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Rahmatpour N, Kuo LY, Kang J, Herman E, Lei L, Li M, Srinivasan S, Zipper R, Wolniak SM, Delwiche CF, Mount S, Li FW. Analyses of Marsilea vestita genome and transcriptomes do not support widespread intron retention during spermatogenesis. THE NEW PHYTOLOGIST 2023; 237:1490-1494. [PMID: 36451524 DOI: 10.1111/nph.18652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Affiliation(s)
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Jessica Kang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Eliana Herman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Lily Lei
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Sruthi Srinivasan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Richard Zipper
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Stephen M Wolniak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Stephen Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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Szövényi P, Gunadi A, Li FW. Charting the genomic landscape of seed-free plants. NATURE PLANTS 2021; 7:554-565. [PMID: 33820965 DOI: 10.1038/s41477-021-00888-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 05/02/2023]
Abstract
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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Kuo LY, Tang TY, Li FW, Su HJ, Chiou WL, Huang YM, Wang CN. Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales). FRONTIERS IN PLANT SCIENCE 2018; 9:486. [PMID: 29755486 PMCID: PMC5932399 DOI: 10.3389/fpls.2018.00486] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/29/2018] [Indexed: 05/19/2023]
Abstract
Organelle genomes of land plants are predominately inherited maternally but in some cases can also be transmitted paternally or biparentally. Compared to seed plants (>83% genera of angiosperms and >12% genera of gymnosperms), plastid genome (plastome) inheritance has only been investigated in fewer than 2% of fern genera, and mitochondrial genome (mitogenome) from only one fern genus. We developed a new and efficient method to examine plastome and mitogenome inheritance in a fern species-Deparia lancea (Athyriaceae, Aspleniineae, Polypodiales), and found that plastid and mitochondrial DNAs were transmitted from only the maternal parentage to a next generation. To further examine whether both organelle genomes have the same manner of inheritance in other Deparia ferns, we sequenced both plastid and mitochondrial DNA regions of inter-species hybrids, and performed phylogenetic analyses to identify the origins of organellar DNA. Evidence from our experiments and phylogenetic analyses support that both organelle genomes in Deparia are uniparentally and maternally inherited. Most importantly, our study provides the first report of mitogenome inheritance in eupolypod ferns, and the second one among all ferns.
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Affiliation(s)
- Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- *Correspondence: Li-Yaung Kuo, Yao-Moan Huang, Chun-Neng Wang,
| | - Te-Yen Tang
- Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Biology Section, Cornell University, Ithaca, NY, United States
| | - Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
| | - Wen-Liang Chiou
- Taiwan Forestry Research Institute, Taipei, Taiwan
- Dr. Cecilia Koo Botanic Conservation Center, Pingtung, Taiwan
| | - Yao-Moan Huang
- Taiwan Forestry Research Institute, Taipei, Taiwan
- *Correspondence: Li-Yaung Kuo, Yao-Moan Huang, Chun-Neng Wang,
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- *Correspondence: Li-Yaung Kuo, Yao-Moan Huang, Chun-Neng Wang,
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Tomei EJ, Wolniak SM. Kinesin-2 and kinesin-9 have atypical functions during ciliogenesis in the male gametophyte of Marsilea vestita. BMC Cell Biol 2016; 17:29. [PMID: 27421907 PMCID: PMC4947347 DOI: 10.1186/s12860-016-0107-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/07/2016] [Indexed: 11/28/2022] Open
Abstract
Background Spermatogenesis in the semi-aquatic fern, Marsilea vestita, is a rapid, synchronous process that is initiated when dry microspores are placed in water. Development is post-transcriptionally driven and can be divided into two phases. The first phase consists of nine mitotic division cycles that produce 7 sterile cells and 32 spermatids. During the second phase, each spermatid differentiates into a corkscrew-shaped motile spermatozoid with ~140 cilia. Results Analysis of the transcriptome from the male gametophyte of Marsilea revealed that one kinesin-2 (MvKinesin-2) and two kinesin-9 s (MvKinesin-9A and MvKinesin-9B) are present during spermatid differentiation and ciliogenesis. RNAi knockdowns show that MvKinesin-2 is required for mitosis and cytokinesis in spermatogenous cells. Without MvKinesin-2, most spermatozoids contain two or more coiled microtubule ribbons with attached cilia and very large cell bodies. MvKinesin-9A is required for the correct placement of basal bodies along the organelle coil. Knockdowns of MvKinesin-9A have basal bodies and cilia that are irregularly positioned. Spermatozoid swimming behavior in MvKinesin-2 and -9A knockdowns is altered because of defects in axonemal placement or ciliogenesis. MvKinesin-2 knockdowns only quiver in place while MvKinesin-9A knockdowns swim erratically compared to controls. In contrast, spermatozoids