151
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Shi C, Liu Y, Huang H, Xia EH, Zhang HB, Gao LZ. Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PLoS One 2013; 8:e59620. [PMID: 23527231 PMCID: PMC3601113 DOI: 10.1371/journal.pone.0059620] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/15/2013] [Indexed: 11/19/2022] Open
Abstract
Plant chloroplast genes are usually co-transcribed while its posttranscriptional splicing is fairly complex and remains largely unsolved. On basis of sequencing the three complete Camellia (Theaceae) chloroplast genomes for the first time, we comprehensively analyzed the evolutionary patterns of ycf15, a plastid gene quite paradoxical in terms of its function and evolution, along the inferred angiosperm phylogeny. Although many species in separate lineages including the three species reported here contained an intact ycf15 gene in their chloroplast genomes, the phylogenetic mixture of both intact and obviously disabled ycf15 genes imply that they are all non-functional. Both intracellular gene transfer (IGT) and horizontal gene transfer (HGT) failed to explain such distributional anomalies. While, transcriptome analyses revealed that ycf15 was transcribed as precursor polycistronic transcript which contained ycf2, ycf15 and antisense trnL-CAA. The transcriptome assembly was surprisingly found to cover near the complete Camellia chloroplast genome. Many non-coding regions including pseudogenes were mapped by multiple transcripts, indicating the generality of pseudogene transcriptions. Our results suggest that plastid DNA posttranscriptional splicing may involve complex cleavage of non-functional genes.
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Affiliation(s)
- Chao Shi
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yuan Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- * E-mail:
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152
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Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Rest JS, Davis CC. Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet 2013; 9:e1003265. [PMID: 23459037 PMCID: PMC3573108 DOI: 10.1371/journal.pgen.1003265] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/07/2012] [Indexed: 11/18/2022] Open
Abstract
Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms. Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Here, using phylogenomic approaches, we demonstrate that as much as ∼40% of the mitochondrial genes in the parasitic plant species Rafflesiaceae are acquired from their hosts via HGT. These transgenes are likely functional in their recipient species and in some cases appear to have displaced native copies in the same genomic location. These results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in parasitic plants, HGT involving mitochondrial genes is substantially higher.
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Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
- Department of Ecology and Evolutionary Biology, School of Life Science, Fudan University, Shanghai, China
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Sugumaran
- Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Joshua S. Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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153
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Plasmodesmata: intercellular tunnels facilitating transport of macromolecules in plants. Cell Tissue Res 2013; 352:49-58. [DOI: 10.1007/s00441-012-1550-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 12/18/2012] [Indexed: 01/15/2023]
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154
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Tripp EA, Fatimah S, Darbyshire I, McDade LA. Origin of African Physacanthus (Acanthaceae) via wide hybridization. PLoS One 2013; 8:e55677. [PMID: 23383261 PMCID: PMC3559597 DOI: 10.1371/journal.pone.0055677] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 01/03/2013] [Indexed: 11/24/2022] Open
Abstract
Gene flow between closely related species is a frequent phenomenon that is known to play important roles in organismal evolution. Less clear, however, is the importance of hybridization between distant relatives. We present molecular and morphological evidence that support origin of the plant genus Physacanthus via “wide hybridization” between members of two distantly related lineages in the large family Acanthaceae. These two lineages are well characterized by very different morphologies yet, remarkably, Physacanthus shares features of both. Chloroplast sequences from six loci indicate that all three species of Physacanthus contain haplotypes from both lineages, suggesting that heteroplasmy likely predated speciation in the genus. Although heteroplasmy is thought to be unstable and thus transient, multiple haplotypes have been maintained through time in Physacanthus. The most likely scenario to explain these data is that Physacanthus originated via an ancient hybridization event that involved phylogenetically distant parents. This wide hybridization has resulted in the establishment of an independently evolving clade of flowering plants.
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Affiliation(s)
- Erin A Tripp
- Rancho Santa Ana Botanic Garden, Claremont, California, United States of America.
