřová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
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Osterman WHA, Hill A, Hagan JG, Whitton J, Bacon CD, Bjorkman AD. Rethinking pathways to the dioecy-polyploidy association: Genera with many dioecious species have fewer polyploids. Am J Bot 2024:e16318. [PMID: 38654555 DOI: 10.1002/ajb2.16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024]
Abstract
PREMISE Numerous studies have found a positive association between dioecy and polyploidy; however, this association presents a theoretical conflict: While polyploids are predicted to benefit from self-reproduction for successful establishment, dioecious species cannot self-reproduce. We propose a theoretical framework to resolve this apparent conflict. We hypothesize that the inability of dioecious species to self-reproduce hinders their establishment as polyploids. We therefore expect that genera with many dioecious species have fewer polyploids, leading to a negative association between polyploidy and dioecy across genera. METHODS We used three publicly available databases to determine ploidy and sexual systems for 131 genera and 546 species. We quantified (1) the relationship between the frequency of polyploid species and the frequency of dioecious species across genera, and (2) the proportion of polyploids with hermaphroditism and dioecy across species, adjusting for phylogenetic history. RESULTS Across genera, we found a negative relationship between the proportion of polyploids and the proportion of dioecious species, a consistent trend across clades. Across all species, we found that sexual system (dioecious or not) was not associated with polyploidy. CONCLUSIONS Polyploids are rare in genera in which the majority of species are dioecious, consistent with the theory that self-reproduction favors polyploid establishment. The low frequency of polyploidy among dioecious species indicates the association is not as widespread as previously suggested. Our findings are consistent with previous studies identifying a positive relationship between the two traits, but only if polyploidy promotes a transition to dioecy, and not the reverse.
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Affiliation(s)
- Wilhelm H A Osterman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Adrian Hill
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - James G Hagan
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jeannette Whitton
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, Vancouver, Canada
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Anne D Bjorkman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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Vaz de Sousa D, Greve M, Oberlander KC. Friends without benefits: Extensive cytotype sympatry and polyploid persistence in an African geophyte. Am J Bot 2024:e16291. [PMID: 38439133 DOI: 10.1002/ajb2.16291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 03/06/2024]
Abstract
PREMISE Polyploidy is a major factor in plant adaptation and speciation. Multiple mechanisms contribute to autopolyploid frequency within populations, but uncertainties remain regarding mechanisms that facilitate polyploid establishment and persistence. Here we aimed to document and predict cytotype distributions of Oxalis obliquifolia Steud. ex A. Rich. across Gauteng, South Africa, and test for evidence of possible mechanisms, including morphological, phenological, and reproductive traits, that may potentially facilitate polyploid persistence. METHODS Over 320 O. obliquifolia plants from 25 sites were cytotyped using flow cytometry, and DNA ploidy was confirmed using meiotic chromosome squashes. Cytotypes were mapped and correlations with abiotic variables assessed using ordinations. To assess morphological and phenological associations with cytotype, we grew multiple cytotypes in a common garden, measured phenotypic traits and compared them using linear models and discriminant analyses. Intercytotype reproductive isolation was assessed using crossing experiments, and AMOVAs based on ITS DNA sequences tested for cytogeographic structure. RESULTS Six cytotypes were identified, and most sites had multiple cytotypes. Abiotic variables were not predictive of cytotype distribution. A clear gigas effect was present. Differences in flower size and phenology suggested pollinator interactions could play a role in polyploid persistence. Intercytotype crosses produced seed at low frequency. DNA data suggested diploids and polyploids were largely reproductively isolated in situ, and polyploidization events were not frequent enough to explain high cytotype sympatry. CONCLUSIONS Diploids and polyploids are behaving as separate species, despite little observable niche differentiation and non-zero potential intercytotype seed set. Tests on biotic interactions and intercytotype F1 fitness may provide insights into diploid and polyploid coexistence.
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Affiliation(s)
- Damian Vaz de Sousa
- Department of Plant and Soil Science, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa
- H.G.W.J. Schweickerdt Herbarium, Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
| | - Michelle Greve
- Department of Plant and Soil Science, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - Kenneth C Oberlander
- H.G.W.J. Schweickerdt Herbarium, Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
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Li T, Zheng J, Nousias O, Yan Y, Meinhardt LW, Goenaga R, Zhang D, Yin Y. The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of Magnoliales, and a Putative Gene Cluster for Acetogenin Biosynthesis. Plants (Basel) 2024; 13:636. [PMID: 38475482 DOI: 10.3390/plants13050636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Annona cherimola (cherimoya) is a species renowned for its delectable fruit and medicinal properties. In this study, we developed a chromosome-level genome assembly for the cherimoya 'Booth' cultivar from the United States. The genome assembly has a size of 794 Mb with a N50 = 97.59 Mb. The seven longest scaffolds account for 87.6% of the total genome length, which corresponds to the seven pseudo-chromosomes. A total of 45,272 protein-coding genes (≥30 aa) were predicted with 92.9% gene content completeness. No recent whole genome duplications were identified by an intra-genome collinearity analysis. Phylogenetic analysis supports that eudicots and magnoliids are more closely related to each other than to monocots. Moreover, the Magnoliales was found to be more closely related to the Laurales than the Piperales. Genome comparison revealed that the 'Booth' cultivar has 200 Mb less repeats than the Spanish cultivar 'Fino de Jete', despite their highly similar (>99%) genome sequence identity and collinearity. These two cultivars were diverged during the early Pleistocene (1.93 Mya), which suggests a different origin and domestication of the cherimoya. Terpene/terpenoid metabolism functions were found to be enriched in Magnoliales, while TNL (Toll/Interleukin-1-NBS-LRR) disease resistance gene has been lost in Magnoliales during evolution. We have also identified a gene cluster that is potentially responsible for the biosynthesis of acetogenins, a class of natural products found exclusively in Annonaceae. The cherimoya genome provides an invaluable resource for supporting characterization, conservation, and utilization of Annona genetic resources.
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Affiliation(s)
- Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Yuchen Yan
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Ricardo Goenaga
- Tropical Agriculture Research Station, United States Department of Agriculture, Agriculture Research Service, Mayaguez 00680, Puerto Rico
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
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Wang M, Zhang R, Shu JP, Zheng XL, Wu XY, Chen JB, Wang MN, Shen H, Yan YH. Whole Genome Duplication Events Likely Contributed to the Aquatic Adaptive Evolution of Parkerioideae. Plants (Basel) 2024; 13:521. [PMID: 38498522 PMCID: PMC10893450 DOI: 10.3390/plants13040521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
As the only aquatic lineage of Pteridaceae, Parkerioideae is distinct from many xeric-adapted species of the family and consists of the freshwater Ceratopteris species and the only mangrove ferns from the genus Acrostichum. Previous studies have shown that whole genome duplication (WGD) has occurred in Parkerioideae at least once and may have played a role in their adaptive evolution; however, more in-depth research regarding this is still required. In this study, comparative and evolutionary transcriptomics analyses were carried out to identify WGDs and explore their roles in the environmental adaptation of Parkerioideae. Three putative WGD events were identified within Parkerioideae, two of which were specific to Ceratopteris and Acrostichum, respectively. The functional enrichment analysis indicated that the lineage-specific WGD events have played a role in the adaptation of Parkerioideae to the low oxygen concentrations of aquatic habitats, as well as different aquatic environments of Ceratopteris and Acrostichum, such as the adaptation of Ceratopteris to reduced light levels and the adaptation of Acrostichum to high salinity. Positive selection analysis further provided evidence that the putative WGD events may have facilitated the adaptation of Parkerioideae to changes in habitat. Moreover, the gene family analysis indicated that the plasma membrane H+-ATPase (AHA), vacuolar H+-ATPase (VHA), and suppressor of K+ transport growth defect 1 (SKD1) may have been involved in the high salinity adaptation of Acrostichum. Our study provides new insights into the evolution and adaptations of Parkerioideae in different aquatic environments.
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Affiliation(s)
- Meng Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Rui Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (R.Z.); (H.S.)
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Jiang-Ping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xi-Long Zheng
- School of Traditional Medicine Materials Resource, Guangdong Pharmaceutical University, Yunfu 527322, China;
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Jian-Bing Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Mei-Na Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Hui Shen
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (R.Z.); (H.S.)
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yue-Hong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
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Ryu T, Okamoto K, Ansai S, Nakao M, Kumar A, Iguchi T, Ogino Y. Gene Duplication of Androgen Receptor As An Evolutionary Driving Force Underlying the Diversity of Sexual Characteristics in Teleost Fishes. Zoolog Sci 2024; 41:68-76. [PMID: 38587519 DOI: 10.2108/zs230098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/15/2024] [Indexed: 04/09/2024]
Abstract
Sexual dimorphism allows species to meet their fitness optima based on the physiological availability of each sex. Although intralocus sexual conflict appears to be a genetic constraint for the evolution of sex-specific traits, sex-linked genes and the regulation of sex steroid hormones contribute to resolving this conflict by allowing sex-specific developments. Androgens and their receptor, androgen receptor (Ar), regulate male-biased phenotypes. In teleost fish, ar ohnologs have emerged as a result of teleost-specific whole genome duplication (TSGD). Recent studies have highlighted the evolutionary differentiation of ar ohnologs responsible for the development of sexual characteristics, which sheds light on the need for comparative studies on androgen regulation among different species. In this review, we discuss the importance of ar signaling as a regulator of male-specific traits in teleost species because teleost species are suitable experimental models for comparative studies owing to their great diversity in male-biased morphological and physiological traits. To date, both in vivo and in vitro studies on teleost ar ohnologs have shown a substantial influence of ars as a regulator of male-specific reproductive traits such as fin elongation, courtship behavior, and nuptial coloration. In addition to these sexual characteristics, ar substantially influences immunity, inducing a sex-biased immune response. This review aims to provide a comprehensive understanding of the current state of teleost ar studies and emphasizes the potential of teleost fishes, given their availability, to find molecular evidence about what gives rise to the spectacular diversity among fish species.
