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Schröpfer S, Flachowsky H. Tracing CRISPR/Cas12a Mediated Genome Editing Events in Apple Using High-Throughput Genotyping by PCR Capillary Gel Electrophoresis. Int J Mol Sci 2021; 22:ijms222212611. [PMID: 34830492 PMCID: PMC8619667 DOI: 10.3390/ijms222212611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 01/03/2023] Open
Abstract
The use of the novel CRISPR/Cas12a system is advantageous, as it expands the possibilities for genome editing (GE) applications due to its different features compared to the commonly used CRISPR/Cas9 system. In this work, the CRISPR/Cas12a system was applied for the first time to apple to investigate its general usability for GE applications. Efficient guide RNAs targeting different exons of the endogenous reporter gene MdPDS, whose disruption leads to the albino phenotype, were pre-selected by in vitro cleavage assays. A construct was transferred to apple encoding for a CRISPR/Cas12a system that simultaneously targets two loci in MdPDS. Using fluorescent PCR capillary electrophoresis and amplicon deep sequencing, all identified GE events of regenerated albino shoots were characterized as deletions. Large deletions between the two neighboring target sites were not observed. Furthermore, a chimeric composition of regenerates and shoots that exhibited multiple GE events was observed frequently. By comparing both analytical methods, it was shown that fluorescent PCR capillary gel electrophoresis is a sensitive high-throughput genotyping method that allows accurate predictions of the size and proportion of indel mutations for multiple loci simultaneously. Especially for species exhibiting high frequencies of chimerism, it can be recommended as a cost-effective method for efficient selection of homohistont GE lines.
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Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). ANNALS OF BOTANY 2021; 128:281-299. [PMID: 33729490 PMCID: PMC8389469 DOI: 10.1093/aob/mcab042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. METHODS Using next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization. KEY RESULTS Full-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4-7.2 million years ago. CONCLUSIONS Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kathrin M Seibt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Beatrice Weber
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, PR China
| | - Thomas Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
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Chang J, Chen X, Zhang T, Wang R, Wang A, Lan X, Zhou Y, Ma S, Xia Q. The novel insight into the outcomes of CRISPR/Cas9 editing intra- and inter-species. Int J Biol Macromol 2020; 163:711-717. [PMID: 32652159 DOI: 10.1016/j.ijbiomac.2020.07.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
The CRISPR/Cas (clustered regularly interspaced short palindromic repeat technology/CRISPR-associated protein) is a widely used and powerful research tool in biosciences and a promising therapeutic agent for treating genetic diseases. Mutations induced by Cas9 are generally considered stochastic and unpredictable, thus hindering its applications where precise genetic alternations are required. Here, through deep sequencing and analysis of genome editing outcomes of multiple sites in four distinct species, we found that Cas9-induced mutations are coincident in mutation types but are significantly different in indel patterns among species. In human and mouse cells, indels were almost evenly distributed at both ends of the cleavage sites. However, the indels mainly appeared at the upstream of cleavage sites in Bombyx mori, while they predominantly occurred downstream of the cleavage sites in the zebrafish Danio rerio. We also found that within a species, indel patterns are sequence dependent, wherein deletions between two adjacent micro-homology sequences were the most frequently observed mutations in the repair spectrum. These results suggested the species differences in DNA repair processes during Cas9-induced gene editing, and the important role of sequence structure at the target site in predicting the gene editing outcome.
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Affiliation(s)
- Jiasong Chang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Xiaoxu Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Tong Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Ruolin Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Aoming Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Xinhui Lan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Yuyu Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China.
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China.
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Comparison and Characterization of Mutations Induced by Gamma-Ray and Carbon-Ion Irradiation in Rice ( Oryza sativa L.) Using Whole-Genome Resequencing. G3-GENES GENOMES GENETICS 2019; 9:3743-3751. [PMID: 31519747 PMCID: PMC6829151 DOI: 10.1534/g3.119.400555] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gamma-rays are the most widely used mutagenic radiation in plant mutation breeding, but detailed characteristics of mutated DNA sequences have not been clarified sufficiently. In contrast, newly introduced physical mutagens, e.g., heavy-ion beams, have attracted geneticists’ and breeders’ interest and many studies on their mutation efficiency and mutated DNA characteristics have been conducted. In this study, we characterized mutations induced by gamma rays and carbon(C)-ion beams in rice (Oryza sativa L.) mutant lines at M5 generation using whole-genome resequencing. On average, 57.0 single base substitutions (SBS), 17.7 deletions, and 5.9 insertions were detected in each gamma-ray-irradiated mutant, whereas 43.7 single SBS, 13.6 deletions, and 5.3 insertions were detected in each C-ion-irradiated mutant. The structural variation (SV) analysis detected 2.0 SVs (including large deletions or insertions, inversions, duplications, and reciprocal translocations) on average in each C-ion-irradiated mutant, while 0.6 SVs were detected on average in each gamma-ray-irradiated mutant. Furthermore, complex SVs presumably having at least two double-strand breaks (DSBs) were detected only in C-ion-irradiated mutants. In summary, gamma-ray irradiation tended to induce larger numbers of small mutations than C-ion irradiation, whereas complex SVs were considered to be the specific characteristics of the mutations induced by C-ion irradiation, which may be due to their different radiation properties. These results could contribute to the application of radiation mutagenesis to plant mutation breeding.
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Huang TK, Puchta H. CRISPR/Cas-mediated gene targeting in plants: finally a turn for the better for homologous recombination. PLANT CELL REPORTS 2019; 38:443-453. [PMID: 30673818 DOI: 10.1007/s00299-019-02379-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/09/2019] [Indexed: 05/22/2023]
Abstract
We summarize recent progress of CRISPR/Cas9-mediated gene targeting in plants, provide recommendations for designing gene-targeting vectors and highlight the potential of new technologies applicable to plants. Gene targeting (GT) is a tool of urgent need for plant biotechnology and breeding. It is based on homologous recombination that is able to precisely introduce desired modifications within a target locus. However, its low efficiency in higher plants is a major barrier for its application. Using site-specific nucleases, such as the recent CRISPR/Cas system, GT has become applicable in plants, via the induction of double-strand breaks, although still at a too low efficiency for most practical applications in crops. Recently, a variety of promising new improvements regarding the efficiency of GT has been reported by several groups. It turns out that GT can be enhanced by cell-type-specific expression of Cas nucleases, by the use of self-amplified GT-vector DNA or by manipulation of DNA repair pathways. Here, we highlight the most recent progress of GT in plants. Moreover, we provide suggestions on how to use the technology efficiently, based on the mechanisms of DNA repair, and highlight several of the newest GT strategies in yeast or mammals that are potentially applicable to plants. Using the full potential of GT technology will definitely help us pave the way in enhancing crop yields and food safety for an ecologically friendly agriculture.
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Affiliation(s)
- Teng-Kuei Huang
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany.
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6
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Grohmann L, Keilwagen J, Duensing N, Dagand E, Hartung F, Wilhelm R, Bendiek J, Sprink T. Detection and Identification of Genome Editing in Plants: Challenges and Opportunities. FRONTIERS IN PLANT SCIENCE 2019; 10:236. [PMID: 30930911 PMCID: PMC6423494 DOI: 10.3389/fpls.2019.00236] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/12/2019] [Indexed: 05/21/2023]
Abstract
Conventional genetic engineering techniques generate modifications in the genome via stable integration of DNA elements which do not occur naturally in this combination. Therefore, the resulting organisms and (most) products thereof can unambiguously be identified with event-specific PCR-based methods targeting the insertion site. New breeding techniques such as genome editing diversify the toolbox to generate genetic variability in plants. Several of these techniques can introduce single nucleotide changes without integrating foreign DNA and thereby generate organisms with intended phenotypes. Consequently, such organisms and products thereof might be indistinguishable from naturally occurring or conventionally bred counterparts with established analytical tools. The modifications can entirely resemble random mutations regardless of being spontaneous or induced chemically or via irradiation. Therefore, if an identification of these organisms or products thereof is demanded, a new challenge will arise for (official) seed, food, and feed testing laboratories and enforcement institutions. For detailed consideration, we distinguish between the detection of sequence alterations - regardless of their origin - the identification of the process that generated a specific modification and the identification of a genotype, i.e., an organism produced by genome editing carrying a specific genetic alteration in a known background. This article briefly reviews the existing and upcoming detection and identification strategies (including the use of bioinformatics and statistical approaches) in particular for plants developed with genome editing techniques.