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155
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Greiner S, Bock R. Tuning a ménage à trois: Co-evolution and co-adaptation of nuclear and organellar genomes in plants. Bioessays 2013; 35:354-65. [DOI: 10.1002/bies.201200137] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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156
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Parry MAJ, Andralojc PJ, Scales JC, Salvucci ME, Carmo-Silva AE, Alonso H, Whitney SM. Rubisco activity and regulation as targets for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:717-30. [PMID: 23162118 DOI: 10.1093/jxb/ers336] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rubisco (ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase) enables net carbon fixation through the carboxylation of RuBP. However, some characteristics of Rubisco make it surprisingly inefficient and compromise photosynthetic productivity. For example, Rubisco catalyses a wasteful reaction with oxygen that leads to the release of previously fixed CO(2) and NH(3) and the consumption of energy during photorespiration. Furthermore, Rubisco is slow and large amounts are needed to support adequate photosynthetic rates. Consequently, Rubisco has been studied intensively as a prime target for manipulations to 'supercharge' photosynthesis and improve both productivity and resource use efficiency. The catalytic properties of Rubiscos from diverse sources vary considerably, suggesting that changes in turnover rate, affinity, or specificity for CO(2) can be introduced to improve Rubisco performance in specific crops and environments. While attempts to manipulate plant Rubisco by nuclear transformation have had limited success, modifying its catalysis by targeted changes to its catalytic large subunit via chloroplast transformation have been much more successful. However, this technique is still in need of development for most major food crops including maize, wheat, and rice. Other bioengineering approaches for improving Rubisco performance include improving the activity of its ancillary protein, Rubisco activase, in addition to modulating the synthesis and degradation of Rubisco's inhibitory sugar phosphate ligands. As the rate-limiting step in carbon assimilation, even modest improvements in the overall performance of Rubisco pose a viable pathway for obtaining significant gains in plant yield, particularly under stressful environmental conditions.
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Affiliation(s)
- Martin A J Parry
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK.
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157
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Thyssen G, Svab Z, Maliga P. Exceptional inheritance of plastids via pollen in Nicotiana sylvestris with no detectable paternal mitochondrial DNA in the progeny. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:84-8. [PMID: 22612300 DOI: 10.1111/j.1365-313x.2012.05057.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plastids and mitochondria, the DNA-containing cytoplasmic organelles, are maternally inherited in the majority of angiosperm species. Even in plants with strict maternal inheritance, exceptional paternal transmission of plastids has been observed. Our objective was to detect rare leakage of plastids via pollen in Nicotiana sylvestris and to determine if pollen transmission of plastids results in co-transmission of paternal mitochondria. As father plants, we used N. sylvestris plants with transgenic, selectable plastids and wild-type mitochondria. As mother plants, we used N. sylvestris plants with Nicotiana undulata cytoplasm, including the CMS-92 mitochondria that cause cytoplasmic male sterility (CMS) by homeotic transformation of the stamens. We report here exceptional paternal plastid DNA in approximately 0.002% of N. sylvestris seedlings. However, we did not detect paternal mitochondrial DNA in any of the six plastid-transmission lines, suggesting independent transmission of the cytoplasmic organelles via pollen. When we used fertile N. sylvestris as mothers, we obtained eight fertile plastid transmission lines, which did not transmit their plastids via pollen at higher frequencies than their fathers. We discuss the implications for transgene containment and plant evolutionary histories inferred from cytoplasmic phylogenies.
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Affiliation(s)
- Gregory Thyssen
- Waksman Institute, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
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158
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Abstract
The flow of genes between different species represents a form of genetic variation whose implications have not been fully appreciated. Here I examine some key findings on the extent of horizontal gene transfer (HGT) revealed by comparative genome analysis and their theoretical implications. In theoretical terms, HGT affects ideas pertaining to the tree of life, the notion of a last universal common ancestor, and the biological unities, as well as the rules of taxonomic nomenclature. This review discusses the emergence of the eukaryotic cell and the occurrence of HGT among metazoan phyla involving both transposable elements and structural genes for normal housekeeping functions. I also discuss the bacterial pangenome, which provides an important case study on the permeability of species boundaries. An interesting observation about bdelloid rotifers and their reversion to asexual reproduction as it pertains to HGT is included.