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Affiliation(s)
- Tsukasa Ryu
- Laboratory of Marine Biochemistry, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Keigo Okamoto
- Laboratory of Aquatic Molecular Developmental Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Satoshi Ansai
- Laboratory of Genome Editing Breeding, Graduate School of Agriculture, Kyoto University, Kyoto 606-8507, Japan
| | - Miki Nakao
- Laboratory of Marine Biochemistry, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Anu Kumar
- Commonwealth Scientific and Industrial Research Organization, CSIRO Environment, PMB2, Glen Osmond, 5064 South Australia, Australia
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ishikawa 927-0553, Japan
| | - Yukiko Ogino
- Laboratory of Aquatic Molecular Developmental Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan,
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
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8
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Li C, Wickell D, Kuo LY, Chen X, Nie B, Liao X, Peng D, Ji J, Jenkins J, Williams M, Shu S, Plott C, Barry K, Rajasekar S, Grimwood J, Han X, Sun S, Hou Z, He W, Dai G, Sun C, Schmutz J, Leebens-Mack JH, Li FW, Wang L. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. Proc Natl Acad Sci U S A 2024; 121:e2312607121. [PMID: 38236735 PMCID: PMC10823260 DOI: 10.1073/pnas.2312607121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.
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Affiliation(s)
- Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - David Wickell
- Boyce Thompson Institute, Ithaca, NY14853
- Plant Biology Section, Cornell University, Ithaca, NY14853
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Xueqing Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Mellissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ85721
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Weijun He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Guanhua Dai
- Research Station of Changbai Mountain Forest Ecosystems, Chinese Academy of Sciences, Yanji133000, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing100048, China
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY14853
- Plant Biology Section, Cornell University, Ithaca, NY14853
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing100700, China
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9
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Aase-Remedios ME, Janssen R, Leite DJ, Sumner-Rooney L, McGregor AP. Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication. Mol Biol Evol 2023; 40:msad239. [PMID: 37935059 PMCID: PMC10726417 DOI: 10.1093/molbev/msad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.
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Affiliation(s)
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Daniel J Leite
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom
| | - Lauren Sumner-Rooney
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, 10115, Germany
| | - Alistair P McGregor
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom
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10
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Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event. bioRxiv 2023:2023.10.02.560513. [PMID: 37873368 PMCID: PMC10592909 DOI: 10.1101/2023.10.02.560513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Whole genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in S. cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post WGD. In S. cerevisiae, HRR25 encodes the casein kinase (CK) 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post and non-WGD species, and have non-conserved cellular localization, consistent with their ongoing loss of function. The analysis in N. castelli shows that the non-complementing ohnolog is expressed at a lower level and has become non-essential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.
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Affiliation(s)
- Daniel Evans-Yamamoto
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Gourav Saha
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani K K Birla Goa campus, Zuarinagar, South Goa, Goa, India
- Current address: Department of Bioengineering, University of California, CA 90095, United States
| | - Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Current address: Département de Biochimie, Université de Sherbrooke, Québec, J1K 0A5, Canada
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
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11
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Du X, Yu H, Wang Y, Liu J, Zhang Q. Comparative Studies on Duplicated foxl2 Paralogs in Spotted Knifejaw Oplegnathus punctatus Show Functional Diversification. Genes (Basel) 2023; 14:1847. [PMID: 37895196 PMCID: PMC10606028 DOI: 10.3390/genes14101847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
As a member of the forkhead box L gene family, foxl2 plays a significant role in gonadal development and the regulation of reproduction. During the evolution of deuterostome, whole genome duplication (WGD)-enriched lineage diversifications and regulation mechanisms occurs. However, only limited research exists on foxl2 duplication in teleost or other vertebrate species. In this study, two foxl2 paralogs, foxl2 and foxl2l, were identified in the transcriptome of spotted knifejaw (Oplegnathus punctatus), which had varying expressions in the gonads. The foxl2 was expressed higher in the ovary, while foxl2l was expressed higher in the testis. Phylogenetic reconstruction, synteny analysis, and the molecular evolution test confirmed that foxl2 and foxl2l likely originated from the first two WGD. The expression patterns test using qRT-PCR and ISH as well as motif scan analysis revealed evidence of potentially functional divergence between the foxl2 and foxl2l paralogs in spotted knifejaw. Our results indicate that foxl2 and foxl2l may originate from the first two WGD, be active in transcription, and have undergone functional divergence. These results shed new light on the evolutionary trajectories of foxl2 and foxl2l and highlights the need for further detailed functional analysis of these two duplicated paralogs.
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Affiliation(s)
- Xinxin Du
- School of Life Science and Bioengineering, Jining University, Jining 273155, China; (X.D.); (H.Y.)
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, China; (Y.W.); (J.L.)
| | - Haiyang Yu
- School of Life Science and Bioengineering, Jining University, Jining 273155, China; (X.D.); (H.Y.)
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, China; (Y.W.); (J.L.)
| | - Yujue Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, China; (Y.W.); (J.L.)
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, China; (Y.W.); (J.L.)
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, China; (Y.W.); (J.L.)
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12
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Rao SR, Protheroe A, Cerundolo L, Maldonado-Perez D, Browning L, Lamb AD, Bryant RJ, Mills IG, Woodcock DJ, Hamdy FC, Tomlinson IPM, Verrill C. Genomic Evolution and Transcriptional Changes in the Evolution of Prostate Cancer into Neuroendocrine and Ductal Carcinoma Types. Int J Mol Sci 2023; 24:12722. [PMID: 37628903 PMCID: PMC10454593 DOI: 10.3390/ijms241612722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Prostate cancer is typically of acinar adenocarcinoma type but can occasionally present as neuroendocrine and/or ductal type carcinoma. These are associated with clinically aggressive disease, and the former often arises on a background of androgen deprivation therapy, although it can also arise de novo. Two prostate cancer cases were sequenced by exome capture from archival tissue. Case 1 was de novo small cell neuroendocrine carcinoma and ductal adenocarcinoma with three longitudinal samples over 5 years. Case 2 was a single time point after the development of treatment-related neuroendocrine prostate carcinoma. Case 1 showed whole genome doubling in all samples and focal amplification of AR in all samples except the first time point. Phylogenetic analysis revealed a common ancestry for ductal and small cell carcinoma. Case 2 showed 13q loss (involving RB1) in both adenocarcinoma and small cell carcinoma regions, and 3p gain, 4p loss, and 17p loss (involving TP53) in the latter. By using highly curated samples, we demonstrate for the first time that small-cell neuroendocrine and ductal prostatic carcinoma can have a common ancestry. We highlight whole genome doubling in a patient with prostate cancer relapse, reinforcing its poor prognostic nature.
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Affiliation(s)
- Srinivasa R. Rao
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Andrew Protheroe
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | | | - Lisa Browning
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Alastair D. Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Richard J. Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Ian G. Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Dan J. Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
| | | | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; (S.R.R.)
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
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13
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Casanova EL. Ancient roots: A Cambrian explosion of autism susceptibility genes. Autism Res 2023; 16:1480-1487. [PMID: 37421164 DOI: 10.1002/aur.2984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/27/2023] [Indexed: 07/09/2023]
Abstract
Functional gene groups often share unique evolutionary patterns. The present study addresses whether autism susceptibility genes, which frequently share functional overlap, display unusual gene age and conservation patterns compared to other gene groups. Using phylostratigraphically-derived and other genetic data, the investigator explores average gene age, Ohnolog status, evolutionary rate, variation intolerance, and numbers of protein-protein (PPI) interactions across autism susceptibility, nervous system, developmental regulatory, immune, housekeeping, and luxury gene groups. Autism susceptibility genes are unusually old compared to controls, many genes having radiated in the Cambrian period in early vertebrates from whole genome duplication events. They are also tightly conserved across the animal kingdom, are highly variation intolerant, and have more PPI than other genes-all features suggesting extreme dosage sensitivity. The results of the current study indicate that autism susceptibility genes display unique radiation and conservation patterns, which may be a reflection of the major transitions in nervous system evolution that were occurring in early animals and which are still foundational in brain development today.
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Affiliation(s)
- Emily L Casanova
- Department of Psychology, Loyola University, New Orleans, Louisiana, USA
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14
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Schvarzstein M, Alam F, Toure M, Yanowitz JL. An Emerging Animal Model for Querying the Role of Whole Genome Duplication in Development, Evolution, and Disease. J Dev Biol 2023; 11:26. [PMID: 37367480 PMCID: PMC10299280 DOI: 10.3390/jdb11020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Whole genome duplication (WGD) or polyploidization can occur at the cellular, tissue, and organismal levels. At the cellular level, tetraploidization has been proposed as a driver of aneuploidy and genome instability and correlates strongly with cancer progression, metastasis, and the development of drug resistance. WGD is also a key developmental strategy for regulating cell size, metabolism, and cellular function. In specific tissues, WGD is involved in normal development (e.g., organogenesis), tissue homeostasis, wound healing, and regeneration. At the organismal level, WGD propels evolutionary processes such as adaptation, speciation, and crop domestication. An essential strategy to further our understanding of the mechanisms promoting WGD and its effects is to compare isogenic strains that differ only in their ploidy. Caenorhabditis elegans (C. elegans) is emerging as an animal model for these comparisons, in part because relatively stable and fertile tetraploid strains can be produced rapidly from nearly any diploid strain. Here, we review the use of Caenorhabditis polyploids as tools to understand important developmental processes (e.g., sex determination, dosage compensation, and allometric relationships) and cellular processes (e.g., cell cycle regulation and chromosome dynamics during meiosis). We also discuss how the unique characteristics of the C. elegans WGD model will enable significant advances in our understanding of the mechanisms of polyploidization and its role in development and disease.
