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McElroy KE, Müller S, Lamatsch DK, Bankers L, Fields PD, Jalinsky JR, Sharbrough J, Boore JL, Logsdon JM, Neiman M. Asexuality Associated with Marked Genomic Expansion of Tandemly Repeated rRNA and Histone Genes. Mol Biol Evol 2021; 38:3581-3592. [PMID: 33885820 PMCID: PMC8382920 DOI: 10.1093/molbev/msab121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
How does asexual reproduction influence genome evolution? Although is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits-mode of genomic inheritance-influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S-5.8S-28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA-histone copies than sexuals, which we validated through molecular and cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction-with potential functional consequences related to the loss of sexual reproduction.
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Affiliation(s)
- Kyle E McElroy
- Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondsee, Mondsee, Austria
| | - Laura Bankers
- Division of Infectious Diseases, University of Colorado—Anschutz Medical Campus, Aurora, CO, USA
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, Seattle, WA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA, USA
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Kiefer M, Nauerth BH, Volkert C, Ibberson D, Loreth A, Schmidt A. Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera. Genome Biol Evol 2020; 12:656-673. [PMID: 32302391 PMCID: PMC7250504 DOI: 10.1093/gbe/evaa078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2020] [Indexed: 12/20/2022] Open
Abstract
In higher plants, sexual and asexual reproductions through seeds (apomixis) have evolved as alternative strategies. Evolutionary advantages leading to coexistence of both reproductive modes are currently not well understood. It is expected that accumulation of deleterious mutations leads to a rapid elimination of apomictic lineages from populations. In this line, apomixis originated repeatedly, likely from deregulation of the sexual pathway, leading to alterations in the development of reproductive lineages (germlines) in apomicts as compared with sexual plants. This potentially involves mutations in genes controlling reproduction. Increasing evidence suggests that RNA helicases are crucial regulators of germline development. To gain insights into the evolution of 58 members of this diverse gene family in sexual and apomictic plants, we applied target enrichment combined with next-generation sequencing to identify allelic variants from 24 accessions of the genus Boechera, comprising sexual, facultative, and obligate apomicts. Interestingly, allelic variants from apomicts did not show consistently increased mutation frequency. Either sequences were highly conserved in any accession, or allelic variants preferentially harbored mutations in evolutionary less conserved C- and N-terminal domains, or presented high mutation load independent of the reproductive mode. Only for a few genes allelic variants harboring deleterious mutations were only identified in apomicts. To test if high sequence conservation correlates with roles in fundamental cellular or developmental processes, we analyzed Arabidopsis thaliana mutant lines in VASA-LIKE (VASL), and identified pleiotropic defects during ovule and reproductive development. This indicates that also in apomicts mechanisms of selection are in place based on gene function.
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Affiliation(s)
- Markus Kiefer
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Berit H Nauerth
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Christopher Volkert
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, Heidelberg, Germany
| | - Anna Loreth
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Anja Schmidt
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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Costa J, Torices R, Barrett SCH. Evolutionary history of the buildup and breakdown of the heterostylous syndrome in Plumbaginaceae. THE NEW PHYTOLOGIST 2019; 224:1278-1289. [PMID: 30825331 DOI: 10.1111/nph.15768] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/23/2019] [Indexed: 05/27/2023]
Abstract
The evolutionary pathways leading to the heterostylous syndrome are not well understood, and models concerning the origins of distyly differ in the order in which reciprocal herkogamy and self-incompatibility evolve. We investigated the evolution and breakdown of distyly in Plumbaginaceae, a family with considerable diversity of floral traits and reproductive systems. Using Bayesian Markov chain Monte Carlo analyses and stochastic character mapping, we examined the evolutionary assembly and breakdown of the heterostylous syndrome based on a well-resolved phylogeny of 121 species of Plumbaginaceae and six outgroup taxa using five nuclear and plastid gene regions. We used the distribution of reproductive traits and reconstructed ancestral characters across phylogenies to evaluate competing models for the evolution of distyly. The most likely common ancestor of Plumbaginaceae was self-incompatible and monomorphic for sex-organ arrangement and pollen-stigma characters. Character state reconstructions indicated that reciprocal herkogamy evolved at least three times and that shifts to selfing and apomixis occurred on multiple occasions. Our results provide comparative support for the early ideas of H. G. Baker on evolutionary pathways in Plumbaginaceae, and the more recent selfing avoidance model by D. & B. Charlesworth in which distyly evolves from self-incompatible ancestors.