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Affiliation(s)
- Michael Syvanen
- Department of Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA.
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159
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Xi Z, Bradley RK, Wurdack KJ, Wong K, Sugumaran M, Bomblies K, Rest JS, Davis CC. Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics 2012; 13:227. [PMID: 22681756 PMCID: PMC3460754 DOI: 10.1186/1471-2164-13-227] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association between the parasite and its host. HGT in these systems has been invoked when a DNA sequence obtained from a parasite is placed phylogenetically very near to its host rather than with its closest relatives. Studies of HGT in parasitic plants have relied largely on the fortuitous discovery of gene phylogenies that indicate HGT, and no broad systematic search for HGT has been undertaken in parasitic systems where it is most expected to occur. RESULTS We analyzed the transcriptomes of the holoparasite Rafflesia cantleyi Solms-Laubach and its obligate host Tetrastigma rafflesiae Miq. using phylogenomic approaches. Our analyses show that several dozen actively transcribed genes, most of which appear to be encoded in the nuclear genome, are likely of host origin. We also find that hundreds of vertically inherited genes (VGT) in this parasitic plant exhibit codon usage properties that are more similar to its host than to its closest relatives. CONCLUSIONS Our results establish for the first time a substantive number of HGTs in a plant host-parasite system. The elevated rate of unidirectional host-to- parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesia for maintaining these genes. Finally, a similar convergence in codon usage of VGTs has been shown in microbes with high HGT rates, which may help to explain the increase of HGTs in these parasitic plants.
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Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
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160
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Heslop-Harrison JSP. Genome evolution: extinction, continuation or explosion? CURRENT OPINION IN PLANT BIOLOGY 2012; 15:115-21. [PMID: 22465161 DOI: 10.1016/j.pbi.2012.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/05/2012] [Accepted: 03/06/2012] [Indexed: 05/24/2023]
Abstract
Darwin recognised the processes of speciation and the frequent extinction of species. We now understand many of the genome-scale processes occurring during evolution involving mutations, amplification, loss or homogenisation of DNA sequences; rearrangement, fusion and fission of chromosomes; and horizontal transfer of genes or genomes, including processes involving hybridisation and polyploidy. DNA sequence information, combined with appropriate informatic tools and experimental approaches such as generation of synthetic hybrids, comparison of genotypes across environments, and modelling of genomic responses, is now letting us link genome behaviour with its consequences. The understanding of genome evolution will be of critical value both for conservation of the biodiversity of the plant kingdom and addressing the challenges of breeding new and more sustainable crops to feed the human population.
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161
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Abstract
Our objective was to test whether or not plastids and mitochondria, the two DNA-containing organelles, move between cells in plants. As our experimental approach, we grafted two different species of tobacco, Nicotiana tabacum and Nicotiana sylvestris. Grafting triggers formation of new cell-to-cell contacts, creating an opportunity to detect cell-to-cell organelle movement between the genetically distinct plants. We initiated tissue culture from sliced graft junctions and selected for clonal lines in which gentamycin resistance encoded in the N. tabacum nucleus was combined with spectinomycin resistance encoded in N. sylvestris plastids. Here, we present evidence for cell-to-cell movement of the entire 161-kb plastid genome in these plants, most likely in intact plastids. We also found that the related mitochondria were absent, suggesting independent movement of the two DNA-containing organelles. Acquisition of plastids from neighboring cells provides a mechanism by which cells may be repopulated with functioning organelles. Our finding supports the universality of intercellular organelle trafficking and may enable development of future biotechnological applications.
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Affiliation(s)
- Gregory Thyssen
- Waksman Institute, Rutgers University, Piscataway, NJ 08854; and
| | - Zora Svab
- Waksman Institute, Rutgers University, Piscataway, NJ 08854; and
| | - Pal Maliga
- Waksman Institute, Rutgers University, Piscataway, NJ 08854; and
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
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