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Affiliation(s)
- Mara Schvarzstein
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
- Biology Department, The Graduate Center at the City University of New York, New York, NY 10016, USA
- Biochemistry Department, The Graduate Center at the City University of New York, New York, NY 10016, USA
| | - Fatema Alam
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
| | - Muhammad Toure
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
| | - Judith L. Yanowitz
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA;
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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15
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Gout JF, Hao Y, Johri P, Arnaiz O, Doak TG, Bhullar S, Couloux A, Guérin F, Malinsky S, Potekhin A, Sawka N, Sperling L, Labadie K, Meyer E, Duharcourt S, Lynch M. Dynamics of gene loss following ancient whole-genome duplication in the cryptic Paramecium complex. Mol Biol Evol 2023:7156828. [PMID: 37154524 DOI: 10.1093/molbev/msad107] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD-derived paralogs are maintained over long evolutionary periods, and the relative contributions of different selective pressures to their maintenance is still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliate Paramecium tetraurelia and two of its sister species from the P. aurelia complex. Here, we report the genome sequence and analysis of 10 additional P. aurelia species and one additional outgroup, revealing aspects of post-WGD evolution in 13 species sharing a common ancestral WGD. Contrary to the morphological radiation of vertebrates that putatively followed two WGD events, members of the cryptic P. aurelia complex have remained morphologically indistinguishable after hundreds of millions of years. Biases in gene retention compatible with dosage constraints appear to play a major role opposing post-WGD gene loss across all 13 species. In addition, post-WGD gene loss has been slower in Paramecium than in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong in Paramecium. A near complete lack of recent single-gene duplications in Paramecium provides additional evidence for strong selective pressures against gene-dosage changes. This exceptional dataset of 13 species sharing an ancestral WGD and two closely related outgroup species will be a useful resource for future studies on Paramecium as a major model organism in the evolutionary cell biology.
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Affiliation(s)
- Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Yue Hao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Parul Johri
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Simran Bhullar
- Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, 75005 Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Fréderic Guérin
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Sophie Malinsky
- Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, 75005 Paris, France
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, 199034 Saint Petersburg, Russia
| | - Natalia Sawka
- Institute of Systematic and Evolution of Animals, Polish Academy of Science, 31-016 Krakow, Poland
| | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Eric Meyer
- Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, 75005 Paris, France
| | - Sandra Duharcourt
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
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16
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Anneberg TJ, Segraves KA. Neopolyploidy causes increased nutrient requirements and a shift in plant growth strategy in Heuchera cylindrica. Ecology 2023:e4054. [PMID: 37082928 DOI: 10.1002/ecy.4054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 04/22/2023]
Abstract
Functional traits fall along a continuum from resource-conservative to acquisitive and are powerful predictors of the ecological settings necessary for a species to persist and establish. As a consequence, a major problem that functional trait analysis could address is understanding the ecological contexts necessary for the persistence of polyploid plants, because early generation polyploids, or "neopolyploids", are at a high extinction risk. Since neopolyploidy could increase nutrient limitation, growth strategies should shift to accommodate the increased need for resources, but this prediction is untested. To address this gap, we compared the functional trait responses of diploids, synthetic neotetraploids, and naturally occurring tetraploids of Heuchera cylindrica, an herbaceous perennial plant, to nutrient manipulations in a greenhouse experiment. We found strong support for the hypothesis that neotetraploidy increases nutrient requirements, as evidenced by reduced productivity and increased tissue concentrations of nitrogen and phosphorus in neotetraploids. We also found that repeated formation of independent origins of neotetraploidy led to differing responses to nutrient supply, but neotetraploidy generally shifted functional traits to be more resource-acquisitive and inefficient. Taken together, our results suggest that shifts in functional trait responses may constrain the ability of neopolyploids to establish in nutrient-poor habitats. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Thomas J Anneberg
- Department of Biology, Syracuse University, Syracuse, NY, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kari A Segraves
- Department of Biology, Syracuse University, Syracuse, NY, USA
- Archbold Biological Station, Venus, FL, USA
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17
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Dimos B, Phelps M. A homology guide for Pacific salmon genus Oncorhynchus resolves patterns of ohnolog retention, resolution and local adaptation following the salmonid-specific whole-genome duplication event. Ecol Evol 2023; 13:e9994. [PMID: 37091557 PMCID: PMC10119027 DOI: 10.1002/ece3.9994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/25/2023] Open
Abstract
Salmonid fishes have emerged as a tractable model to study whole-genome duplications (WGDs) as this group has undergone four rounds of WGDs. While most of the salmonid genome has returned to a diploid state, a significant proportion of genes are maintained as duplicates and are referred to as ohnologs. The fact that much of the modern salmonid gene repertoire is comprised of ohnologs, while other genes have returned to their singleton state creates complications for genetic studies by obscuring homology relationships. The difficulty this creates is particularly prominent in Pacific salmonids belonging to genus Oncorhynchus who are the focus of intense genetics-based conservation and management efforts owing to the important ecological and cultural roles these fish play. To address this gap, we generated a homology guide for six species of Oncorhynchus with available genomes and used this guide to describe patterns of ohnolog retention and resolution. Overall, we find that ohnologs comprise approximately half of each species modern gene repertoires, which are functionally enriched for genes involved in DNA binding, while the less numerous singleton genes are heavily enriched in dosage-sensitive processes such as mitochondrial metabolism. Additionally, by reanalyzing published expression data from locally adapted strains of O. mykiss, we show that numerous ohnologs exhibit adaptive expression profiles; however, ohnologs are not more likely to display adaptive signatures than either paralogs or singletons. Finally, we demonstrate the utility of our homology guide by investigating the evolutionary relationship among genes highlighted as playing a role in salmonid life-history traits or gene editing targets.
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Affiliation(s)
- Bradford Dimos
- Department of Animal SciencesWashington State UniversityPullmanWashingtonUSA
| | - Michael Phelps
- Department of Animal SciencesWashington State UniversityPullmanWashingtonUSA
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18
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Sahlström HM, Datsomor AK, Monsen Ø, Hvidsten TR, Sandve SR. Functional validation of transposable element derived cis-regulatory elements in Atlantic salmon. G3 (Bethesda) 2023; 13:7031732. [PMID: 36753570 PMCID: PMC10085797 DOI: 10.1093/g3journal/jkad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023]
Abstract
Transposable elements (TEs) are hypothesized to play important roles in shaping genome evolution following whole genome duplications (WGD), including rewiring of gene regulation. In a recent analysis, duplicate gene copies that had evolved higher expression in liver following the salmonid WGD ∼100 million years ago were associated with higher numbers of predicted TE-derived cis-regulatory elements (TE-CREs). Yet, the ability of these TE-CREs to recruit transcription factors (TFs) in vivo and impact gene expression remains unknown. Here, we evaluated the gene regulatory functions of 11 TEs using luciferase promoter reporter assays in Atlantic salmon (Salmo salar) primary liver cells. Canonical Tc1-Mariner elements from intronic regions showed no or small repressive effects on transcription. However, other TE-derived cis-regulatory elements upstream of transcriptional start sites increased expression significantly. Our results question the hypothesis that TEs in the Tc1-Mariner superfamily, which were extremely active following WGD in salmonids, had a major impact on regulatory rewiring of gene duplicates, but highlights the potential of other TEs in post-WGD rewiring of gene regulation in the Atlantic salmon genome.