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Affiliation(s)
- Joana Costa
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Rubén Torices
- Area of Biodiversity and Conservation, Universidad Rey Juan Carlos, c/Tulipán s/n., Móstoles, Madrid, E-28933, Spain
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada, M5S 3B2
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Zühl L, Volkert C, Ibberson D, Schmidt A. Differential activity of F-box genes and E3 ligases distinguishes sexual versus apomictic germline specification in Boechera. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5643-5657. [PMID: 31294816 PMCID: PMC6812705 DOI: 10.1093/jxb/erz323] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
Germline specification is the first step during sexual and apomictic plant reproduction, and takes place in the nucellus of the ovule, a specialized domain of the reproductive flower tissues. In each case, a sporophytic cell is determined to form the sexual megaspore mother cell (MMC) or an apomictic initial cell (AIC). These differ in their developmental fates: while the MMC undergoes meiosis, the AIC modifies or omits meiosis to form the female gametophyte. Despite great interest in these distinct developmental processes, little is known about their gene regulatory basis. To elucidate the gene regulatory networks underlying germline specification, we conducted tissue-specific transcriptional profiling using laser-assisted microdissection and RNA sequencing to compare the transcriptomes of nucellar tissues between different sexual and apomictic Boechera accessions representing four species and two ploidy levels. This allowed us to distinguish between expression differences caused by genetic background or reproductive mode. Statistical data analysis revealed 45 genes that were significantly differentially expressed, and which potentially play a role for determination of the reproductive mode. Based on annotations, these included F-box genes and E3 ligases that most likely relate to genes previously described as regulators important for germline development. Our findings provide novel insights into the transcriptional basis of sexual and apomictic reproduction.
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Affiliation(s)
- Luise Zühl
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld, Heidelberg
- Present address: Max Planck Institute for Plant Breeding Research, Department of Comparative Development and Genetics, Carl-von-Linné-Weg 10, D-50829 Cologne
| | - Christopher Volkert
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld, Heidelberg
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, Im Neuenheimer Feld, Heidelberg
| | - Anja Schmidt
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld, Heidelberg
- Correspondence:
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Carman JG, Mateo de Arias M, Gao L, Zhao X, Kowallis BM, Sherwood DA, Srivastava MK, Dwivedi KK, Price BJ, Watts L, Windham MD. Apospory and Diplospory in Diploid Boechera (Brassicaceae) May Facilitate Speciation by Recombination-Driven Apomixis-to-Sex Reversals. FRONTIERS IN PLANT SCIENCE 2019; 10:724. [PMID: 31214233 PMCID: PMC6555261 DOI: 10.3389/fpls.2019.00724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/16/2019] [Indexed: 05/08/2023]
Abstract
Apomixis (asexual seed formation) in angiosperms occurs either sporophytically, through adventitious embryony, or gametophytically, where an unreduced female gametophyte (embryo sac) forms and produces an unreduced egg that develops into an embryo parthenogenetically. Multiple types of gametophytic apomixis occur, and these are differentiated based on where and when the unreduced gametophyte forms, a process referred to as apomeiosis. Apomeiotic gametophytes form directly from ameiotic megasporocytes, as in Antennaria-type diplospory, from unreduced spores derived from 1st division meiotic restitutions, as in Taraxacum-type diplospory, or from cells of the ovule wall, as in Hieracium-type apospory. Multiple types of apomeiosis occasionally occur in the same plant, which suggests that the different types occur in response to temporal and/or spatial shifts in termination of sexual processes and onset timing of apomeiosis processes. To better understand the origins and evolutionary implications of apomixis in Boechera (Brassicaceae), we determined apomeiosis type for 64 accessions representing 44 taxonomic units. Plants expressing apospory and diplospory were equally common, and these generally produced reduced and unreduced pollen, respectively. Apospory and diplospory occurred simultaneously in individual plants of seven taxa. In Boechera, apomixis perpetuates otherwise sterile or semisterile interspecific hybrids (allodiploids) through multiple generations. Accordingly, ample time, in these multigenerational clones, is available for rare meioses to produce haploid, intergenomically recombined male and female gametes. The fusion of such gametes could then produce segmentally autoploidized progeny. If sex re-emerges among such progeny, then new and genomically unique sexual species could evolve. Herein, we present evidence that such apomixis-facilitated speciation is occurring in Boechera, and we hypothesize that it might also be occurring in facultatively apomictic allodiploids of other angiospermous taxa.