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Affiliation(s)
- Lutz Grohmann
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
- *Correspondence: Lutz Grohmann,
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Nina Duensing
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Emilie Dagand
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Frank Hartung
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Joachim Bendiek
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Thorben Sprink
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
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7
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Schmidt C, Pacher M, Puchta H. DNA Break Repair in Plants and Its Application for Genome Engineering. Methods Mol Biol 2019; 1864:237-266. [PMID: 30415341 DOI: 10.1007/978-1-4939-8778-8_17] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome engineering is a biotechnological approach to precisely modify the genetic code of a given organism in order to change the context of an existing sequence or to create new genetic resources, e.g., for obtaining improved traits or performance. Efficient targeted genome alterations are mainly based on the induction of DNA double-strand breaks (DSBs) or adjacent single-strand breaks (SSBs). Naturally, all organisms continuously have to deal with DNA-damaging factors challenging the genetic integrity, and therefore a wide range of DNA repair mechanisms have evolved. A profound understanding of the different repair pathways is a prerequisite to control and enhance targeted gene modifications. DSB repair can take place by nonhomologous end joining (NHEJ) or homology-dependent repair (HDR). As the main outcome of NHEJ-mediated repair is accompanied by small insertions and deletions, it is applicable to specifically knock out genes or to rearrange linkage groups or whole chromosomes. The basic requirement for HDR is the presence of a homologous template; thus this process can be exploited for targeted integration of ectopic sequences into the plant genome. The development of different types of artificial site-specific nucleases allows for targeted DSB induction in the plant genome. Such synthetic nucleases have been used for both qualitatively studying DSB repair in vivo with respect to mechanistic differences and quantitatively in order to determine the role of key factors for NHEJ and HR, respectively. The conclusions drawn from these studies allow for a better understanding of genome evolution and help identifying synergistic or antagonistic genetic interactions while supporting biotechnological applications for transiently modifying the plant DNA repair machinery in favor of targeted genome engineering.
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Affiliation(s)
- Carla Schmidt
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Michael Pacher
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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8
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Que Q, Chen Z, Kelliher T, Skibbe D, Dong S, Chilton MD. Plant DNA Repair Pathways and Their Applications in Genome Engineering. Methods Mol Biol 2019; 1917:3-24. [PMID: 30610624 DOI: 10.1007/978-1-4939-8991-1_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Remarkable progress in the development of technologies for sequence-specific modification of primary DNA sequences has enabled the precise engineering of crops with novel characteristics. These programmable sequence-specific modifiers include site-directed nucleases (SDNs) and base editors (BEs). Currently, these genome editing machineries can be targeted to specific chromosomal locations to induce sequence changes. However, the sequence mutation outcomes are often greatly influenced by the type of DNA damage being generated, the status of host DNA repair machinery, and the presence and structure of DNA repair donor molecule. The outcome of sequence modification from repair of DNA double-strand breaks (DSBs) is often uncontrollable, resulting in unpredictable sequence insertions or deletions of various sizes. For base editing, the precision of intended edits is much higher, but the efficiency can vary greatly depending on the type of BE used or the activity of the endogenous DNA repair systems. This article will briefly review the possible DNA repair pathways present in the plant cells commonly used for generating edited variants for genome engineering applications. We will discuss the potential use of DNA repair mechanisms for developing and improving methodologies to enhance genome engineering efficiency and to direct DNA repair processes toward the desired outcomes.
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Affiliation(s)
- Qiudeng Que
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA.
| | - Zhongying Chen
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Tim Kelliher
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - David Skibbe
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Shujie Dong
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Mary-Dell Chilton
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
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9
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Birth and Death of LTR-Retrotransposons in Aegilops tauschii. Genetics 2018; 210:1039-1051. [PMID: 30158124 DOI: 10.1534/genetics.118.301198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/20/2018] [Indexed: 11/18/2022] Open
Abstract
Long terminal repeat-retrotransposons (LTR-RTs) are a major component of all flowering plant genomes. To analyze the time dynamics of LTR-RTs, we modeled the insertion rates of the 35 most abundant LTR-RT families in the genome of Aegilops tauschii, one of the progenitors of wheat. Our model of insertion rate (birth) takes into account random variation in LTR divergence and the deletion rate (death) of LTR-RTs. Modeling the death rate is crucial because ignoring it would underestimate insertion rates in the distant past. We rejected the hypothesis of constancy of insertion rates for all 35 families and showed by simulations that our hypothesis test controlled the false-positive rate. LTR-RT insertions peaked from 0.064 to 2.39 MYA across the 35 families. Among other effects, the average age of elements within a family was negatively associated with recombination rate along a chromosome, with proximity to the closest gene, and weakly associated with the proximity to its 5' end. Elements within a family that were near genes colinear with genes in the genome of tetraploid emmer wheat tended to be younger than those near noncolinear genes. We discuss these associations in the context of genome evolution and stability of genome sizes in the tribe Triticeae. We demonstrate the general utility of our models by analyzing the two most abundant LTR-RT families in Arabidopsis lyrata, and show that these families differed in their insertion dynamics. Our estimation methods are available in the R package TE on CRAN.
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10
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Zhang G, Hua Z. Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation. PeerJ 2018; 6:e4678. [PMID: 29707435 PMCID: PMC5918131 DOI: 10.7717/peerj.4678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/09/2018] [Indexed: 02/01/2023] Open
Abstract
Wheat streak mosaic virus (WSMV) causes streak mosaic disease in wheat (Triticum aestivum L.) and has been an important constraint limiting wheat production in many regions around the world. Wsm2 is the only resistance gene discovered in wheat genome and has been located in a short genomic region of its chromosome 3B. However, the sequence nature and the biological function of Wsm2 remain unknown due to the difficulty of genetic manipulation in wheat. In this study, we tested WSMV infectivity among wheat and its two closely related grass species, rice (Oryza sativa) and Brachypodium distachyon. Based on the phenotypic result and previous genomic studies, we developed a novel bioinformatics pipeline for interpreting a potential biological function of Wsm2 and its ancestor locus in wheat. In the WSMV resistance tests, we found that rice has a WMSV resistance gene while Brachypodium does not, which allowed us to hypothesize the presence of a Wsm2 ortholog in rice. Our OrthoMCL analysis of protein coding genes on wheat chromosome 3B and its syntenic chromosomes in rice and Brachypodium discovered 4,035 OrthoMCL groups as preliminary candidates of Wsm2 orthologs. Given that Wsm2 is likely duplicated through an intrachromosomal illegitimate recombination and that Wsm2 is dominant, we inferred that this new WSMV-resistance gene acquired an activation domain, lost an inhibition domain, or gained high expression compared to its ancestor locus. Through comparison, we identified that 67, 16, and 10 out of 4,035 OrthoMCL orthologous groups contain a rice member with 25% shorter or longer in length, or 10 fold more expression, respectively, than those from wheat and Brachypodium. Taken together, we predicted a total of 93 good candidates for a Wsm2 ancestor locus. All of these 93 candidates are not tightly linked with Wsm2, indicative of the role of illegitimate recombination in the birth of Wsm2. Further sequence analysis suggests that the protein products of Wsm2 may combat WSMV disease through a molecular mechanism involving protein degradation and/or membrane trafficking. The 93 putative Wsm2 ancestor loci discovered in this study could serve as good candidates for future genetic isolation of the true Wsm2 locus.