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Affiliation(s)
- Hanna M Sahlström
- Department of Animal and Aquacultural Sciences, Faculty of Bioscience, Norwegian University of Life Sciences, 1430, Aas, Norway
| | - Alex K Datsomor
- Department of Animal and Aquacultural Sciences, Faculty of Bioscience, Norwegian University of Life Sciences, 1430, Aas, Norway
| | - Øystein Monsen
- Department of Animal and Aquacultural Sciences, Faculty of Bioscience, Norwegian University of Life Sciences, 1430, Aas, Norway
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430, Aas, Norway
| | - Simen Rød Sandve
- Department of Animal and Aquacultural Sciences, Faculty of Bioscience, Norwegian University of Life Sciences, 1430, Aas, Norway
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19
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Zhong Y, Wu W, Sun C, Zou P, Liu Y, Dai S, Zhou R. Chromosomal-level genome assembly of Melastoma candidum provides insights into trichome evolution. Front Plant Sci 2023; 14:1126319. [PMID: 36778698 PMCID: PMC9911893 DOI: 10.3389/fpls.2023.1126319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Melastoma, consisting of ~100 species diversified in tropical Asia and Oceania in the past 1-2 million years, represents an excellent example of rapid speciation in flowering plants. Trichomes on hypanthia, twigs and leaves vary markedly among species of this genus and are the most important diagnostic traits for species identification. These traits also play critical roles in contributing to differential adaptation of these species to their own habitats. Here we sequenced the genome of M. candidum, a common, erect-growing species from southern China, with the aim to provide genomic insights into trichome evolution in this genus. We generated a high-quality, chromosome-level genome assembly of M. candidum, with the genome size of 256.2 Mb and protein-coding gene number of 40,938. The gene families specific to, and significantly expanded in Melastoma are enriched for GO terms related to trichome initiation and differentiation. We provide evidence that Melastoma and its sister genus Osbeckia have undergone two whole genome duplications (WGDs) after the triplication event (γ) shared by all core eudicots. Preferential retention of trichome development-related transcription factor genes such as C2H2, bHLH, HD-ZIP, WRKY, and MYB after both WGDs might provide raw materials for trichome evolution and thus contribute to rapid species diversification in Melastoma. Our study provides candidate transcription factor genes related to trichome evolution in Melastoma, which can be used to evolutionary and functional studies of trichome diversification among species of this genus.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chenyu Sun
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peishan Zou
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Seping Dai
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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20
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Coate JE, Chen JT, Meru G. Editorial: Artificial polyploidy in plants, Volume II. Front Plant Sci 2023; 13:1124292. [PMID: 36714720 PMCID: PMC9879002 DOI: 10.3389/fpls.2022.1124292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Affiliation(s)
- Jeremy E. Coate
- Department of Biology, Reed College, Portland, OR, United States
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Geoffrey Meru
- Horticultural Sciences Department and Tropical Research & Education Center, University of Florida, Gainesville, FL, United States
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21
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Wang B, Lv R, Zhang Z, Yang C, Xun H, Liu B, Gong L. Homoeologous exchange enables rapid evolution of tolerance to salinity and hyper-osmotic stresses in a synthetic allotetraploid wheat. J Exp Bot 2022; 73:7488-7502. [PMID: 36055762 DOI: 10.1093/jxb/erac355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The link between polyploidy and enhanced adaptation to environmental stresses could be a result of polyploidy itself harbouring higher tolerance to adverse conditions, or polyploidy possessing higher evolvability than diploids under stress conditions. Natural polyploids are inherently unsuitable to disentangle these two possibilities. Using selfed progenies of a synthetic allotetraploid wheat AT3 (AADD) along with its diploid parents, Triticum urartu TMU38 (AA) and Aegilops tauschii TQ27 (DD), we addressed the foregoing issue under abiotic salinity and hyper-osmotic (drought-like) stress. Under short duration of both stresses, euploid plants of AT3 showed intermediate tolerance of diploid parents; under life-long duration of both stresses, tolerant individuals to either stress emerged from selfed progenies of AT3, but not from comparable-sized diploid parent populations. Tolerance to both stresses were conditioned by the same two homoeologous exchanges (HEs; 2DS/2AS and 3DL/3AL), and at least one HE needed to be at the homozygous state. Transcriptomic analyses revealed that hyper-up-regulation of within-HE stress responsive genes of the A sub-genome origin is likely responsible for the dual-stress tolerant phenotypes. Our results suggest that HE-mediated inter-sub-genome rearrangements can be an important mechanism leading to adaptive evolution in allopolyploids as well as a promising target for genetic manipulation in crop improvement.
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Affiliation(s)
- Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongwei Xun
- 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
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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22
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Wighard SS, Athanasouli M, Witte H, Rödelsperger C, Sommer RJ. A New Hope: A Hermaphroditic Nematode Enables Analysis of a Recent Whole Genome Duplication Event. Genome Biol Evol 2022; 14:6868937. [PMID: 36461901 PMCID: PMC9763058 DOI: 10.1093/gbe/evac169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/03/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Whole genome duplication (WGD) is often considered a major driver of evolution that leads to phenotypic novelties. However, the importance of WGD for evolution is still controversial because most documented WGD events occurred anciently and few experimental systems amenable to genetic analysis are available. Here, we report a recent WGD event in the hermaphroditic nematode Allodiplogaster sudhausi and present a comparison with a gonochoristic (male/female) sister species that did not undergo WGD. Self-fertilizing reproduction of A. sudhausi makes it amenable to functional analysis and an ideal system to study WGD events. We document WGD in A. sudhausi through karyotype analysis and whole genome sequencing, the latter of which allowed us to 1) identify functional bias in retention of protein domains and metabolic pathways, 2) show most duplicate genes are under evolutionary constraint, 3) show a link between sequence and expression divergence, and 4) characterize differentially expressed duplicates. We additionally show WGD is associated with increased body size and an abundance of repeat elements (36% of the genome), including a recent expansion of the DNA-hAT/Ac transposon family. Finally, we demonstrate the use of CRISPR/Cas9 to generate mutant knockouts, whereby two WGD-derived duplicate genes display functional redundancy in that they both need to be knocked out to generate a phenotype. Together, we present a novel experimental system that is convenient for examining and characterizing WGD-derived genes both computationally and functionally.
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Affiliation(s)
- Sara S Wighard
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Marina Athanasouli
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
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23
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Flamio R, Swift DG, Portnoy DS, Chojnacki KA, DeLonay AJ, Powell J, Braaten PJ, Heist EJ. Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons. Mol Ecol Resour 2022. [PMID: 36453984 DOI: 10.1111/1755-0998.13742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Acipenseriformes (sturgeons and paddlefishes) are of substantial conservation concern, and development of genomic resources for these species is difficult due to past whole genome duplication. Development of disomic markers for polyploid organisms can be challenging due to difficulty in resolving alleles at a single locus from those among duplicated loci. In this study, we detail the development of disomic markers for the endangered pallid sturgeon (Scaphirhynchus albus) found in North America. One of the strategies for pallid sturgeon conservation is to stock U.S. rivers with offspring of pure pallid sturgeon, but introgression with the sympatric shovelnose sturgeon (S. platorynchus) threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite loci are used to differentiate between both species and their hybrids, but the markers are insufficient to robustly identify backcrosses. We performed double digest restriction site-associated DNA sequencing (ddRADseq) on shovelnose sturgeon haploid gynogens to produce a reduced-representation genomic reference. Contiguous sequences that were heterozygous within a haploid individual were flagged as potentially encompassing multiple loci. Approximately 60 individuals of each species from two management units were sequenced, and reads were mapped to the haploid reference to identify single nucleotide polymorphisms (SNPs) at individual loci. The final data set contained 11,082 microhaplotyped loci which offer at least an order of magnitude greater resolution for species discrimination than the current panel of 19 microsatellites. These markers will be used to examine a larger sample of Scaphirhynchus individuals throughout their ranges to determine the extent and trajectory of hybridization.
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Affiliation(s)
- Richard Flamio
- Department of Zoology, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Dominic G Swift
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, Texas, USA
| | - David S Portnoy
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, Texas, USA
| | - Kimberly A Chojnacki
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Aaron J DeLonay
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Jeffrey Powell
- U.S. Fish and Wildlife Service, Gavins Point National Fish Hatchery, Yankton, South Dakota, USA
| | - Patrick J Braaten
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Edward J Heist
- Department of Zoology, Southern Illinois University Carbondale, Carbondale, Illinois, USA
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
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24
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Zhong S, Li B, Chen W, Wang L, Guan J, Wang Q, Yang Z, Yang H, Wang X, Yu X, Fu P, Liu H, Chen C, Tan F, Ren T, Shen J, Luo P. The chromosome-level genome of Akebia trifoliata as an important resource to study plant evolution and environmental adaptation in the Cretaceous. Plant J 2022; 112:1316-1330. [PMID: 36305286 DOI: 10.1111/tpj.16011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
The environmental adaptation of eudicots is the most reasonable explanation for why they compose the largest clade of modern plants (>70% of angiosperms), which indicates that the basal eudicots would be valuable and helpful to study their survival and ability to thrive throughout evolutionary processes. Here, we detected two whole-genome duplication (WGD) events in the high-quality assembled Akebia trifoliata genome (652.73 Mb) with 24 138 protein-coding genes based on the evidence of intragenomic and intergenomic collinearity, synonymous substitution rate (KS ) values and polyploidization and diploidization traces; these events putatively occurred at 85.15 and 146.43 million years ago (Mya). The integrated analysis of 16 species consisting of eight basal and eight core eudicots further revealed that there was a putative ancient WGD at the early stage of eudicots (temporarily designated θ) at 142.72 Mya, similar to the older WGD of Akebia trifoliata, and a putative core eudicot-specific WGD (temporarily designated ω). Functional enrichment analysis of retained duplicate genes following the θ event is suggestive of adaptation to the extreme environment change in both the carbon dioxide concentration and desiccation around the Jurassic-Cretaceous boundary, while the retained duplicate genes following the ω event is suggestive of adaptation to the extreme droughts, possibly leading to the rapid spread of eudicots in the mid-Cretaceous. Collectively, the A. trifoliata genome experienced two WGD events, and the older event may have occurred at the early stage of eudicots, which likely increased plant environmental adaptability and helped them survive in ancient extreme environments.
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Affiliation(s)
- Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road in Haidian District, 100193, Beijing, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Bin Li
- State Key Laboratory of Tree Breeding and Forest Genetics, Research Institute of Forestry, Chinese Academy of Forestry, 1 Dongxiaofu Xiangshan Road in Haidian District, 100091, Beijing, China
| | - Wei Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Lili Wang
- Biomarker Technologies Co., Ltd, 12 Fuqian Street in Shunyi District, 101300, Beijing, China
| | - Ju Guan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Zujun Yang
- Center for Information in Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 2006 Xiyuan Avenue in West Hi-Tech Zone, 611731, Chengdu, Sichuan Province, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Xianshu Wang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Xiaojiao Yu
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Peng Fu
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Hongchang Liu
- Guizhou Key Laboratory for Propagation and Cultivation of Medicinal Plants, Guizhou University, 2708 Huaxi South Avenue in Huaxi District, 550025, Guiyang, Guizhou province, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Tianheng Ren
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road in Haidian District, 100193, Beijing, China
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25
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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Nie S, Tian XC, Kong L, Zhao SW, Chen ZY, Jiao SQ, El-Kassaby YA, Porth I, Yang FS, Zhao W, Mao JF. Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation. Front Plant Sci 2022; 13:1006904. [PMID: 36457535 PMCID: PMC9706204 DOI: 10.3389/fpls.2022.1006904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/27/2022] [Indexed: 05/31/2023]
Abstract
Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.