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Affiliation(s)
- John G. Carman
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
| | - Mayelyn Mateo de Arias
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
- Instituto Tecnológico de Santo Domingo, Santo Domingo, Dominican Republic
| | - Lei Gao
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
| | - Xinghua Zhao
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
- College of Desert Control Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | | | - David A. Sherwood
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
| | - Manoj K. Srivastava
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
- Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Krishna K. Dwivedi
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
- Caisson Laboratories, Inc., Smithfield, UT, United States
- Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Bo J. Price
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
| | - Landon Watts
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
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Brukhin V, Osadtchiy JV, Florez-Rueda AM, Smetanin D, Bakin E, Nobre MS, Grossniklaus U. The Boechera Genus as a Resource for Apomixis Research. FRONTIERS IN PLANT SCIENCE 2019; 10:392. [PMID: 31001306 PMCID: PMC6454215 DOI: 10.3389/fpls.2019.00392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/14/2019] [Indexed: 05/03/2023]
Abstract
The genera Boechera (A. Löve et D. Löve) and Arabidopsis, the latter containing the model plant Arabidopsis thaliana, belong to the same clade within the Brassicaceae family. Boechera is the only among the more than 370 genera in the Brassicaceae where apomixis is well documented. Apomixis refers to the asexual reproduction through seed, and a better understanding of the underlying mechanisms has great potential for applications in agriculture. The Boechera genus currently includes 110 species (of which 38 are reported to be triploid and thus apomictic), which are distributed mostly in the North America. The apomictic lineages of Boechera occur at both the diploid and triploid level and show signs of a hybridogenic origin, resulting in a modification of their chromosome structure, as reflected by alloploidy, aneuploidy, substitutions of homeologous chromosomes, and the presence of aberrant chromosomes. In this review, we discuss the advantages of the Boechera genus to study apomixis, consider its modes of reproduction as well as the inheritance and possible mechanisms controlling apomixis. We also consider population genetic aspects and a possible role of hybridization at the origin of apomixis in Boechera. The molecular tools available to study Boechera, such as transformation techniques, laser capture microdissection, analysis of transcriptomes etc. are also discussed. We survey available genome assemblies of Boechera spp. and point out the challenges to assemble the highly heterozygous genomes of apomictic species. Due to these challenges, we argue for the application of an alternative reference-free method for the comparative analysis of such genomes, provide an overview of genomic sequencing data in the genus Boechera suitable for such analysis, and provide examples of its application.
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Affiliation(s)
- Vladimir Brukhin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Saint Petersburg, Russia
- Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, Saint Petersburg, Russia
| | - Jaroslaw V. Osadtchiy
- Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, Saint Petersburg, Russia
| | - Ana Marcela Florez-Rueda
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Evgeny Bakin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Saint Petersburg, Russia
- Bioinformatics Institute, Saint Petersburg, Russia
| | - Margarida Sofia Nobre
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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Rushworth CA, Windham MD, Keith RA, Mitchell-Olds T. Ecological differentiation facilitates fine-scale coexistence of sexual and asexual Boechera. AMERICAN JOURNAL OF BOTANY 2018; 105:2051-2064. [PMID: 30548985 PMCID: PMC6685206 DOI: 10.1002/ajb2.1201] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/10/2018] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Ecological differentiation (ED) between sexual and asexual organisms may permit the maintenance of reproductive polymorphism. Several studies of sexual/asexual ED in plants have shown that the geographic ranges of asexuals extend beyond those of sexuals, often in areas of higher latitude or elevation. But very little is known about ED at fine scales, wherein coexistence of sexuals and asexuals may be permitted by differential niche occupation. METHODS We used 149 populations of sexual and apomictic lineages in the genus Boechera (rock cress) collected across a portion of this mustard's vast range. We characterized reproductive mode, ploidy, and species identity or hybrid parentage of each individual, and then used a multipronged statistical approach to (1) identify ED between sexuals and asexuals; (2) investigate the impacts of two confounding factors, polyploidy and hybridization, on ED; and (3) determine the environmental variables underlying ED. KEY RESULTS We found that sexuals and asexuals are significantly ecologically differentiated across the landscape, despite fine-scale interdigitation of these two reproductive forms. Asexual reproduction was strongly associated with greater disturbance, reduced slope, and greater environmental variability. Although ploidy had little effect on the patterns observed, hybridization has a unique impact on the relationships between asexual reproduction and specific environmental variables. CONCLUSIONS Ecological differentiation along the axes of disturbance, slope, and climatic variability, as well as the effects of heterozygosity, may contribute to the maintenance of sexuality and asexuality across the landscape, ultimately impacting the establishment and spread of asexual lineages.