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Affiliation(s)
- Guorong Zhang
- Agricultural Research Center-Hays, Kansas State University, Hays, KS, United States of America
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States of America.,Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, United States of America
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11
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Grover CE, Arick MA, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing. Genome Biol Evol 2017; 9:3328-3344. [PMID: 29194487 PMCID: PMC5737505 DOI: 10.1093/gbe/evx248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2017] [Indexed: 12/19/2022] Open
Abstract
Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple transoceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic disjunction, being restricted to the Hawaiian Islands and Madagascar/East Africa, respectively. We assembled and use de novo genome sequences to address questions regarding the divergence of these two genera from each other and from their sister-group, Gossypium. In addition, we explore processes underlying the genome downsizing that characterizes Kokia and Gossypioides relative to other genera in the tribe. Using 13,000 gene orthologs and synonymous substitution rates, we show that the two disjuncts last shared a common ancestor ∼5 Ma, or half as long ago as their divergence from Gossypium. We report relative stasis in the transposable element fraction. In comparison to Gossypium, there is loss of ∼30% of the gene content in the two disjunct genera and a history of genome-wide accumulation of deletions. In both genera, there is a genome-wide bias toward deletions over insertions, and the number of gene losses exceeds the number of gains by ∼2- to 4-fold. The genomic analyses presented here elucidate genomic consequences of the demographic and biogeographic history of these closest relatives of Gossypium, and enhance their value as phylogenetic outgroups.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Mark A Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Adam Thrash
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - William S Sanders
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
- Department of Computer Science & Engineering, Mississippi State University, Mississippi State, MS
- The Jackson Laboratory, Connecticut, Farmington, CT
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico
| | | | - Joshua A Udall
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
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12
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Vu GTH, Cao HX, Fauser F, Reiss B, Puchta H, Schubert I. Endogenous sequence patterns predispose the repair modes of CRISPR/Cas9-induced DNA double-stranded breaks in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:57-67. [PMID: 28696528 DOI: 10.1111/tpj.13634] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 05/20/2023]
Abstract
The possibility to predict the outcome of targeted DNA double-stranded break (DSB) repair would be desirable for genome editing. Furthermore the consequences of mis-repair of potentially cell-lethal DSBs and the underlying pathways are not yet fully understood. Here we study the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-induced mutation spectra at three selected endogenous loci in Arabidopsis thaliana by deep sequencing of long amplicon libraries. Notably, we found sequence-dependent genomic features that affected the DNA repair outcome. Deletions of 1-bp to <1000-bp size and/or very short insertions, deletions >1 kbp (all due to NHEJ) and deletions combined with insertions between 5-bp to >100 bp [caused by a synthesis-dependent strand annealing (SDSA)-like mechanism] occurred most frequently at all three loci. The appearance of single-stranded annealing events depends on the presence and distance between repeats flanking the DSB. The frequency and size of insertions is increased if a sequence with high similarity to the target site was available in cis. Most deletions were linked to pre-existing microhomology. Deletion and/or insertion mutations were blunt-end ligated or via de novo generated microhomology. While most mutation types and, to some degree, their predictability are comparable with animal systems, the broad range of deletion mutations seems to be a peculiar feature of the plant A. thaliana.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D 06466, Gatersleben, Stadt Seeland, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D 06466, Gatersleben, Stadt Seeland, Germany
| | - Friedrich Fauser
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, Karlsruhe, 76049, Germany
| | - Bernd Reiss
- Max Planck Institute for Plant Breeding Research, 50829, Köln, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, Karlsruhe, 76049, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D 06466, Gatersleben, Stadt Seeland, Germany
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An Insight into T-DNA Integration Events in Medicago sativa. Int J Mol Sci 2017; 18:ijms18091951. [PMID: 28895894 PMCID: PMC5618600 DOI: 10.3390/ijms18091951] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/24/2017] [Accepted: 09/06/2017] [Indexed: 11/16/2022] Open
Abstract
The molecular mechanisms of transferred DNA (T-DNA) integration into the plant genome are still not completely understood. A large number of integration events have been analyzed in different species, shedding light on the molecular mechanisms involved, and on the frequent transfer of vector sequences outside the T-DNA borders, the so-called vector backbone (VB) sequences. In this work, we characterized 46 transgenic alfalfa (Medicago sativa L.) plants (events), generated in previous works, for the presence of VB tracts, and sequenced several T-DNA/genomic DNA (gDNA) junctions. We observed that about 29% of the transgenic events contained VB sequences, within the range reported in other species. Sequence analysis of the T-DNA/gDNA junctions evidenced larger deletions at LBs compared to RBs and insertions probably originated by different integration mechanisms. Overall, our findings in alfalfa are consistent with those in other plant species. This work extends the knowledge on the molecular events of T-DNA integration and can help to design better transformation protocols for alfalfa.
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Hu Y, Chen Z, Zhuang C, Huang J. Cascade of chromosomal rearrangements caused by a heterogeneous T-DNA integration supports the double-stranded break repair model for T-DNA integration. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:954-965. [PMID: 28244154 DOI: 10.1111/tpj.13523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/15/2017] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Transferred DNA (T-DNA) from Agrobacterium tumefaciens can be integrated into the plant genome. The double-stranded break repair (DSBR) pathway is a major model for T-DNA integration. From this model, we expect that two ends of a T-DNA molecule would invade into a single DNA double-stranded break (DSB) or independent DSBs in the plant genome. We call the later phenomenon a heterogeneous T-DNA integration, which has never been observed. In this work, we demonstrated it in an Arabidopsis T-DNA insertion mutant seb19. To resolve the chromosomal structural changes caused by T-DNA integration at both the nucleotide and chromosome levels, we performed inverse PCR, genome resequencing, fluorescence in situ hybridization and linkage analysis. We found, in seb19, a single T-DNA connected two different chromosomal loci and caused complex chromosomal rearrangements. The specific break-junction pattern in seb19 is consistent with the result of heterogeneous T-DNA integration but not of recombination between two T-DNA insertions. We demonstrated that, in seb19, heterogeneous T-DNA integration evoked a cascade of incorrect repair of seven DSBs on chromosomes 4 and 5, and then produced translocation, inversion, duplication and deletion. Heterogeneous T-DNA integration supports the DSBR model and suggests that two ends of a T-DNA molecule could be integrated into the plant genome independently. Our results also show a new origin of chromosomal abnormalities.
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Affiliation(s)
- Yufei Hu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiyu Chen
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chuxiong Zhuang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
| | - Jilei Huang
- Instrumental Analysis and Research Center, South China Agricultural University, Guangzhou, 510642, China
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15
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Vu GTH, Cao HX, Reiss B, Schubert I. Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage. THE NEW PHYTOLOGIST 2017; 214:1712-1721. [PMID: 28245065 DOI: 10.1111/nph.14490] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/22/2017] [Indexed: 06/06/2023]
Abstract
In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate. We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution. Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break-end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome. Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion-biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Bernd Reiss
- Max Planck Institute for Plant Breeding Research, 50829, Köln, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
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16
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Singh KK, Choudhury AR, Tiwari HK. Numtogenesis as a mechanism for development of cancer. Semin Cancer Biol 2017; 47:101-109. [PMID: 28511886 DOI: 10.1016/j.semcancer.2017.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/20/2017] [Accepted: 10/14/2016] [Indexed: 01/10/2023]
Abstract
Transfer of genetic material from cytoplasmic organelles to the nucleus, an ongoing process, has implications in evolution, aging, and human pathologies such as cancer. The transferred mitochondrial DNA (mtDNA) fragments in the nuclear genome are called nuclear mtDNA or NUMTs. We have named the process numtogenesis, defining the term as the transfer of mtDNA into the nuclear genome, or, less specifically, the transfer of mitochondria or mitochondrial components into the nucleus. There is increasing evidence of the involvement of NUMTs in human biology and pathology. Although information pertaining to NUMTs and numtogenesis is sparse, the role of this aspect of mitochondrial biology to human cancers is apparent. In this review, we present available knowledge about the origin and mechanisms of numtogenesis, with special emphasis on the role of NUMTs in human malignancies. We describe studies undertaken in our laboratory and in others and discuss the influence of NUMTs in tumor initiation and progression and in survival of cancer patients. We describe suppressors of numtogenesis and evolutionary conserved mechanisms underlying numtogenesis in cancer. An understanding the emerging field of numtogenesis should allow comprehension of this process in various malignancies and other diseases and, more generally, in human health.