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Affiliation(s)
- Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Chan Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Kong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhao-Yang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, Canada
| | - Fu-Sheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Shen G, Luo Y, Yao Y, Meng G, Zhang Y, Wang Y, Xu C, Liu X, Zhang C, Ding G, Pang Y, Zhang H, Guo B. The discovery of a key prenyltransferase gene assisted by a chromosome-level Epimedium pubescens genome. Front Plant Sci 2022; 13:1034943. [PMID: 36452098 PMCID: PMC9702526 DOI: 10.3389/fpls.2022.1034943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
Abstract
Epimedium pubescens is a species of the family Berberidaceae in the basal eudicot lineage, and a main plant source for the traditional Chinese medicine "Herba Epimedii". The current study achieved a chromosome-level genome assembly of E. pubescens with the genome size of 3.34 Gb, and the genome guided discovery of a key prenyltransferase (PT) in E. pubescens. Our comparative genomic analyses confirmed the absence of Whole Genome Triplication (WGT-γ) event shared in core eudicots and further revealed the occurrence of an ancient Whole Genome Duplication (WGD) event approximately between 66 and 81 Million Years Ago (MYA). In addition, whole genome search approach was successfully applied to identify 19 potential flavonoid PT genes and an important flavonoid PT (EpPT8) was proven to be an enzyme for the biosynthesis of medicinal compounds, icaritin and its derivatives in E. pubescens. Therefore, our results not only provide a good reference genome to conduct further molecular biological studies in Epimedium genus, but also give important clues for synthetic biology and industrial production of related prenylated flavonoids in future.
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Affiliation(s)
- Guoan Shen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Yanjiao Luo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- Institute of Animal Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Yao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Guoqing Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yixin Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Yuanyue Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- Chongqing Key Laboratory of Traditional Chinese Medicine Resource, Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Cheng Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- Key Laboratory of Biodiversity Science and Ecological Engineering, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Gang Ding
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Yongzhen Pang
- Institute of Animal Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Baolin Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
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Zhong S, Guan J, Chen C, Tan F, Luo P. Multiomics analysis elucidated molecular mechanism of aromatic amino acid biosynthesis in Akebia trifoliata fruit. Front Plant Sci 2022; 13:1039550. [PMID: 36426151 PMCID: PMC9680012 DOI: 10.3389/fpls.2022.1039550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Akebia trifoliata is a novel edible and healthy fruit. Here, we found that this fruit had the highest content of total free amino acids and three aromatic amino acids (AAAs) compared with the other popular fruits, and there was an obvious inverse relationship between AAA and flavonoid levels in various fruit tissues. Multiomics analysis revealed that the evolutionarily strengthened synthetic pathway of all three AAAs, the largely regulating ability conferred by ASP5 in the arogenate pathway and the complementary phenylpyruvate pathway endorsed by ADT of both Phe and Tyr biosynthesis provided reasonable explanations for the high AAA content in the flesh of A. trifoliata fruit. Gene-specific expression could be the main reason for the inverse relationship between AAAs and flavonoids. This study will help us understand the metabolic mechanism of AAAs and to develop A. trifoliata as a fresh fruit crop and medicinal plant by molecular breeding strategies.
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Fan W, Wang S, Wang H, Wang A, Jiang F, Liu H, Zhao H, Xu D, Zhang Y. The genomes of chicory, endive, great burdock and yacon provide insights into Asteraceae palaeo-polyploidization history and plant inulin production. Mol Ecol Resour 2022; 22:3124-3140. [PMID: 35751596 DOI: 10.1111/1755-0998.13675] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
Inulin is an important reserve polysaccharide in Asteraceae plants, and is also widely used as a sweetener, a source of dietary fibre and prebiotic. Nevertheless, a lack of genomic resources for inulin-producing plants has hindered extensive studies on inulin metabolism and regulation. Here, we present chromosome-level reference genomes for four inulin-producing plants: chicory (Cichorium intybus), endive (Cichorium endivia), great burdock (Arctium lappa) and yacon (Smallanthus sonchifolius), with assembled genome sizes of 1.28, 0.89, 1.73 and 2.72 Gb, respectively. We found that the chicory, endive and great burdock genomes were shaped by whole genome triplication (WGT-1), and the yacon genome was shaped by WGT-1 and two subsequent whole genome duplications (WGD-2 and WGD-3). A yacon unique whole genome duplication (WGD-3) occurred 5.6-5.8 million years ago. Our results also showed the genome size difference between chicory and endive is largely due to LTR retrotransposons, and rejected a previous hypothesis that chicory is an ancestor of endive. Furthermore, we identified fructan-active-enzyme and transcription-factor genes, and found there is one copy in chicory, endive and great burdock but two copies in yacon for most of these genes, except for the 1-FEH II gene which is significantly expanded in chicory. Interestingly, inulin synthesis genes 1-SST and 1-FFT are located close to each other, as are the degradation genes 1-FEH I and 1-FEH II. Finally, we predicted protein structures for 1-FFT genes to explore the mechanism determining inulin chain length.
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Affiliation(s)
- Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hanbo Zhao
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
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Zhong S, Yang H, Guan J, Shen J, Ren T, Li Z, Tan F, Li Q, Luo P. Characterization of the MADS-Box Gene Family in Akebia trifoliata and Their Evolutionary Events in Angiosperms. Genes (Basel) 2022; 13:genes13101777. [PMID: 36292662 PMCID: PMC9601569 DOI: 10.3390/genes13101777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
As the largest clade of modern plants, flower plants have evolved a wide variety of flowers and fruits. MADS-box genes play key roles in regulating plant morphogenesis, while basal eudicots have an evolutionarily important position of acting as an evolutionary bridge between basal angiosperms and core eudicots. Akebia trifoliata is an important member of the basal eudicot group. To study the early evolution of angiosperms, we identified and characterized the MADS-Box gene family on the whole-genome level of A. trifoliata. There were 47 MADS-box genes (13 type I and 34 type II genes) in the A. trifoliata genome; type I genes had a greater gene length and coefficient of variation and a smaller exon number than type II genes. A total of 27 (57.4%) experienced whole or segmental genome duplication and purifying selection. A transcriptome analysis suggested that three and eight genes were involved in whole fruit and seed development, respectively. The diversification and phylogenetic analysis of 1479 type II MADS-box genes of 22 angiosperm species provided some clues indicating that a γ whole genome triplication event of eudicots possibility experienced a two-step process. These results are valuable for improving A. trifoliata fruit traits and theoretically elucidating evolutionary processes of angiosperms, especially eudicots.
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Affiliation(s)
- Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Ju Guan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianheng Ren
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi Li
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Li
- Department of Biology and Chemistry, Chongqing Industry and Trade Polytechnic, Chongqing 408000, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence:
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Zhong Y, Liu Y, Wu W, Chen J, Sun C, Liu H, Shu J, Ebihara A, Yan Y, Zhou R, Schneider H. Genomic insights into genetic diploidization in the homosporous fern Adiantum nelumboides. Genome Biol Evol 2022; 14:evac127. [PMID: 35946426 PMCID: PMC9387920 DOI: 10.1093/gbe/evac127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Whole genome duplication has been recognized as a major process in speciation of land plants, especially in ferns. Whereas genome downsizing contributes greatly to the post-genome shock responses of polyploid flowering plants, diploidization of polyploid ferns diverges by maintaining most of the duplicated DNA and is thus expected to be dominated by genic processes. As a consequence, fern genomes provide excellent opportunities to study ecological speciation enforced by expansion of protein families via polyploidy. To test the key predictions of this hypothesis, we reported the de novo genome sequence of Adiantum nelumboides, a tetraploid homosporous fern. The obtained draft genome had a size of 6.27 Gb assembled into 11,767 scaffolds with the contig N50 of 1.37 Mb. Repetitive DNA sequences contributed with about 81.7%, a remarkably high proportion of the genome. With 69,568 the number of predicted protein-coding genes exceeded those reported in most other land plant genomes. Intragenomic synteny analyses recovered 443 blocks with the average block size of 1.29 Mb and the average gene content of 16 genes. The results are consistent with the hypothesis of high ancestral chromosome number, lack of substantial genome downsizing, and dominance of genic diploidization. As expected in the calciphilous plants, a notable number of detected genes were involved in calcium uptake and transport. In summary, the genome sequence of a tetraploid homosporous fern not only provides access to a genomic resource of a derived fern, but also supports the hypothesis of maintenance of high chromosome numbers and duplicated DNA in young polyploid ferns.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - Wei Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jingfang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenyu Sun
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hongmei Liu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Jiangping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, and the Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, and the Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
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Pelosi JA, Kim EH, Barbazuk WB, Sessa EB. Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. Front Plant Sci 2022; 13:882441. [PMID: 35909764 PMCID: PMC9330400 DOI: 10.3389/fpls.2022.882441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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Affiliation(s)
- Jessie A. Pelosi
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Emily H. Kim
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
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Morales‐Briones DF, Lin N, Huang EY, Grossenbacher DL, Sobel JM, Gilmore CD, Tank DC, Yang Y. Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades. Am J Bot 2022; 109:1035-1046. [PMID: 35462411 PMCID: PMC9328367 DOI: 10.1002/ajb2.1860] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny as a basis for a stable taxonomy and for macroevolutionary comparisons. METHODS We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and a cloudogram, and carried out reticulation analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distances, and gene duplication events as evidence. RESULTS Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, the monophyly of Mimulus s.l. is rejected, and no individual reticulation event among the Phrymaceae tribes is well-supported. Reticulation likely occurred among Erythranthe bicolor and closely related species. No ancient WGD was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. CONCLUSIONS We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that phylogenomic datasets using genomes and transcriptomes present rich opportunities to investigate gene family evolution and genome duplication events involved in lineage diversification and adaptation.