produced after the silencing of MvKinesin-9B exhibit normal morphology and swimming behavior, though development is slower than normal for these gametes. Conclusions Our results show that MvKinesin-2 and MvKinesin-9A are required for ciliogenesis and motility in the Marsilea male gametophyte; however, these kinesins display atypical roles during these processes. MvKinesin-2 is required for cytokinesis, a role not typically associated with this protein, as well as for ciliogenesis during rapid development and MvKinesin-9A is needed for the correct orientation of basal bodies. Our results are the first to investigate the kinesin-linked mechanisms that regulate ciliogenesis in a land plant. Electronic supplementary material The online version of this article (doi:10.1186/s12860-016-0107-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erika J Tomei
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, MD, 20742, USA
| | - Stephen M Wolniak
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, MD, 20742, USA.
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Tomei EJ, Wolniak SM. Transcriptome analysis reveals a diverse family of kinesins essential for spermatogenesis in the fern
M
arsilea. Cytoskeleton (Hoboken) 2016; 73:145-59. [DOI: 10.1002/cm.21285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Erika J. Tomei
- Department of Cell Biology and Molecular GeneticsUniversity of Maryland at College ParkCollege Park Maryland
| | - Stephen M. Wolniak
- Department of Cell Biology and Molecular GeneticsUniversity of Maryland at College ParkCollege Park Maryland
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Wolniak SM, Boothby TC, van der Weele CM. Posttranscriptional control over rapid development and ciliogenesis in Marsilea. Methods Cell Biol 2015; 127:403-44. [PMID: 25837402 DOI: 10.1016/bs.mcb.2015.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Marsilea vestita is a semiaquatic fern that produces its spores (meiotic products) as it undergoes a process of natural desiccation. During the period of desiccation, the spores mature, and produce large quantities of pre-mRNA, which is partially processed and stored in nuclear speckles and can remain stable during a period of extended quiescence in the dry spore. Rehydration of the spores initiates a highly coordinated developmental program, featuring nine successive mitotic division cycles that occur at precise times and in precise planes within the spore wall to produce 39 cells, 32 of which are spermatids. The spermatids then undergo de novo basal body formation, the assembly of a massive cytoskeleton, nuclear and cell elongation, and finally ciliogenesis, before being released from the spore wall. The entire developmental program requires only 11 h to reach completion, and is synchronous in a population of spores rehydrated at the same time. Rapid development in this endosporic gametophyte is controlled posttranscriptionally, where stored pre-mRNAs, many of which are intron-retaining transcripts, are unmasked, processed, and translated under tight spatial and temporal control. Here, we describe posttranscriptional mechanisms that exert temporal and spatial control over this developmental program, which culminates in the production of ∼140 ciliary axonemes in each spermatozoid.
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Affiliation(s)
- Stephen M Wolniak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
| | - Thomas C Boothby
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
| | - Corine M van der Weele
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
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Chapman KM, Powell HM, Chaudhary J, Shelton JM, Richardson JA, Richardson TE, Hamra FK. Linking spermatid ribonucleic acid (RNA) binding protein and retrogene diversity to reproductive success. Mol Cell Proteomics 2013; 12:3221-36. [PMID: 23938467 DOI: 10.1074/mcp.m113.030585] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Spermiogenesis is a postmeiotic process that drives development of round spermatids into fully elongated spermatozoa. Spermatid elongation is largely controlled post-transcriptionally after global silencing of mRNA synthesis from the haploid genome. Here, rats that differentially express EGFP from a lentiviral transgene during early and late steps of spermiogenesis were used to flow sort fractions of round and elongating spermatids. Mass-spectral analysis of 2D gel protein spots enriched >3-fold in each fraction revealed a heterogeneous RNA binding proteome (hnRNPA2/b1, hnRNPA3, hnRPDL, hnRNPK, hnRNPL, hnRNPM, PABPC1, PABPC4, PCBP1, PCBP3, PTBP2, PSIP1, RGSL1, RUVBL2, SARNP2, TDRD6, TDRD7) abundantly expressed in round spermatids prior to their elongation. Notably, each protein within this ontology cluster regulates alternative splicing, sub-cellular transport, degradation and/or translational repression of mRNAs. In contrast, elongating spermatid fractions were enriched with glycolytic enzymes, redox enzymes and protein synthesis factors. Retrogene-encoded proteins were over-represented among the most abundant elongating spermatid factors identified. Consistent with these biochemical activities, plus corresponding histological profiles, the identified RNA processing factors are predicted to collectively drive post-transcriptional expression of an alternative exome that fuels finishing steps of sperm maturation and fitness.