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Affiliation(s)
- Catherine A. Rushworth
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Michael D. Windham
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
| | - Rose A. Keith
- Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Tom Mitchell-Olds
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
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Sears CJ, Whitton J. A reexamination of the North American Crepis agamic complex and comparison with the findings of Babcock and Stebbins' classic biosystematic monograph. AMERICAN JOURNAL OF BOTANY 2016; 103:1289-99. [PMID: 27313196 DOI: 10.3732/ajb.1600057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 04/12/2016] [Indexed: 05/22/2023]
Abstract
PREMISE OF THE STUDY Babcock and Stebbins coined the term agamic complex in their 1938 monograph of the North American Crepis agamic complex. Despite the historical role that this complex holds in the evolutionary literature, it has not been reexamined in over 75 years. We present a thorough reevaluation of the complex to test hypotheses proposed by Babcock and Stebbins about its origins and spread, the relationships of diploids, and the nature and origins of polyploids. METHODS We used flow cytometry to infer ploidy of roughly 600 samples spanning the morphological and taxonomic diversity of the complex and a phylogenetic analysis of plastid DNA variation to infer maternal relationships among diploids and to infer maternal origins of polyploids. KEY RESULTS We identified populations of all seven recognized diploids plus one new lineage. Phylogenetic analysis of plastid DNA variation in diploids revealed a well-resolved, but moderately supported phylogeny, with evidence for monophyly of the North America Crepis agamic complex and no evidence of widespread homoploid hybridization. Polyploids showed evidence of multiple origins and a pattern of frequent local co-occurrence consistent with repeated colonization of suitable sites. CONCLUSIONS Our findings agree broadly with the distribution and variation of ploidy within and among species described by Babcock and Stebbins. One key difference is finding support for monophyly of North American species, and refuting their hypothesis of polyphyly. Our results provide an explicit phylogenetic framework for further study of this classic agamic complex.
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Affiliation(s)
- Christopher J Sears
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4 Canada
| | - Jeannette Whitton
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4 Canada
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Florez Rueda AM, Grossniklaus U, Schmidt A. Laser-assisted Microdissection (LAM) as a Tool for Transcriptional Profiling of Individual Cell Types. J Vis Exp 2016. [PMID: 27213843 DOI: 10.3791/53916] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The understanding of developmental processes at the molecular level requires insights into transcriptional regulation, and thus the transcriptome, at the level of individual cell types. While the methods described here are generally applicable to a wide range of species and cell types, our research focuses on plant reproduction. Plant cultivation and seed production is of crucial importance for human and animal nutrition. A detailed understanding of the regulatory networks that govern the formation of the reproductive lineage (germline) and ultimately of seeds is a precondition for the targeted manipulation of plant reproduction. In particular, the engineering of apomixis (asexual reproduction through seeds) into crop plants promises great improvements, as it leads to the formation of clonal seeds that are genetically identical to the mother plant. Consequently, the cell types of the female germline are of major importance for the understanding and engineering of apomixis. However, as the corresponding cells are deeply embedded within the floral tissues, they are very difficult to access for experimental analyses, including cell-type specific transcriptomics. To overcome this limitation, sections of individual cells can be isolated by laser-assisted microdissection (LAM). While LAM in combination with transcriptional profiling allows the identification of genes and pathways active in any cell type with high specificity, establishing a suitable protocol can be challenging. Specifically, the quality of RNA obtained after LAM can be compromised, especially when small, single cells are targeted. To circumvent this problem, we have established a workflow for LAM that reproducibly results in high RNA quality that is well suitable for transcriptomics, as exemplified here by the isolation of cells of the female germline in apomictic Boechera. In this protocol, procedures are described for tissue preparation and LAM, also with regard to RNA extraction and quality control.