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Affiliation(s)
- Diego F. Morales‐Briones
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
- Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig‐Maximilians‐Universität MünchenMenzinger Strasse 6780638MunichGermany
| | - Nan Lin
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
- College of Life ScienceHenan Agricultural University63 Nongye RoadZhengzhouHenan450002China
| | - Eileen Y. Huang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
| | - Dena L. Grossenbacher
- Biological Sciences DepartmentCalifornia Polytechnic State University, 1 Grand Avenue, San Luis ObispoCalifornia93407USA
| | - James M. Sobel
- Department of Biological SciencesBinghamton University (State University of New York), 4400 Vestal Parkway E, BinghamtonNew York13902USA
| | - Caroline D. Gilmore
- Department of Biological SciencesBinghamton University (State University of New York), 4400 Vestal Parkway E, BinghamtonNew York13902USA
| | - David C. Tank
- Department of Botany & Rocky Mountain HerbariumUniversity of Wyoming, 1000 E. University Avenue, LaramieWyoming82071USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
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Trujillo JT, Long J, Aboelnour E, Ogas J, Wisecaver JH. CHD chromatin remodeling protein diversification yields novel clades and domains absent in classic model organisms. Genome Biol Evol 2022; 14:6582301. [PMID: 35524943 PMCID: PMC9113485 DOI: 10.1093/gbe/evac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
Chromatin remodelers play a fundamental role in the assembly of chromatin, regulation of transcription, and DNA repair. Biochemical and functional characterizations of the CHD family of chromatin remodelers from a variety of model organisms have shown that these remodelers participate in a wide range of activities. However, because the evolutionary history of CHD homologs is unclear, it is difficult to predict which of these activities are broadly conserved and which have evolved more recently in individual eukaryotic lineages. Here, we performed a comprehensive phylogenetic analysis of 8,042 CHD homologs from 1,894 species to create a model for the evolution of this family across eukaryotes with a particular focus on the timing of duplications that gave rise to the diverse copies observed in plants, animals, and fungi. Our analysis confirms that the three major subfamilies of CHD remodelers originated in the eukaryotic last common ancestor, and subsequent losses occurred independently in different lineages. Improved taxon sampling identified several subfamilies of CHD remodelers in plants that were absent or highly divergent in the model plant Arabidopsis thaliana. Whereas the timing of CHD subfamily expansions in vertebrates corresponds to whole genome duplication events, the mechanisms underlying CHD diversification in land plants appear more complicated. Analysis of protein domains reveals that CHD remodeler diversification has been accompanied by distinct transitions in domain architecture, contributing to the functional differences observed between these remodelers. This study demonstrates the importance of proper taxon sampling when studying ancient evolutionary events to prevent misinterpretation of subsequent lineage-specific changes and provides an evolutionary framework for functional and comparative analysis of this critical chromatin remodeler family across eukaryotes.
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Affiliation(s)
- Joshua T Trujillo
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jiaxin Long
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Erin Aboelnour
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA.,Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Joseph Ogas
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jennifer H Wisecaver
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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Ogawa S, Yamamoto N, Hagio H, Oka Y, Parhar IS. Multiple gonadotropin-releasing hormone systems in non-mammalian vertebrates: Ontogeny, anatomy, and physiology. J Neuroendocrinol 2022; 34:e13068. [PMID: 34931380 DOI: 10.1111/jne.13068] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 01/08/2023]
Abstract
Three paralogous genes for gonadotropin-releasing hormone (GnRH; gnrh1, gnrh2, and gnrh3) and GnRH receptors exist in non-mammalian vertebrates. However, there are some vertebrate species in which one or two of these paralogous genes have become non-functional during evolution. The developmental migration of GnRH neurons in the brain is evolutionarily conserved in mammals, reptiles, birds, amphibians, and jawed teleost fish. The three GnRH paralogs have specific expression patterns in the brain and originate from multiple sites. In acanthopterygian teleosts (medaka, cichlid, etc.), the preoptic area (POA)-GnRH1 and terminal nerve (TN)-GnRH3 neuronal types originate from the olfactory regions. In other fish species (zebrafish, goldfish and salmon) with only two GnRH paralogs (GnRH2 and GnRH3), the TN- and POA-GnRH3 neuronal types share the same olfactory origin. However, the developmental origin of midbrain (MB)-GnRH2 neurons is debatable between mesencephalic or neural crest site. Each GnRH system has distinctive anatomical and physiological characteristics, and functions differently. The POA-GnRH1 neurons are hypophysiotropic in nature and function in the neuroendocrine control of reproduction. The non-hypophysiotropic GnRH2/GnRH3 neurons probably play neuromodulatory roles in metabolism (MB-GnRH2) and the control of motivational state for sexual behavior (TN-GnRH3).
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Affiliation(s)
- Satoshi Ogawa
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - Naoyuki Yamamoto
- Laboratory of Fish Biology, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hanako Hagio
- Laboratory of Fish Biology, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Yoshitaka Oka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ishwar S Parhar
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Selangor, Malaysia
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Vacca F, Gomes AS, Murashita K, Cinquetti R, Roseti C, Barca A, Rønnestad I, Verri T, Bossi E. Functional characterization of Atlantic salmon (Salmo salar L.) PepT2 transporters. J Physiol 2022; 600:2377-2400. [PMID: 35413133 PMCID: PMC9321897 DOI: 10.1113/jp282781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/16/2022] [Indexed: 11/24/2022] Open
Abstract
Abstract The high‐affinity/low‐capacity system Slc15a2 (PepT2) is responsible for the reuptake of di/tripeptides from the renal proximal tubule, but it also operates in many other tissues and organs. Information regarding PepT2 in teleost fish is limited and, to date, functional data are available from the zebrafish (Danio rerio) only. Here, we report the identification of two slc15a2 genes in the Atlantic salmon (Salmo salar) genome, namely slc15a2a and slc15a2b. The two encoded PepT2 proteins share 87% identity and resemble both structurally and functionally the canonical vertebrate PepT2 system. The mRNA tissue distribution analyses reveal a widespread distribution of slc15a2a transcripts, being more abundant in the brain and gills, while slc15a2b transcripts are mainly expressed in the kidney and the distal part of the gastrointestinal tract. The function of the two transporters was investigated by heterologous expression in Xenopus laevis oocytes and two‐electrode voltage‐clamp recordings of transport and presteady‐state currents. Both PepT2a and PepT2b in the presence of Gly‐Gln elicit pH‐dependent and Na+ independent inward currents. The biophysical and kinetic analysis of the recorded currents defined the transport properties, confirming that the two Atlantic salmon PepT2 proteins behave as high‐affinity/low‐capacity transporters. The recent structures and the previous kinetic schemes of rat and human PepT2 qualitatively account for the characteristics of the two Atlantic salmon proteins. This study is the first to report on the functional expression of two PepT2‐type transporters that operate in the same vertebrate organism as a result of (a) gene duplication process(es). Key points Two slc15a2‐type genes, slc15a2a and slc15a2b coding for PepT2‐type peptide transporters were found in the Atlantic salmon. slc15a2a
transcripts, widely distributed in the fish tissues, are abundant in the brain and gills, while slc15a2b transcripts are mainly expressed in the kidney and distal gastrointestinal tract. Amino acids involved in vertebrate Slc15 transport function are conserved in PepT2a and PepT2b proteins. Detailed kinetic analysis indicates that both PepT2a and PepT2b operate as high‐affinity transporters. The kinetic schemes and structures proposed for the mammalian models of PepT2 are suitable to explain the function of the two Atlantic salmon transporters.
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Affiliation(s)
- Francesca Vacca
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, via Dunant 3, Varese, I-21100, Italy
| | - Ana S Gomes
- Department of Biological Sciences, University of Bergen, Po. Box 7803, Bergen, NO-5020, Norway
| | - Koji Murashita
- Research Center for Aquaculture Systems, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, 516-0193, Japan
| | - Raffella Cinquetti
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, via Dunant 3, Varese, I-21100, Italy
| | - Cristina Roseti
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, via Dunant 3, Varese, I-21100, Italy
| | - Amilcare Barca
- Laboratory of Applied Physiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, via Provinciale Lecce-Monteroni, Lecce, I-73100, Italy
| | - Ivar Rønnestad
- Department of Biological Sciences, University of Bergen, Po. Box 7803, Bergen, NO-5020, Norway
| | - Tiziano Verri
- Laboratory of Applied Physiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, via Provinciale Lecce-Monteroni, Lecce, I-73100, Italy
| | - Elena Bossi
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, via Dunant 3, Varese, I-21100, Italy
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Mandal K, Dutta S, Upadhyay A, Panda A, Tripathy S. Comparative Genome Analysis Across 128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution and Localized Evolution of Compartmentalized Genomes. Front Microbiol 2022; 13:806398. [PMID: 35369471 PMCID: PMC8967354 DOI: 10.3389/fmicb.2022.806398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Phytophthora sp. are invasive groups of pathogens belonging to class Oomycetes. In order to contain and control them, a deep knowledge of their biology and infection strategy is imperative. With the availability of large-scale sequencing data, it has been possible to look directly into their genetic material and understand the strategies adopted by them for becoming successful pathogens. Here, we have studied the genomes of 128 Phytophthora species available publicly with reasonable quality. Our analysis reveals that the simple sequence repeats (SSRs) of all Phytophthora sp. follow distinct isolate specific patterns. We further show that TG/CA dinucleotide repeats are far more abundant in Phytophthora sp. than other classes of repeats. In case of tri- and tetranucleotide SSRs also, TG/CA-containing motifs always dominate over others. The GC content of the SSRs are stable without much variation across the isolates of Phytophthora. Telomeric repeats of Phytophthora follow a pattern of (TTTAGGG)n or (TTAGGGT)n rather than the canonical (TTAGGG)n. RxLR (arginine-any amino acid-leucine-arginine) motifs containing effectors diverge rapidly in Phytophthora and do not show any core common group. The RxLR effectors of some Phytophthora isolates have a tendency to form clusters with RxLRs from other species than within the same species. An analysis of the flanking intergenic distance clearly indicates a two-speed genome organization for all the Phytophthora isolates. Apart from effectors and the transposons, a large number of other virulence genes such as carbohydrate-active enzymes (CAZymes), transcriptional regulators, signal transduction genes, ATP-binding cassette transporters (ABC), and ubiquitins are also present in the repeat-rich compartments. This indicates a rapid co-evolution of this powerful arsenal for successful pathogenicity. Whole genome duplication studies indicate that the pattern followed is more specific to a geographic location. To conclude, the large-scale genomic studies of Phytophthora have thrown light on their adaptive evolution, which is largely guided by the localized host-mediated selection pressure.