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Affiliation(s)
- Keshav K Singh
- Departments of Genetics, Birmingham, AL, 35294, USA; Departments of Pathology, Birmingham, AL, 35294, USA; Departments of Environmental Health, Center for Free Radical Biology, Birmingham, AL, 35294, USA; Center for Aging, Birmingham, AL, 35294, USA; UAB Comprehensive Cancer Center, University of Alabama at Birmingham, AL, 35294, USA; Birmingham Veterans Affairs Medical Center, AL, 35294, USA.
| | | | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
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17
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Puchta H. Applying CRISPR/Cas for genome engineering in plants: the best is yet to come. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:1-8. [PMID: 27914284 DOI: 10.1016/j.pbi.2016.11.011] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/13/2016] [Indexed: 05/18/2023]
Abstract
Less than 5 years ago the CRISPR/Cas nuclease was first introduced into eukaryotes, shortly becoming the most efficient and widely used tool for genome engineering. For plants, efforts were centred on obtaining heritable changes in most transformable crop species by inducing mutations into open reading frames of interest, via non-homologous end joining. Now it is important to take the next steps and further develop the technology to reach its full potential. For breeding, besides using DNA-free editing and avoiding off target effects, it will be desirable to apply the system for the mutation of regulatory elements and for more complex genome rearrangements. Targeting enzymatic activities, like transcriptional regulators or DNA modifying enzymes, will be important for plant biology in the future.
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Affiliation(s)
- Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany.
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19
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Schubert I, Vu GTH. Genome Stability and Evolution: Attempting a Holistic View. TRENDS IN PLANT SCIENCE 2016; 21:749-757. [PMID: 27427334 DOI: 10.1016/j.tplants.2016.06.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/06/2016] [Accepted: 06/15/2016] [Indexed: 05/02/2023]
Abstract
The reason why the DNA content, chromosome number and shape, and gene content of eukaryotic genomes vary independently remains a matter of speculation. The same is true for the questions of whether there is a general tendency for increase or decrease of genome size and chromosome number and whether genome size and/or chromosome number have an adaptive value and, if so, what this value is. Here we assume that three strategies of genome evolution (shrinkage, expansion, and equilibrium) have developed to find the optimal balance between genomic stability and plasticity. We suggest various modes of DNA double-strand break (DSB) repair in combination with whole-genome duplication (WGD) and dysploid chromosome number alteration to explain the different strategies of genome size and karyotype evolution.
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Affiliation(s)
- Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D 06466 Gatersleben, Stadt Seeland, Germany.
| | - Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D 06466 Gatersleben, Stadt Seeland, Germany
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20
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Puchta H. Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:5-15. [PMID: 26677816 DOI: 10.1111/tpj.13100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 05/21/2023]
Abstract
It is possible to target individual sequence motives within genomes by using synthetic DNA-binding domains. This one-dimensional approach has been used successfully in plants to induce mutations or for the transcriptional regulation of single genes. When the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system was discovered, a tool became available allowing the extension of this approach from one to three dimensions and to construct at least partly synthetic entities on the genome, epigenome and transcriptome levels. The second dimension can be obtained by targeting the Cas9 protein to multiple unique genomic sites by applying multiple different single guiding (sg) RNAs, each defining a different DNA-binding site. Finally, the simultaneous use of phylogenetically different Cas9 proteins or sgRNAs that harbour different types of protein binding motives, allows for a third dimension of control. Thus, different types of enzyme activities - fused either to one type of Cas9 orthologue or to one type of RNA-binding domain specific to one type of sgRNA - can be targeted to multiple different genomic sites simultaneously. Thus, it should be possible to induce quantitatively different levels of expression of certain sets of genes and at the same time to repress other genes, redefining the nuclear transcriptome. Likewise, by the use of different types of histone-modifying and/or DNA (de)methylating activities, the epigenome of plants should be reprogrammable. On our way to synthetic plant genomes, the next steps will be to use complex genome engineering approaches within or between species borders to restructure and recombine natural or artificial chromosomes.
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Affiliation(s)
- Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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21
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Repair of adjacent single-strand breaks is often accompanied by the formation of tandem sequence duplications in plant genomes. Proc Natl Acad Sci U S A 2016; 113:7266-71. [PMID: 27307441 DOI: 10.1073/pnas.1603823113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Duplication of existing sequences is a major mechanism of genome evolution. It has been previously shown that duplications can occur by replication slippage, unequal sister chromatid exchange, homologous recombination, and aberrant double-strand break-induced synthesis-dependent strand annealing reactions. In a recent study, the abundant presence of short direct repeats was documented by comparative bioinformatics analysis of different rice genomes, and the hypothesis was put forward that such duplications might arise due to the concerted repair of adjacent single-strand breaks (SSBs). Applying the CRISPR/Cas9 technology, we were able to test this hypothesis experimentally in the model plant Arabidopsis thaliana Using a Cas9 nickase to induce adjacent genomic SSBs in different regions of the genome (genic, intergenic, and heterochromatic) and at different distances (∼20, 50, and 100 bps), we analyzed the repair outcomes by deep sequencing. In addition to deletions, we regularly detected the formation of direct repeats close to the break sites, independent of the genomic context. The formation of these duplications as well as deletions may be associated with the presence of microhomologies. Most interestingly, we found that even the induction of two SSBs on the same DNA strand can cause genome alterations, albeit at a much lower level. Because such a scenario reflects a natural step during nucleotide excision repair, and given that the germline is set aside only late during development in plants, the repair of adjacent SSBs indeed seems to have an important influence on the shaping of plant genomes during evolution.
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Puchta H. Breaking DNA in plants: how I almost missed my personal breakthrough. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:437-440. [PMID: 26096544 DOI: 10.1111/pbi.12420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
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23
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Vu GTH, Schmutzer T, Bull F, Cao HX, Fuchs J, Tran TD, Jovtchev G, Pistrick K, Stein N, Pecinka A, Neumann P, Novak P, Macas J, Dear PH, Blattner FR, Scholz U, Schubert I. Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus. THE PLANT GENOME 2015; 8:eplantgenome2015.04.0021. [PMID: 33228273 DOI: 10.3835/plantgenome2015.04.0021] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/19/2015] [Indexed: 06/11/2023]
Abstract
The C-value paradox remains incompletely resolved after >40 yr and is exemplified by 2,350-fold variation in genome sizes of flowering plants. The carnivorous Lentibulariaceae genus Genlisea, displaying a 25-fold range of genome sizes, is a promising subject to study mechanisms and consequences of evolutionary genome size variation. Applying genomic, phylogenetic, and cytogenetic approaches, we uncovered bidirectional genome size evolution within the genus Genlisea. The Genlisea nigrocaulis Steyerm. genome (86 Mbp) has probably shrunk by retroelement silencing and deletion-biased double-strand break (DSB) repair, from an ancestral size of 400 to 800 Mbp to become one of the smallest among flowering plants. The G. hispidula Stapf genome has expanded by whole-genome duplication (WGD) and retrotransposition to 1550 Mbp. Genlisea hispidula became allotetraploid after the split from the G. nigrocaulis clade ∼29 Ma. Genlisea pygmaea A. St.-Hil. (179 Mbp), a close relative of G. nigrocaulis, proved to be a recent (auto)tetraploid. Our analyses suggest a common ancestor of the genus Genlisea with an intermediate 1C value (400-800 Mbp) and subsequent rapid genome size evolution in opposite directions. Many abundant repeats of the larger genome are absent in the smaller, casting doubt on their functionality for the organism, while recurrent WGD seems to safeguard against the loss of essential elements in the face of genome shrinkage. We cannot identify any consistent differences in habitat or life strategy that correlate with genome size changes, raising the possibility that these changes may be selectively neutral.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Fabian Bull
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Trung D Tran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Gabriele Jovtchev
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Institute for Biodiversity and Ecosystem Research, 2 Yurii Gagarin Street, Sofia, 1113, Bulgaria
| | - Klaus Pistrick
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Pavel Neumann
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Petr Novak
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Jiri Macas
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Paul H Dear
- MRC Lab. of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Faculty of Science and Central European Institute of Technology, Masaryk Univ., 61137, Brno, Czech Republic
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Manova V, Gruszka D. DNA damage and repair in plants - from models to crops. FRONTIERS IN PLANT SCIENCE 2015; 6:885. [PMID: 26557130 PMCID: PMC4617055 DOI: 10.3389/fpls.2015.00885] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 10/05/2015] [Indexed: 05/17/2023]
Abstract
The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction. It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity. DNA repair processes have been characterized in bacterial, fungal, and mammalian model systems. The description of these processes in plants, in contrast, was initiated relatively recently and has been focused largely on the model plant Arabidopsis thaliana. Consequently, our knowledge about DNA repair in plant genomes - particularly in the genomes of crop plants - is by far more limited. However, the relatively small size of the Arabidopsis genome, its rapid life cycle and availability of various transformation methods make this species an attractive model for the study of eukaryotic DNA repair mechanisms and mutagenesis. Moreover, abnormalities in DNA repair which proved to be lethal for animal models are tolerated in plant genomes, although sensitivity to DNA damaging agents is retained. Due to the high conservation of DNA repair processes and factors mediating them among eukaryotes, genes and proteins that have been identified in model species may serve to identify homologous sequences in other species, including crop plants, in which these mechanisms are poorly understood. Crop breeding programs have provided remarkable advances in food quality and yield over the last century. Although the human population is predicted to "peak" by 2050, further advances in yield will be required to feed this population. Breeding requires genetic diversity. The biological impact of any mutagenic agent used for the creation of genetic diversity depends on the chemical nature of the induced lesions and on the efficiency and accuracy of their repair. More recent targeted mutagenesis procedures also depend on host repair processes, with different pathways yielding different products. Enhanced understanding of DNA repair processes in plants will inform and accelerate the engineering of crop genomes via both traditional and targeted approaches.