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Affiliation(s)
| | | | - Anja Schmidt
- University of Zürich & Zürich-Basel Plant Science Center;
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10
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Ferreira de Carvalho J, Oplaat C, Pappas N, Derks M, de Ridder D, Verhoeven KJF. Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants. BMC Genomics 2016; 17:203. [PMID: 26956152 PMCID: PMC4782324 DOI: 10.1186/s12864-016-2524-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/24/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Asexual reproduction has the potential to enhance deleterious mutation accumulation and to constrain adaptive evolution. One source of mutations that can be especially relevant in recent asexuals is activity of transposable elements (TEs), which may have experienced selection for high transposition rates in sexual ancestor populations. Predictions of genomic divergence under asexual reproduction therefore likely include a large contribution of transposable elements but limited adaptive divergence. For plants empirical insight into genome divergence under asexual reproduction remains limited. Here, we characterize expression divergence between clone members of a single apomictic lineage of the common dandelion (Taraxacum officinale) to contribute to our knowledge of genome evolution under asexuality. RESULTS Using RNA-Seq, we show that about one third of heritable divergence within the apomictic lineage is driven by TEs and TE-related gene activity. In addition, we identify non-random transcriptional differences in pathways related to acyl-lipid and abscisic acid metabolisms which might reflect functional divergence within the apomictic lineage. We analyze SNPs in the transcriptome to assess genetic divergence between the apomictic clone members and reveal that heritable expression differences between the accessions are not explained simply by genome-wide genetic divergence. CONCLUSION The present study depicts a first effort towards a more complete understanding of apomictic plant genome evolution. We identify abundant TE activity and ecologically relevant functional genes and pathways affecting heritable within-lineage expression divergence. These findings offer valuable resources for future work looking at epigenetic silencing and Cis-regulation of gene expression with particular emphasis on the effects of TE activity on asexual species' genome.
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Affiliation(s)
- Julie Ferreira de Carvalho
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
| | - Carla Oplaat
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
| | - Nikolaos Pappas
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Martijn Derks
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
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Gu C, Wang L, Wang W, Zhou H, Ma B, Zheng H, Fang T, Ogutu C, Vimolmangkang S, Han Y. Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1993-2005. [PMID: 26850878 PMCID: PMC4783375 DOI: 10.1093/jxb/erw021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Texture is an important attribute affecting consumer perception of fruit quality. Peach melting flesh and flesh adhesion to stone (endocarp) are simply inherited and controlled by the F-M locus on linkage group (LG) 4. Here, we report that two genes encoding endopolygalacturonase (endoPG) in the F-M locus, designated PpendoPGF and PpendoPGM, are associated with the melting flesh and stone adhesion traits. PpendoPGM controls melting flesh while PpendoPGF has pleiotropic effects on both melting flesh and stone adhesion. The F-M locus has three allelic copy number variants of endoPG, H1 (PpendoPGF and PpendoPGM), H2 (PpendoPGM), and H3 (null). The H2 haplotype represents the ancestral one while the H1 and H3 haplotypes are two variants due to duplication and deletion of PpendoPGM, respectively. Accessions with H1H1, H1H2, or H1H3 genotypes show the freestone or semi-freestone and melting flesh phenotype, while both H2H2 and H2H3 accessions have the clingstone and melting flesh phenotype. The H3H3 accessions have the clingstone and non-melting flesh phenotype. Our study not only demonstrates a driving role of gene copy number variations in flesh texture diversification in fruit trees, but also provides a useful diagnostic tool for early seedling selection in peach breeding programmes.
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Affiliation(s)
- Chao Gu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
| | - Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
| | - Wei Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Baiquan Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Hongyu Zheng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Collins Ogutu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Sornkanok Vimolmangkang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
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Mau M, Lovell JT, Corral JM, Kiefer C, Koch MA, Aliyu OM, Sharbel TF. Hybrid apomicts trapped in the ecological niches of their sexual ancestors. Proc Natl Acad Sci U S A 2015; 112:E2357-65. [PMID: 25902513 PMCID: PMC4426457 DOI: 10.1073/pnas.1423447112] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Asexual reproduction is expected to reduce the adaptive potential to novel or changing environmental conditions, restricting or altering the ecological niche of asexual lineages. Asexual lineages of plants and animals are typically polyploid, an attribute that may influence their genetic variation, plasticity, adaptive potential, and niche breadth. The genus Boechera (Brassicaceae) represents an ideal model to test the relative ecological and biogeographic impacts of reproductive mode and ploidy because it is composed of diploid sexual and both diploid and polyploid asexual (i.e., apomictic) lineages. Here, we demonstrate a strong association between a transcriptionally conserved allele and apomictic seed formation. We then use this allele as a proxy apomixis marker in 1,649 accessions to demonstrate that apomixis is likely to be a common feature across the Boechera phylogeny. Phylogeographic analyses of these data demonstrate (i) species-specific niche differentiation in sexuals, (ii) extensive niche conservation between differing reproductive modes of the same species, (iii) ploidy-specific niche differentiation within and among species, and (iv) occasional niche drift between apomicts and their sexual ancestors. We conclude that ploidy is a substantially stronger and more common driver of niche divergence within and across Boechera species although variation in both traits may not necessarily lead to niche evolution on the species scale.