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Affiliation(s)
- Kajal Mandal
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Subhajeet Dutta
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Upadhyay
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Arijit Panda
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN, United States
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Niu Y, Li G, Ni S, He X, Zheng C, Liu Z, Gong L, Kong G, Li W, Liu J. The Chromosome-Scale Reference Genome of Macadamia tetraphylla Provides Insights Into Fatty Acid Biosynthesis. Front Genet 2022; 13:835363. [PMID: 35281801 PMCID: PMC8906886 DOI: 10.3389/fgene.2022.835363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/08/2022] [Indexed: 12/28/2022] Open
Abstract
Macadamia is an evergreen tree belonging to the Proteaceae family. The two commercial macadamia species, Macadamia integrifolia and M. tetraphylla, are highly prized for their edible kernels. The M. integrifolia genome was recently sequenced, but the genome of M. tetraphylla has to date not been published, which limits the study of biological research and breeding in this species. This study reports a high-quality genome sequence of M. tetraphylla based on the Oxford Nanopore Technologies technology and high-throughput chromosome conformation capture techniques (Hi-C). An assembly of 750.87 Mb with 51.11 Mb N50 length was generated, close to the 740 and 758 Mb size estimates by flow cytometry and k-mer analysis, respectively. Genome annotation indicated that 61.42% of the genome is composed of repetitive sequences and 34.95% is composed of long terminal repeat retrotransposons. Up to 31,571 protein-coding genes were predicted, of which 92.59% were functionally annotated. The average gene length was 6,055 bp. Comparative genome analysis revealed that the gene families associated with defense response, lipid transport, steroid biosynthesis, triglyceride lipase activity, and fatty acid metabolism are expanded in the M. tetraphylla genome. The distribution of fourfold synonymous third-codon transversion showed a recent whole-genome duplication event in M. tetraphylla. Genomic and transcriptomic analysis identified 187 genes encoding 33 crucial oil biosynthesis enzymes, depicting a comprehensive map of macadamia lipid biosynthesis. Besides, the 55 identified WRKY genes exhibited preferential expression in root as compared to that in other tissues. The genome sequence of M. tetraphylla provides novel insights for breeding novel varieties and genetic improvement of agronomic traits.
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Affiliation(s)
- Yingfeng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Guohua Li
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Shubang Ni
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Xiyong He
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Ziyan Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Lidan Gong
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Guanghong Kong
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
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Tossi VE, Martínez Tosar LJ, Laino LE, Iannicelli J, Regalado JJ, Escandón AS, Baroli I, Causin HF, Pitta-Álvarez SI. Impact of polyploidy on plant tolerance to abiotic and biotic stresses. Front Plant Sci 2022; 13:869423. [PMID: 36072313 PMCID: PMC9441891 DOI: 10.3389/fpls.2022.869423] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/25/2022] [Indexed: 05/04/2023]
Abstract
Polyploidy, defined as the coexistence of three or more complete sets of chromosomes in an organism's cells, is considered as a pivotal moving force in the evolutionary history of vascular plants and has played a major role in the domestication of several crops. In the last decades, improved cultivars of economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse species have shown that the anatomical and physiological changes generated by either natural or artificial polyploidization can increase tolerance to abiotic and biotic stresses as well as disease resistance, which may positively impact on plant growth and net production. The aim of this work is to review the current literature regarding the link between plant ploidy level and tolerance to abiotic and biotic stressors, with an emphasis on the physiological and molecular mechanisms responsible for these effects, as well as their impact on the growth and development of both natural and artificially generated polyploids, during exposure to adverse environmental conditions. We focused on the analysis of those types of stressors in which more progress has been made in the knowledge of the putative morpho-physiological and/or molecular mechanisms involved, revealing both the factors in common, as well as those that need to be addressed in future research.
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Affiliation(s)
- Vanesa E. Tossi
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Leandro J. Martínez Tosar
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biotecnología, Alimentos, Agro y Ambiental (DEBAL), Facultad de Ingeniería y Ciencias Exactas, Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
| | - Leandro E. Laino
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Jesica Iannicelli
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - José Javier Regalado
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Alejandro Salvio Escandón
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
| | - Irene Baroli
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Irene Baroli,
| | - Humberto Fabio Causin
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Humberto Fabio Causin,
| | - Sandra Irene Pitta-Álvarez
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- *Correspondence: Sandra Irene Pitta-Álvarez, ;
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Yu L, Ma S, Zhang X, Tian D, Yang S, Jia X, Traw MB. Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication. Plant J 2021; 108:1365-1381. [PMID: 34585814 DOI: 10.1111/tpj.15516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/03/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas-9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30-member DNA-binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20-million-year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50-million-year interval. CRISPR/Cas9 editing revealed widespread fitness-related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.
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Affiliation(s)
- Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shiying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xianqing Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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Oh DH, Kowalski KP, Quach QN, Wijesinghege C, Tanford P, Dassanayake M, Clay K. Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed). Mol Ecol 2021; 31:1142-1159. [PMID: 34839548 PMCID: PMC9300010 DOI: 10.1111/mec.16293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/12/2021] [Accepted: 11/15/2021] [Indexed: 11/06/2022]
Abstract
The rapid invasion of the non‐native Phragmites australis (Poaceae, subfamily Arundinoideae) is a major threat to native wetland ecosystems in North America and elsewhere. We describe the first reference genome for P. australis and compare invasive (ssp. australis) and native (ssp. americanus) genotypes collected from replicated populations across the Laurentian Great Lakes to deduce genomic bases driving its invasive success. Here, we report novel genomic features including a Phragmites lineage‐specific whole genome duplication, followed by gene loss and preferential retention of genes associated with transcription factors and regulatory functions in the remaining duplicates. Comparative transcriptomic analyses revealed that genes associated with biotic stress and defence responses were expressed at a higher basal level in invasive genotypes, but native genotypes showed a stronger induction of defence responses when challenged by a fungal endophyte. The reference genome and transcriptomes, combined with previous ecological and environmental data, add to our understanding of mechanisms leading to invasiveness and support the development of novel, genomics‐assisted management approaches for invasive Phragmites.
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Affiliation(s)
- Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kurt P Kowalski
- U.S. Geological Survey, Great Lakes Science Center, Ann Arbor, Michigan, USA
| | - Quynh N Quach
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
| | - Chathura Wijesinghege
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Philippa Tanford
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Keith Clay
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA.,Department of Biology, Indiana University, Bloomington, Indiana, USA
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Hale I, Ma X, Melo ATO, Padi FK, Hendre PS, Kingan SB, Sullivan ST, Chen S, Boffa JM, Muchugi A, Danquah A, Barnor MT, Jamnadass R, Van de Peer Y, Van Deynze A. Genomic Resources to Guide Improvement of the Shea Tree. Front Plant Sci 2021; 12:720670. [PMID: 34567033 PMCID: PMC8459026 DOI: 10.3389/fpls.2021.720670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/04/2021] [Indexed: 05/25/2023]
Abstract
A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.
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Affiliation(s)
- Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Arthur T. O. Melo
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Francis Kwame Padi
- Plant Breeding Division, Cocoa Research Institute of Ghana, Ghana Cocoa Board, New Tafo, Ghana
| | - Prasad S. Hendre
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | | | | | - Shiyu Chen
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
| | - Jean-Marc Boffa
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | - Alice Muchugi
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- The Forage Genebank, Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Agyemang Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Michael Teye Barnor
- Plant Breeding Division, Cocoa Research Institute of Ghana, Ghana Cocoa Board, New Tafo, Ghana
| | - Ramni Jamnadass
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Allen Van Deynze
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
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43
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Small CD, Davis JP, Crawford BD, Benfey TJ. Early, nonlethal ploidy and genome size quantification using confocal microscopy in zebrafish embryos. J Exp Zool B Mol Dev Evol 2021; 336:496-510. [PMID: 34254444 DOI: 10.1002/jez.b.23069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 11/07/2022]
Abstract
Ploidy transitions through whole genome duplication have shaped evolution by allowing the sub- and neo-functionalization of redundant copies of highly conserved genes to express novel traits. The nuclear:cytoplasmic (n:c) ratio is maintained in polyploid vertebrates resulting in larger cells, but body size is maintained by a concomitant reduction in cell number. Ploidy can be manipulated easily in most teleosts, and the zebrafish, already well established as a model system for biomedical research, is therefore an excellent system in which to study the effects of increased cell size and reduced cell numbers in polyploids on development and physiology. Here we describe a novel technique using confocal microscopy to measure genome size and determine ploidy non-lethally at 48 h post-fertilization (hpf) in transgenic zebrafish expressing fluorescent histones. Volumetric analysis of myofiber nuclei using open-source software can reliably distinguish diploids and triploids from a mixed-ploidy pool of embryos for subsequent experimentation. We present an example of this by comparing heart rate between confirmed diploid and triploid embryos at 54 hpf.