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Affiliation(s)
- Vasilissa Manova
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of SciencesSofia
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, University of SilesiaKatowice, Poland
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25
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Nandy S, Zhao S, Pathak BP, Manoharan M, Srivastava V. Gene stacking in plant cell using recombinases for gene integration and nucleases for marker gene deletion. BMC Biotechnol 2015; 15:93. [PMID: 26452472 PMCID: PMC4600305 DOI: 10.1186/s12896-015-0212-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/01/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Practical approaches for multigene transformation and gene stacking are extremely important for engineering complex traits and adding new traits in transgenic crops. Trait deployment by gene stacking would greatly simplify downstream plant breeding and trait introgression into cultivars. Gene stacking into pre-determined genomic sites depends on mechanisms of targeted DNA integration and recycling of selectable marker genes. Targeted integrations into chromosomal breaks, created by nucleases, require large transformation efforts. Recombinases such as Cre-lox, on the other hand, efficiently drive site-specific integrations in plants. However, the reversibility of Cre-lox recombination, due to the incorporation of two cis-positioned lox sites, presents a major bottleneck in its application in gene stacking. Here, we describe a strategy of resolving this bottleneck through excision of one of the cis-positioned lox, embedded in the marker gene, by nuclease activity. METHODS All transgenic lines were developed by particle bombardment of rice callus with plasmid constructs. Standard molecular approach was used for building the constructs. Transgene loci were analyzed by PCR, Southern hybridization, and DNA sequencing. RESULTS We developed a highly efficient gene stacking method by utilizing powerful recombinases such as Cre-lox and FLP-FRT, for site-specific gene integrations, and nucleases for marker gene excisions. We generated Cre-mediated site-specific integration locus in rice and showed excision of marker gene by I-SceI at ~20 % efficiency, seamlessly connecting genes in the locus. Next, we showed ZFN could be used for marker excision, and the locus can be targeted again by recombinases. Hence, we extended the power of recombinases to gene stacking application in plants. Finally, we show that heat-inducible I-SceI is also suitable for marker excision, and therefore could serve as an important tool in streamlining this gene stacking platform. CONCLUSIONS A practical approach for gene stacking in plant cell was developed that allows targeted gene insertions through rounds of transformation, a method needed for introducing new traits into transgenic lines for their rapid deployment in the field. By using Cre-lox, a powerful site-specific recombination system, this method greatly improves gene stacking efficiency, and through the application of nucleases develops marker-free, seamless stack of genes at pre-determined chromosomal sites.
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Affiliation(s)
- Soumen Nandy
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Shan Zhao
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Bhuvan P Pathak
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Muthusamy Manoharan
- Department of Agriculture, 144 Woodard Hall, University of Arkansas at Pine Bluff, Pine Bluff, AR, 71601, USA.
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
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Henry TA, Bainard JD, Newmaster SG. Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing. Genome 2015; 57:555-66. [PMID: 25727714 DOI: 10.1139/gen-2014-0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.
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Affiliation(s)
- Thomas A Henry
- Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Knoll A, Fauser F, Puchta H. DNA recombination in somatic plant cells: mechanisms and evolutionary consequences. Chromosome Res 2015; 22:191-201. [PMID: 24788060 DOI: 10.1007/s10577-014-9415-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In somatic cells, recombination is a means of DNA damage repair. The most severe type of damage in nuclear DNA is double-strand breaks (DSBs) which may be repaired via either non-homologous end joining (NHEJ) or homologous recombination (HR). In this review, we will summarize the basic features, the mechanisms, and the key players of both repair modes in plants with a focus on the model plant Arabidopsis thaliana. NHEJ may result in insertion of sequences from elsewhere in the genome but is much more often associated with deletions. If more than one DSB is processed simultaneously via NHEJ, besides deletions, inversions or translocations may also arise. As the germ line is only set aside late in plant development, somatic changes may be transferred to the next generation. Thus, NHEJ might influence the evolution of plant genomes and indeed seems to be an important factor of genome shrinking. Deletions may also be due to DSB-induced recombination between tandem duplicated homologous sequences by single-strand annealing (SSA). Moreover, conservative HR using the synthesis-dependent strand annealing (SDSA) mechanism operates in somatic plant cells. The efficiency of SDSA is dependent on the genomic template used as matrix for the repair of the DSB. Besides DSBs, stalled replication forks may also be processed via HR. Several DNA processing enzymes are involved in the regulation of replication initiated HR, mostly in its suppression, and we summarize the current knowledge of these processes in plants.
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Affiliation(s)
- Alexander Knoll
- Karlsruhe Institute of Technology, Botanical Institute II, Hertzstr. 16, 76187, Karlsruhe, Germany
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DNA damage and repair in plants under ultraviolet and ionizing radiations. ScientificWorldJournal 2015; 2015:250158. [PMID: 25729769 PMCID: PMC4333283 DOI: 10.1155/2015/250158] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/27/2014] [Accepted: 11/04/2014] [Indexed: 11/17/2022] Open
Abstract
Being sessile, plants are continuously exposed to DNA-damaging agents present in the environment such as ultraviolet (UV) and ionizing radiations (IR). Sunlight acts as an energy source for photosynthetic plants; hence, avoidance of UV radiations (namely, UV-A, 315–400 nm; UV-B, 280–315 nm; and UV-C, <280 nm) is unpreventable. DNA in particular strongly absorbs UV-B; therefore, it is the most important target for UV-B induced damage. On the other hand, IR causes water radiolysis, which generates highly reactive hydroxyl radicals (OH•) and causes radiogenic damage to important cellular components. However, to maintain genomic integrity under UV/IR exposure, plants make use of several DNA repair mechanisms. In the light of recent breakthrough, the current minireview (a) introduces UV/IR and overviews UV/IR-mediated DNA damage products and (b) critically discusses the biochemistry and genetics of major pathways responsible for the repair of UV/IR-accrued DNA damage. The outcome of the discussion may be helpful in devising future research in the current context.