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Affiliation(s)
- Martin Mau
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany;
| | - John T Lovell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - José M Corral
- Department of Bioanalytics, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Christiane Kiefer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies Heidelberg, 69120 Heidelberg, Germany; and
| | - Olawale M Aliyu
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany; Department of Crop Production, College of Agriculture, Kwara State University, PMB 1530 Ilorin, Kwara State, Nigeria
| | - Timothy F Sharbel
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
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Corral JM, Vogel H, Aliyu OM, Hensel G, Thiel T, Kumlehn J, Sharbel TF. A conserved apomixis-specific polymorphism is correlated with exclusive exonuclease expression in premeiotic ovules of apomictic boechera species. PLANT PHYSIOLOGY 2013; 163:1660-72. [PMID: 24163323 PMCID: PMC3850208 DOI: 10.1104/pp.113.222430] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 10/23/2013] [Indexed: 05/19/2023]
Abstract
Apomixis (asexual seed production) is characterized by meiotically unreduced egg cell production (apomeiosis) followed by its parthenogenetic development into offspring that are genetic clones of the mother plant. Fertilization (i.e. pseudogamy) of the central cell is important for the production of a functional endosperm with a balanced 2:1 maternal:paternal genome ratio. Here, we present the APOLLO (for apomixis-linked locus) gene, an Aspartate Glutamate Aspartate Aspartate histidine exonuclease whose transcripts are down-regulated in sexual ovules entering meiosis while being up-regulated in apomeiotic ovules at the same stage of development in plants of the genus Boechera. APOLLO has both "apoalleles," which are characterized by a set of linked apomixis-specific polymorphisms, and "sexalleles." All apomictic Boechera spp. accessions proved to be heterozygous for the APOLLO gene (having at least one apoallele and one sexallele), while all sexual genotypes were homozygous for sexalleles. Apoalleles contained a 20-nucleotide polymorphism present in the 5' untranslated region that contains specific transcription factor-binding sites for ARABIDOPSIS THALIANA HOMEOBOX PROTEIN5, LIM1 (for LINEAGE ABNORMAL11, INSULIN1, MECHANOSENSORY PROTEIN3), SORLIP1AT (for SEQUENCES OVERREPRESENTED IN LIGHT-INDUCED PROMOTERS IN ARABIDOPSIS THALIANA1), SORLIP2AT, and POLYA SIGNAL1. In the same region, sexalleles contain transcription factor-binding sites for DNA BINDING WITH ONE FINGER2, DNA BINDING WITH ONE FINGER3, and PROLAMIN BOX-BINDING FACTOR. Our results suggest that the expression of a single deregulated allele could induce the cascade of events leading to asexual female gamete formation in an apomictic plant.
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Mau M, Corral JM, Vogel H, Melzer M, Fuchs J, Kuhlmann M, de Storme N, Geelen D, Sharbel TF. The conserved chimeric transcript UPGRADE2 is associated with unreduced pollen formation and is exclusively found in apomictic Boechera species. PLANT PHYSIOLOGY 2013; 163:1640-59. [PMID: 24130193 PMCID: PMC3850206 DOI: 10.1104/pp.113.222448] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In apomictic Boechera spp., meiotic diplospory leads to the circumvention of meiosis and the suppression of recombination to produce unreduced male and female gametes (i.e. apomeiosis). Here, we have established an early flower developmental staging system and have performed microarray-based comparative gene expression analyses of the pollen mother cell stage in seven diploid sexual and seven diploid apomictic genotypes to identify candidate factors for unreduced pollen formation. We identified a transcript unique to apomictic Boechera spp. called UPGRADE2 (BspUPG2), which is highly up-regulated in their pollen mother cells. BspUPG2 is highly conserved among apomictic Boechera spp. genotypes but has no homolog in sexual Boechera spp. or in any other taxa. BspUPG2 undergoes posttranscriptional processing but lacks a prominent open reading frame. Together with the potential of stably forming microRNA-like secondary structures, we hypothesize that BspUPG2 functions as a long regulatory noncoding messenger RNA-like RNA. BspUPG2 has apparently arisen through a three-step process initiated by ancestral gene duplication of the original BspUPG1 locus, followed by sequential insertions of segmentally duplicated gene fragments, with final exonization of its sequence structure. Its genesis reflects the hybridization history that characterizes the genus Boechera.
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