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Boothby TC, Zipper RS, van der Weele CM, Wolniak SM. Removal of retained introns regulates translation in the rapidly developing gametophyte of Marsilea vestita. Dev Cell 2013; 24:517-29. [PMID: 23434411 DOI: 10.1016/j.devcel.2013.01.015] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 11/20/2012] [Accepted: 01/19/2013] [Indexed: 01/12/2023]
Abstract
The utilization of stored RNA is a driving force in rapid development. Here, we show that retention and subsequent removal of introns from pre-mRNAs regulate temporal patterns of translation during rapid and posttranscriptionally controlled spermatogenesis of the fern Marsilea vestita. Analysis of RNAseq-derived transcriptomes revealed a large subset of intron-retaining transcripts (IRTs) that encode proteins essential for gamete development. Genomic and IRT sequence comparisons show that other introns have been previously removed from the IRT pre-mRNAs. Fully spliced isoforms appear at distinct times during development in a spliceosome-dependent and transcription-independent manner. RNA interference knockdowns of 17/17 IRTs produced anomalies after the time points when those transcripts would normally be spliced. Intron retention is a functional mechanism for forestalling precocious translation of transcripts in the male gametophyte of M. vestita. These results have broad implications for plant gene regulation, where intron retention is widespread.
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Affiliation(s)
- Thomas C Boothby
- University of Maryland at College Park, Department of Cell Biology and Molecular Genetics, College Park, MD 20742, USA
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Boothby TC, Wolniak SM. Masked mRNA is stored with aggregated nuclear speckles and its asymmetric redistribution requires a homolog of Mago nashi. BMC Cell Biol 2011; 12:45. [PMID: 21995518 PMCID: PMC3205038 DOI: 10.1186/1471-2121-12-45] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 10/13/2011] [Indexed: 11/22/2022] Open
Abstract
Background Many rapidly developing systems rely on the regulated translation of stored transcripts for the formation of new proteins essential for morphogenesis. The microspores of the water fern Marsilea vestita dehydrate as they mature. During this process both mRNA and proteins required for subsequent development are stored within the microspores as they become fully desiccated and enter into senescence. At this point microspores become transcriptionally silent and remain so upon rehydration and for the remainder of spermatogenesis. Transcriptional silencing coupled with the translation of preformed RNA makes the microspore of M. vestita a useful system in which to study post-transcriptional regulation of RNA. Results We have characterized the distribution of mRNA as well as several conserved markers of subnuclear bodies within the nuclei of desiccating spores. During this period, nuclear speckles containing RNA were seen to aggregate forming a single large coalescence. We found that aggregated speckles contain several masked mRNA species known to be essential for spermatogenesis. During spermatogenesis masked mRNA and associated speckle proteins were shown to fragment and asymmetrically localize to spermatogenous but not sterile cells. This asymmetric localization was disrupted by RNAi knockdown of the Marsilea homolog of the Exon Junction Complex core component Mago nashi. Conclusions A subset of masked mRNA is stored in association with nuclear speckles during the dormant phase of microspore development in M. vestita. The asymmetric distribution of specific mRNAs to spermatogenous but not sterile cells mirrors their translational activities and appears to require the EJC or EJC components. This suggests a novel role for nuclear speckles in the post-transcriptional regulation of transcripts.
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Affiliation(s)
- Thomas C Boothby
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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