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Schiml S, Fauser F, Puchta H. The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:1139-50. [PMID: 25327456 DOI: 10.1111/tpj.12704] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 05/03/2023]
Abstract
The CRISPR/Cas nuclease is becoming a major tool for targeted mutagenesis in eukaryotes by inducing double-strand breaks (DSBs) at pre-selected genomic sites that are repaired by non-homologous end joining (NHEJ) in an error-prone way. In plants, it could be demonstrated that the Cas9 nuclease is able to induce heritable mutations in Arabidopsis thaliana and rice. Gene targeting (GT) by homologous recombination (HR) can also be induced by DSBs. Using a natural nuclease and marker genes, we previously developed an in planta GT strategy in which both a targeting vector and targeting locus are activated simultaneously via DSB induction during plant development. Here, we demonstrate that this strategy can be used for natural genes by CRISPR/Cas-mediated DSB induction. We were able to integrate a resistance cassette into the ADH1 locus of A. thaliana via HR. Heritable events were identified using a PCR-based genotyping approach, characterised by Southern blotting and confirmed on the sequence level. A major concern is the specificity of the CRISPR/Cas nucleases. Off-target effects might be avoided using two adjacent sgRNA target sequences to guide the Cas9 nickase to each of the two DNA strands, resulting in the formation of a DSB. By amplicon deep sequencing, we demonstrate that this Cas9 paired nickase strategy has a mutagenic potential comparable with that of the nuclease, while the resulting mutations are mostly deletions. We also demonstrate the stable inheritance of such mutations in A. thaliana.
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Affiliation(s)
- Simon Schiml
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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30
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Murat F, Zhang R, Guizard S, Flores R, Armero A, Pont C, Steinbach D, Quesneville H, Cooke R, Salse J. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome Biol Evol 2014; 6:12-33. [PMID: 24317974 PMCID: PMC3914691 DOI: 10.1093/gbe/evt200] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named "PlantSyntenyViewer," available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data.
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Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC (Génétique, Diversité et Ecophysiologie des Céréales), Clermont Ferrand, France
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31
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Puchta H, Fauser F. Synthetic nucleases for genome engineering in plants: prospects for a bright future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:727-41. [PMID: 24112784 DOI: 10.1111/tpj.12338] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/13/2013] [Accepted: 09/19/2013] [Indexed: 05/20/2023]
Abstract
By inducing double-strand breaks (DSB), it is possible to initiate DNA recombination. For a long time, it was not possible to use DSB induction for efficient genome engineering due to the lack of a means to target DSBs to specific sites. This limitation was overcome by development of modified meganucleases and synthetic DNA-binding domains. Domains derived from zinc-finger transcription factors or transcription activator-like effectors may be designed to recognize almost any DNA sequence. By fusing these domains to the endonuclease domains of a class II restriction enzyme, an active endonuclease dimer may be formed that introduces a site-specific DSB. Recent studies demonstrate that gene knockouts via non-homologous end joining or gene modification via homologous recombination are becoming routine in many plant species. By creating a single genomic DSB, complete knockout of a gene, sequence-specific integration of foreign DNA or subtle modification of individual amino acids in a specific protein domain may be achieved. The induction of two or more DSBs allows complex genomic rearrangements such as deletions, inversions or the exchange of chromosome arms. The potential for controlled genome engineering in plants is tremendous. The recently discovered RNA-based CRISPR/Cas system, a new tool to induce multiple DSBs, and sophisticated technical applications, such as the in planta gene targeting system, are further steps in this development. At present, the focus remains on engineering of single genes; in the future, engineering of whole genomes will become an option.
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Affiliation(s)
- Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, PO Box 6980, Karlsruhe, 76049, Germany
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Vu GTH, Cao HX, Watanabe K, Hensel G, Blattner FR, Kumlehn J, Schubert I. Repair of Site-Specific DNA Double-Strand Breaks in Barley Occurs via Diverse Pathways Primarily Involving the Sister Chromatid. THE PLANT CELL 2014; 26:2156-2167. [PMID: 24876253 PMCID: PMC4079375 DOI: 10.1105/tpc.114.126607] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 04/24/2014] [Accepted: 05/07/2014] [Indexed: 05/18/2023]
Abstract
DNA double-strand break (DSB) repair mechanisms differ in their requirements for a homologous repair template and in the accuracy of the result. We aimed to quantify the outcome of repair of a single targeted DSB in somatic cells of young barley (Hordeum vulgare) plants. Amplicon sequencing of three reporter constructs revealed 47 to 58% of reads as repaired via nonhomologous end-joining (NHEJ) with deletions and/or small (1 to 3 bp) insertions. Alternative NHEJ revealed 2 to 5 bp microhomology (15.7% of cases) or new replication-mediated short duplications at sealed breaks. Although deletions outweigh insertions in barley, this bias was less pronounced and deleted sequences were shorter than in Arabidopsis thaliana. Between 17 and 33% of reads likely represent restoration of the original sequence. Depending on the construct, 20 to 33% of reads arose via gene conversion (homologous recombination). Remarkably, <1 to >8% of reads apparently display synthesis-dependent strand annealing linked with NHEJ, inserting 4 to 61 bp, mostly originating from the surrounding of breakpoints. Positional coincidence of >81% of sister chromatid exchanges with target loci is unprecedented for higher eukaryotes and indicates that most repair events for staggered DSBs, at least in barley, involve the sister chromatid and occur during S or G2 phase of the cell cycle.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Koichi Watanabe
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany Faculty of Science and Central European Institute of Technology, Masaryk University, CZ-61137 Brno, Czech Republic
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33
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Bennetzen JL, Wang H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:505-30. [PMID: 24579996 DOI: 10.1146/annurev-arplant-050213-035811] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Transposable elements (TEs) are the key players in generating genomic novelty by a combination of the chromosome rearrangements they cause and the genes that come under their regulatory sway. Genome size, gene content, gene order, centromere function, and numerous other aspects of nuclear biology are driven by TE activity. Although the origins and attitudes of TEs have the hallmarks of selfish DNA, there are numerous cases where TE components have been co-opted by the host to create new genes or modify gene regulation. In particular, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes. Most, perhaps all, of this epigenetic regulation is derived from TE insertions near genes or TE-encoded factors that act in trans. Enormous pools of genome data and new technologies for reverse genetics will lead to a powerful new era of TE analysis in plants.
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Affiliation(s)
- Jeffrey L Bennetzen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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34
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Meganuclease-mediated virus self-cleavage facilitates tumor-specific virus replication. Mol Ther 2013; 21:1738-48. [PMID: 23752311 DOI: 10.1038/mt.2013.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 04/30/2013] [Indexed: 12/29/2022] Open
Abstract
Meganucleases can specifically cleave long DNA sequence motifs, a feature that makes them an ideal tool for gene engineering in living cells. In a proof-of-concept study, we investigated the use of the meganuclease I-Sce I for targeted virus self-disruption to generate high-specific oncolytic viruses. For this purpose, we provided oncolytic adenoviruses with a molecular circuit that selectively responds to p53 activation by expression of I-Sce I subsequently leading to self-disruption of the viral DNA via heterologous I-Sce I recognition sites within the virus genome. We observed that virus replication and cell lysis was effectively impaired in p53-normal cells, but not in p53-dysfunctional tumor cells. I-Sce I activity led to effective intracellular processing of viral DNA as confirmed by detection of specific cleavage products. Virus disruption did not interfere with E1A levels indicating that reduction of functional virus genomes was the predominant cause for conditional replication. Consequently, tumor-specific replication was further enhanced when E1A expression was additionally inhibited by targeted transcriptional repression. Finally, we demonstrated p53-dependent oncolysis by I-Sce I-expressing viruses in vitro and in vivo, and demonstrated effective inhibition of tumor growth. In summary, meganuclease-mediated virus cleavage represents a promising approach to provide oncolytic viruses with attractive safety profiles.
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Abstract
It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.
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36
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Lusser M, Davies HV. Comparative regulatory approaches for groups of new plant breeding techniques. N Biotechnol 2013; 30:437-46. [PMID: 23474021 DOI: 10.1016/j.nbt.2013.02.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/31/2013] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
This manuscript provides insights into ongoing debates on the regulatory issues surrounding groups of biotechnology-driven 'New Plant Breeding Techniques' (NPBTs). It presents the outcomes of preliminary discussions and in some cases the initial decisions taken by regulators in the following countries: Argentina, Australia, Canada, EU, Japan, South Africa and USA. In the light of these discussions we suggest in this manuscript a structured approach to make the evaluation more consistent and efficient. The issue appears to be complex as these groups of new technologies vary widely in both the technologies deployed and their impact on heritable changes in the plant genome. An added complication is that the legislation, definitions and regulatory approaches for biotechnology-derived crops differ significantly between these countries. There are therefore concerns that this situation will lead to non-harmonised regulatory approaches and asynchronous development and marketing of such crops resulting in trade disruptions.