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Affiliation(s)
| | - James P Davis
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Bryan D Crawford
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Tillmann J Benfey
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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44
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Hong S, Lim YP, Kwon SY, Shin AY, Kim YM. Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective. Front Plant Sci 2021; 12:702243. [PMID: 34290729 PMCID: PMC8288248 DOI: 10.3389/fpls.2021.702243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/14/2021] [Indexed: 05/03/2023]
Abstract
In polyploids, whole genome duplication (WGD) played a significant role in genome expansion, evolution and diversification. Many gene families are expanded following polyploidization, with the duplicated genes functionally diversified by neofunctionalization or subfunctionalization. These mechanisms may support adaptation and have likely contributed plant survival during evolution. Flowering time is an important trait in plants, which affects critical features, such as crop yields. The flowering-time gene family is one of the largest expanded gene families in plants, with its members playing various roles in plant development. Here, we performed genome-wide identification and comparative analysis of flowering-time genes in three palnt families i.e., Malvaceae, Brassicaceae, and Solanaceae, which indicate these genes were expanded following the event/s of polyploidization. Duplicated genes have been retained during evolution, although genome reorganization occurred in their flanking regions. Further investigation of sequence conservation and similarity network analyses provide evidence for functional diversification of duplicated genes during evolution. These functionally diversified genes play important roles in plant development and provide advantages to plants for adaptation and survival in response to environmental changes encountered during evolution. Collectively, we show that flowering-time genes were expanded following polyploidization and retained as large gene family by providing advantages from functional diversification during evolution.
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Affiliation(s)
- Seongmin Hong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yong-Min Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
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45
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Huang CF, Liu WY, Jade Lu MY, Chen YH, Ku MSB, Li WH. Whole genome duplication facilitated the evolution of C4 photosynthesis in Gynandropsis gynandra. Mol Biol Evol 2021; 38:4715-4731. [PMID: 34191030 PMCID: PMC8557433 DOI: 10.1093/molbev/msab200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In higher plants, whole-genome duplication (WGD) is thought to facilitate the evolution of C4 photosynthesis from C3 photosynthesis. To understand this issue, we used new and existing leaf-development transcriptomes to construct two coding sequence databases for C4Gynandropsis gynandra and C3Tarenaya hassleriana, which shared a WGD before their divergence. We compared duplicated genes in the two species and found that the WGD contributed to four aspects of the evolution of C4 photosynthesis in G. gynandra. First, G. gynandra has retained the duplicates of ALAAT (alanine aminotransferase) and GOGAT (glutamine oxoglutarate aminotransferase) for nitrogen recycling to establish a photorespiratory CO2 pump in bundle sheath (BS) cells for increasing photosynthesis efficiency, suggesting that G. gynandra experienced a C3–C4 intermediate stage during the C4 evolution. Second, G. gynandra has retained almost all known vein-development-related paralogous genes derived from the WGD event, likely contributing to the high vein complexity of G. gynandra. Third, the WGD facilitated the evolution of C4 enzyme genes and their recruitment into the C4 pathway. Fourth, several genes encoding photosystem I proteins were derived from the WGD and are upregulated in G. gynandra, likely enabling the NADH dehydrogenase-like complex to produce extra ATPs for the C4 CO2 concentration mechanism. Thus, the WGD apparently played an enabler role in the evolution of C4 photosynthesis in G. gynandra. Importantly, an ALAAT duplicate became highly expressed in BS cells in G. gynandra, facilitating nitrogen recycling and transition to the C4 cycle. This study revealed how WDG may facilitate C4 photosynthesis evolution.
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Affiliation(s)
- Chi-Fa Huang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Yu Liu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Maurice S B Ku
- Department of Bioagricultural Science, National Chiayi University, Chiayi, 600, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.,Department of Ecology and Evolution, University of Chicago, Chicago, 60637, USA
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Yuan J, Zhang X, Li F, Xiang J. Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species. Front Genet 2021; 12:658619. [PMID: 34012463 PMCID: PMC8126689 DOI: 10.3389/fgene.2021.658619] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/17/2021] [Indexed: 01/27/2023] Open
Abstract
Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies.
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Affiliation(s)
- Jianbo Yuan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xiaojun Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jianhai Xiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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47
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Wang T, Dong Q, Wang W, Chen S, Cheng Y, Tian H, Li X, Hussain S, Wang L, Gong L, Wang S. Evolution of AITR family genes in cotton and their functions in abiotic stress tolerance. Plant Biol (Stuttg) 2021; 23 Suppl 1:58-68. [PMID: 33202099 DOI: 10.1111/plb.13218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/11/2020] [Indexed: 05/18/2023]
Abstract
Abiotic stresses are major environmental factors inhibiting plant growth and development. AITRs (ABA-induced transcription repressors) are a novel family of transcription factors regulating ABA (abscisic acid) signalling and plant responses to abiotic stresses in Arabidopsis. However, the composition and evolution history of AITRs and their roles in the cotton genus are largely unknown. A total of 12 putative AITRs genes were identified in cultivated tetraploid cotton, Gossypium hirsutum. Phylogenetic analysis of GhAITRs in these tetraploid cottons and their closely related species implicate ancient genome-wide duplication occurring after speciation of Gossypium, and Theobroma could generate duplicates of GhAITRs. Duplicated GhAITRs were stably inherited following diploid speciation and further allotetraploidy in Gossypium. Homologous GhAITRs shared common expression patterns in response to ABA, drought and salinity treatments, and drought tolerance induced in transgenic Arabidopsis plants expressing GhAITR-A1. Together, our findings reveal that duplicates in the GhAITRs gene family were achieved by whole genome duplication rather than three individual duplication events, and that GhAITRs function as transcription repressors and are involved in the regulation of plant responses to ABA and drought stress. These results provide insights towards the improvement of abiotic stress tolerance in cotton using GhAITRs.
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Affiliation(s)
- T Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Q Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - W Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - S Chen
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Y Cheng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - H Tian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - X Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - S Hussain
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - L Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China
| | - L Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - S Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China
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48
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Kučera J, Svitok M, Gbúrová Štubňová E, Mártonfiová L, Lafon Placette C, Slovák M. Eunuchs or Females? Causes and Consequences of Gynodioecy on Morphology, Ploidy, and Ecology of Stellaria graminea L. (Caryophyllaceae). Front Plant Sci 2021; 12:589093. [PMID: 33912199 PMCID: PMC8072285 DOI: 10.3389/fpls.2021.589093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Plant speciation results from intricate processes such as polyploidization, reproductive strategy shifts and adaptation. These evolutionary processes often co-occur, blurring their respective contributions and interactions in the speciation continuum. Here, relying on a large-scale study, we tested whether gynodioecy triggers the divergent evolution of flower morphology and genome between sexes, and contributes to the establishment of polyploids and colonization of ecological niches in Stellaria graminea. We found that gynodioecy in S. graminea leads to flower morphology divergence between females and hermaphrodites, likely due to sexual selection. Contrary to our expectations, gynodioecy occurs evenly in diploids and tetraploids, suggesting that this reproductive strategy was not involved in the establishment of polyploids. Both diploid and tetraploid females have a larger genome size than hermaphrodites, suggesting the presence of sex chromosomes. Finally, ecology differs between cytotypes and to a lesser extent between sexes, suggesting that the link between environment and presence of females is indirect and likely explained by other aspects of the species' life history. Our study shows that gynodioecy leads to the consistent evolution of sexual traits across a wide range of populations, cytotypes and environments within a given species, and this likely contributes to the phenotypic and genetic distinctiveness of the species from its sister clades.
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Affiliation(s)
- Jaromír Kučera
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marek Svitok
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, Zvolen, Slovakia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Eliška Gbúrová Štubňová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | | | | | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czechia
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49
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Kolář F. Tracing evolutionary history and admixture in mixed-ploidy systems. Mol Ecol Resour 2021; 21:1413-1415. [PMID: 33749076 DOI: 10.1111/1755-0998.13390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/30/2022]
Abstract
Polyploidy, resulting from whole genome duplication, is a widespread phenomenon throughout Eukaryotic kingdoms. It is estimated that 15% of speciation events in plants is due to polyploidization and 16% of plant species encompass ploidy variation. In spite of the evolutionary and economic significance of polyploidy, there is a limited set of tools that would allow routine population genetic and genomic analysis of polyploid systems, in particular for the inference of population diversity and differentiation from large genome-wide data sets (Dufresne et al., 2014; Meirmans, 2020). Such a shortage is striking especially when compared to the rapid development of such tools in diploid systems over the last decade. Consequently, population genomic research in polyploids is still lagging behind diploids, especially in autopolyploids, for example, polyploids with multiple (>2) similar genome copies. In this issue of Molecular Ecology Resources, Shastry et al. (2021) develops the first software specifically designed to infer population structure and ancestry in large genome-wide mixed-ploidy data sets, opening novel opportunities for polyploid population genomic analysis.
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Affiliation(s)
- Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
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50
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Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. New Phytol 2021; 230:372-386. [PMID: 33452818 DOI: 10.1111/nph.17194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all 'diploid' flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
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Affiliation(s)
- Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tara E Hall
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Chenlu Di
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael T W McKibben
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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