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Affiliation(s)
- Maria Lusser
- European Commission, Institute of Prospective Technological Studies (IPTS), Joint Research Center (JRC), Ed. Expo, c/Inca Garcilaso 3, E-41092 Sevilla, Spain.
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37
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Patterns of nucleotide asymmetries in plant and animal genomes. Biosystems 2013; 111:181-9. [PMID: 23438636 DOI: 10.1016/j.biosystems.2013.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/29/2012] [Accepted: 02/07/2013] [Indexed: 11/20/2022]
Abstract
Symmetry in biology provides many intriguing puzzles to the scientist's mind. Chargaff's second parity rule states a symmetric distribution of oligonucleotides within a single strand of double-stranded DNA. While this rule has been verified in a wide range of microbial genomes, it still awaits explanation. In our study, we inquired into patterns of mono- and trinucleotide intra-strand parity in complex plant genomic sequences that became available during the last few years, and compared these to equally complex animal genomes. The degree and patterns of deviation from Chargaff's second rule were different between plant and animal species. We observed a universal inter-chromosomal homogeneity of mononucleotide skews in coding sequences of plant chromosomes, while the base composition of animal coding sequences differed between chromosomes even within a single species. We also found differences in the base composition of dicot introns in comparison to those of monocots. These genome-wide patterns were limited to genic regions and were not encountered in inter-genic sequences. We discuss the implications of our findings in relation to hypotheses about functional correlations of intra-strand parity which have hitherto been put forward. Furthermore, we propose more recent polyploidization and subsequent homogenization of homoeologues as a possible reason for more homogeneous skew patterns in plants.
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38
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Zhang M, Zhu R, Zhang M, Gao B, Sun D, Wang S. High-energy pulse-electron-beam-induced molecular and cellular damage in Saccharomyces cerevisiae. Res Microbiol 2013; 164:100-9. [DOI: 10.1016/j.resmic.2012.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/25/2012] [Indexed: 10/27/2022]
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Weber N, Halpin C, Hannah LC, Jez JM, Kough J, Parrott W. Editor's choice: Crop genome plasticity and its relevance to food and feed safety of genetically engineered breeding stacks. PLANT PHYSIOLOGY 2012; 160:1842-53. [PMID: 23060369 PMCID: PMC3510115 DOI: 10.1104/pp.112.204271] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/02/2012] [Indexed: 05/22/2023]
Affiliation(s)
- Natalie Weber
- Pioneer Hi-Bred International, Wilmington, Delaware 19880, USA
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40
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Wang D, Lloyd AH, Timmis JN. Nuclear genome diversity in somatic cells is accelerated by environmental stress. PLANT SIGNALING & BEHAVIOR 2012; 7:595-7. [PMID: 22516813 PMCID: PMC3419027 DOI: 10.4161/psb.19871] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA transfer to the nucleus from prokaryotic ancestors of the cytoplasmic organelles (mitochondria and plastids) has occurred during endosymbiotic evolution in eukaryotes. In most eukaryotes, organelle DNA transfer to nucleus is a continuing process. The frequency of DNA transposition from plastid (chloroplast) to nucleus has been measured in tobacco plants (Nicotiana tabacum) experimentally. We have monitored the effects of environmental stress on the rate of DNA transfer from plastid to nucleus by exploiting nucleus-specific reporter genes in two transplastomic tobacco lines. DNA migration from plastids to the nucleus is markedly increased by mild heat stress. In addition, insertions of mitochondrial DNA into induced double-strand breaks are observed after heat treatment. These results show that movement of organelle DNA to the nucleus is remarkably increased by heat stress.
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Affiliation(s)
- Dong Wang
- Discipline of Genetics; School of Molecular and Biomedical Science; The University of Adelaide; South Australia, Australia
| | | | - Jeremy N. Timmis
- Discipline of Genetics; School of Molecular and Biomedical Science; The University of Adelaide; South Australia, Australia
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Lloyd AH, Wang D, Timmis JN. Single molecule PCR reveals similar patterns of non-homologous DSB repair in tobacco and Arabidopsis. PLoS One 2012; 7:e32255. [PMID: 22389691 PMCID: PMC3289645 DOI: 10.1371/journal.pone.0032255] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 01/25/2012] [Indexed: 12/28/2022] Open
Abstract
DNA double strand breaks (DSBs) occur constantly in eukaryotes. These potentially lethal DNA lesions are repaired efficiently by two major DSB repair pathways: homologous recombination and non-homologous end joining (NHEJ). We investigated NHEJ in Arabidopsis thaliana and tobacco (Nicotiana tabacum) by introducing DNA double-strand breaks through inducible expression of I-SceI, followed by amplification of individual repair junction sequences by single-molecule PCR. Using this process over 300 NHEJ repair junctions were analysed in each species. In contrast to previously published variation in DSB repair between Arabidopsis and tobacco, the two species displayed similar DSB repair profiles in our experiments. The majority of repair events resulted in no loss of sequence and small (1-20 bp) deletions occurred at a minority (25-45%) of repair junctions. Approximately ~1.5% of the observed repair events contained larger deletions (>20 bp) and a similar percentage contained insertions. Strikingly, insertion events in tobacco were associated with large genomic deletions at the site of the DSB that resulted in increased micro-homology at the sequence junctions suggesting the involvement of a non-classical NHEJ repair pathway. The generation of DSBs through inducible expression of I-SceI, in combination with single molecule PCR, provides an effective and efficient method for analysis of individual repair junctions and will prove a useful tool in the analysis of NHEJ.
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Affiliation(s)
- Andrew H Lloyd
- School of Molecular and Biomedical Science, The University of Adelaide, South Australia, Australia.
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42
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Environmental stress increases the entry of cytoplasmic organellar DNA into the nucleus in plants. Proc Natl Acad Sci U S A 2012; 109:2444-8. [PMID: 22308419 DOI: 10.1073/pnas.1117890109] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondria and chloroplasts (photosynthetic members of the plastid family of cytoplasmic organelles) in eukaryotic cells originated more than a billion years ago when an ancestor of the nucleated cell engulfed two different prokaryotes in separate sequential events. Extant cytoplasmic organellar genomes contain very few genes compared with their candidate free-living ancestors, as most have functionally relocated to the nucleus. The first step in functional relocation involves the integration of inactive DNA fragments into nuclear chromosomes, and this process continues at high frequency with attendant genetic, genomic, and evolutionary consequences. Using two different transplastomic tobacco lines, we show that DNA migration from chloroplasts to the nucleus is markedly increased by mild heat stress. In addition, we show that insertion of mitochondrial DNA fragments during the repair of induced double-strand breaks is increased by heat stress. The experiments demonstrate that the nuclear influx of organellar DNA is a potentially a source of mutation for nuclear genomes that is highly susceptible to temperature fluctuations that are well within the range experienced naturally.
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Bliss BJ, Suzuki JY. Genome size in Anthurium evaluated in the context of karyotypes and phenotypes. AOB PLANTS 2012; 2012:pls006. [PMID: 22509462 PMCID: PMC3326669 DOI: 10.1093/aobpla/pls006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 02/17/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Anthurium is an important horticultural crop from the family Araceae, order Alismatales, a lineage considered to have diverged from other monocots prior to the cereals. Genome size and its distribution in Anthurium were investigated to gain a basic understanding of genome organization in this large genus and to forge a firm foundation for advancement of molecular approaches for the study of Anthurium. Currently, genome size estimates have been reported for only two Anthurium samples. METHODOLOGY Bulk nuclear DNA content estimates were obtained by flow cell cytometry using leaf tissue collected from Anthurium species of different subgeneric groups and from commercial cultivars. The most current and well-supported topology of subgeneric, sectional relationships was applied to present genome size estimates in the context of reported chromosome counts, karyotypes, putative phylogenetic relationships, observed phenotypes and pedigree. PRINCIPAL RESULTS Genome size estimates based on bulk nuclear DNA content for 77 accessions representing 34 species and 9 cultivars were obtained, including initial estimates for 33 Anthurium species, and both the smallest (Anthurium obtusum; Tetraspermium) and largest (Anthurium roseospadix; Calomystrium) Anthurium genome sizes reported to date. Genome size did not distinguish any subgeneric section, but ranged 5-fold (4.42-20.83 pg/2 C) despite consistent 2N= 30 chromosome counts. Intraspecies genome size variation >20 % is reported for Anthurium ravenii, A. watermaliense and A. gracile. CONCLUSIONS Genome size estimates for Anthurium species spanning 13 recognized subgeneric sections indicate that genome size does not generally correlate with chromosome count or phylogenetic relationships. Mechanisms of genome expansion and contraction, including amplification and reduction of repetitive elements, polyploidy, chromosome reorganization/loss, may be involved in genome evolution in Anthurium as in other species. The new information on Anthurium genome sizes provides a platform for molecular studies supporting further research on genome evolution as well as cultivar development.
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Gaut B, Yang L, Takuno S, Eguiarte LE. The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2011. [DOI: 10.1146/annurev-ecolsys-102710-145119] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brandon Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697; , ,
| | - Liang Yang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697; , ,
| | - Shohei Takuno
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697; , ,
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, CP 04510 Mexico City, Mexico;
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Talianova M, Janousek B. What can we learn from tobacco and other Solanaceae about horizontal DNA transfer? AMERICAN JOURNAL OF BOTANY 2011; 98:1231-42. [PMID: 21795732 DOI: 10.3732/ajb.1000370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In eukaryotic organisms, horizontal gene transfer (HGT) is regarded as an important though infrequent source of reticulate evolution. Many confirmed instances of natural HGT involving multicellular eukaryotes come from flowering plants. This review intends to provide a synthesis of present knowledge regarding HGT in higher plants, with an emphasis on tobacco and other species in the Solanaceae family because there are numerous detailed reports concerning natural HGT events, involving various donors, in this family. Moreover, in-depth experimental studies using transgenic tobacco are of great importance for understanding this process. Valuable insights are offered concerning the mechanisms of HGT, the adaptive role and regulation of natural transgenes, and new routes for gene trafficking. With an increasing amount of data on HGT, a synthetic view is beginning to emerge.
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Affiliation(s)
- Martina Talianova
- Department of Plant Developmental Genetics, Institute of Biophysics AS CR, Kralovopolska 135, 612 65, Brno, Czech Republic.
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Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage. Funct Integr Genomics 2011; 11:599-609. [PMID: 21761280 DOI: 10.1007/s10142-011-0237-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 10/18/2022]
Abstract
The assembly of a 1.3-Mb size region of the wheat genome has provided the opportunity to study a recent nuclear mitochondrial DNA insertion (NUMT). In the present study, we have studied two bacterial artificial chromosomes (BACs) and characterized a 52-kb NUMT segment from the tetraploid and hexaploid wheat BAC libraries. The conserved orthologous NUMT regions from tetraploid and hexaploid wheat Langdon and Chinese Spring shared identical gene haplotypes even though mutations (insertions, deletions, and substitutions) had occurred. The 52-kb NUMT was present in hexaploid variety Chinese Spring, but absent in variety Hope, by sequence comparison of their corresponding region. Amplifying the NUMT junctions using a set of the wheat materials including diploid, tetraploid, and hexaploid lines showed that none of the diploid wheat carried the region and only some tetraploid and hexaploid wheat were positive for the NUMT. Age estimation of the NUMT displayed the mean ages of Langdon NUMT and Chinese Spring NUMT to be 378,000 and 416,000 years ago, respectively. Reverse transcription PCR and sequencing of the nad7 gene showed 28 C → U RNA editing sites and four partial editing sites, as expected for mitochondrial DNA expression. Specific SNPs discriminated between cDNA from the nucleus and the mitochondria and suggested that the nuclear copy was not expressed. The mitochondrial DNA studied was inserted into the genome quite recently within the wheat lineage and gave rise to the non-coding nuclear nad7 gene. The NUMT segment could be lost and acquired frequently during the wheat evolution.
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Schubert I, Lysak MA. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet 2011; 27:207-16. [PMID: 21592609 DOI: 10.1016/j.tig.2011.03.004] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 01/16/2023]
Abstract
Comparative genetics, genomics and cytogenetics provide tools to trace the evolutionary history of extant genomes. Yet, the interpretation of rapidly increasing genomic data is not always done in agreement with constraints determined by chromosome structural features and by insights obtained from chromosome mutagenesis. The terms 'non-reciprocal chromosome translocation', 'chromosome fusion' and 'centromere shift' used to explain genomic differences among organisms are misleading and often do not correctly reflect the mechanisms of chromosome rearrangements underlying the evolutionary karyotypic variation. Here, we (re)interpret evolutionary genome alterations in a parsimonious way and demonstrate that results of comparative genomics and comparative chromosome painting can be explained on the basis of known primary and secondary chromosome rearrangements. Therefore, some widespread terms used in comparative and evolutionary genomics should be either avoided (e.g. non-reciprocal translocation) or redefined (e.g. chromosome fusion and centromere shift).
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Affiliation(s)
- Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany.
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48
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Knoll A, Puchta H. The role of DNA helicases and their interaction partners in genome stability and meiotic recombination in plants. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1565-79. [PMID: 21081662 DOI: 10.1093/jxb/erq357] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA helicases are enzymes that are able to unwind DNA by the use of the energy-equivalent ATP. They play essential roles in DNA replication, DNA repair, and DNA recombination in all organisms. As homologous recombination occurs in somatic and meiotic cells, the same proteins may participate in both processes, albeit not necessarily with identical functions. DNA helicases involved in genome stability and meiotic recombination are the focus of this review. The role of these enzymes and their characterized interaction partners in plants will be summarized. Although most factors are conserved in eukaryotes, plant-specific features are becoming apparent. In the RecQ helicase family, Arabidopsis thaliana RECQ4A has been shown before to be the functional homologue of the well-researched baker's yeast Sgs1 and human BLM proteins. It was surprising to find that its interaction partners AtRMI1 and AtTOP3α are absolutely essential for meiotic recombination in plants, where they are central factors of a formerly underappreciated dissolution step of recombination intermediates. In the expanding group of anti-recombinases, future analysis of plant helicases is especially promising. While no FBH1 homologue is present, the Arabidopsis genome contains homologues of both SRS2 and RTEL1. Yeast and mammals, on the other hand. only possess homologues of either one or the other of these helicases. Plants also contain several other classes of helicases that are known from other organisms to be involved in the preservation of genome stability: FANCM is conserved with parts of the human Fanconi anaemia proteins, as are homologues of the Swi2/Snf2 family and of PIF1.
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Affiliation(s)
- Alexander Knoll
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Enke N, Fuchs J, Gemeinholzer B. Shrinking genomes? Evidence from genome size variation in Crepis (Compositae). PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:185-193. [PMID: 21143740 DOI: 10.1111/j.1438-8677.2010.00341.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Large-scale surveys of genome size evolution in angiosperms show that the ancestral genome was most likely small, with a tendency towards an increase in DNA content during evolution. Due to polyploidisation and self-replicating DNA elements, angiosperm genomes were considered to have a 'one-way ticket to obesity' (Bennetzen & Kellogg 1997). New findings on how organisms can lose DNA challenged the hypotheses of unidirectional evolution of genome size. The present study is based on the classical work of Babcock (1947a) on karyotype evolution within Crepis and analyses karyotypic diversification within the genus in a phylogenetic context. Genome size of 21 Crepis species was estimated using flow cytometry. Additional data of 17 further species were taken from the literature. Within 30 diploid Crepis species there is a striking trend towards genome contraction. The direction of genome size evolution was analysed by reconstructing ancestral character states on a molecular phylogeny based on ITS sequence data. DNA content is correlated to distributional aspects as well as life form. Genome size is significantly higher in perennials than in annuals. Within sampled species, very small genomes are only present in Mediterranean or European species, whereas their Central and East Asian relatives have larger 1C values.
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Affiliation(s)
- N Enke
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany.
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Genetically modified myths and realities. N Biotechnol 2010; 27:545-51. [DOI: 10.1016/j.nbt.2010.05.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 05/23/2010] [Indexed: 11/17/2022]
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