1
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Hunter CT, McCarty DR, Koch KE. Independent evolution of transposase and TIRs facilitated by recombination between Mutator transposons from divergent clades in maize. Proc Natl Acad Sci U S A 2023; 120:e2305298120. [PMID: 37490540 PMCID: PMC10401008 DOI: 10.1073/pnas.2305298120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 07/27/2023] Open
Abstract
Nearly all eukaryotes carry DNA transposons of the Robertson's Mutator (Mu) superfamily, a widespread source of genome instability and genetic variation. Despite their pervasive impact on host genomes, much remains unknown about the evolution of these transposons. Transposase recognition of terminal inverted repeats (TIRs) is thought to drive and constrain coevolution of MuDR transposase genes and TIRs. To address the extent of this relationship and its impact, we compared separate phylogenies of TIRs and MuDR gene sequences from Mu elements in the maize genome. Five major clades were identified. As expected, most Mu elements were bound by highly similar TIRs from the same clade (homomorphic type). However, a subset of elements contained dissimilar TIRs derived from divergent clades. These "heteromorphs" typically occurred in multiple copies indicating active transposition in the genome. In addition, analysis of internal sequences showed that exchanges between elements having divergent TIRs produced new mudra and mudrb gene combinations. In several instances, TIR homomorphs had been regenerated within a heteromorph clade with retention of distinctive internal MuDR sequence combinations. Results reveal that recombination between divergent clades facilitates independent evolution of transposase (mudra), transposase-binding targets (TIRs), and capacity for insertion (mudrb) of active Mu elements. This mechanism would be enhanced by the preference of Mu insertions for recombination-rich regions near the 5' ends of genes. We suggest that cycles of recombination give rise to alternating homo- and heteromorph forms that enhance the diversity on which selection for Mu fitness can operate.
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Affiliation(s)
- Charles T. Hunter
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, United States Department of Agriculture - Agricultural Research Service, Gainesville, FL32608
| | - Donald R. McCarty
- Horticultural Sciences Department, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL32611
| | - Karen E. Koch
- Horticultural Sciences Department, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL32611
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2
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Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:172-192. [PMID: 35959634 PMCID: PMC9804982 DOI: 10.1111/tpj.15938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a basal eudicot plant with a unique lifestyle, physiological features, and evolutionary characteristics. Here we report the unique profile of transposable elements (TEs) in the genome, using a manually curated repeat library. TEs account for 59% of the genome, and hAT (Ac/Ds) elements alone represent 8%, more than in any other known plant genome. About 18% of the lotus genome is comprised of Copia LTR retrotransposons, and over 25% of them are associated with non-canonical termini (non-TGCA). Such high abundance of non-canonical LTR retrotransposons has not been reported for any other organism. TEs are very abundant in genic regions, with retrotransposons enriched in introns and DNA transposons primarily in flanking regions of genes. The recent insertion of TEs in introns has led to significant intron size expansion, with a total of 200 Mb in the 28 455 genes. This is accompanied by declining TE activity in intergenic regions, suggesting distinct control efficacy of TE amplification in different genomic compartments. Despite the prevalence of TEs in genic regions, some genes are associated with fewer TEs, such as those involved in fruit ripening and stress responses. Other genes are enriched with TEs, and genes in epigenetic pathways are the most associated with TEs in introns, indicating a dynamic interaction between TEs and the host surveillance machinery. The dramatic differential abundance of TEs with genes involved in different biological processes as well as the variation of target preference of different TEs suggests the composition and activity of TEs influence the path of evolution.
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Affiliation(s)
- Stefan Cerbin
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Ecology & Evolutionary BiologyUniversity of Kansas1200 Sunnyside AvenueLawrenceKS66045USA
| | - Shujun Ou
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yang Li
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Yanni Sun
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Ning Jiang
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
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3
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Gisby JS, Catoni M. The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution. PLoS Genet 2022; 18:e1010078. [PMID: 35202390 PMCID: PMC8903248 DOI: 10.1371/journal.pgen.1010078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 03/08/2022] [Accepted: 02/06/2022] [Indexed: 11/29/2022] Open
Abstract
Pack-TYPE transposable elements (TEs) are a group of non-autonomous DNA transposons found in plants. These elements can efficiently capture and shuffle coding DNA across the host genome, accelerating the evolution of genes. Despite their relevance for plant genome plasticity, the detection and study of Pack-TYPE TEs are challenging due to the high similarity these elements have with genes. Here, we produced an automated annotation pipeline designed to study Pack-TYPE elements and used it to successfully annotate and analyse more than 10,000 new Pack-TYPE TEs in the rice and maize genomes. Our analysis indicates that Pack-TYPE TEs are an abundant and heterogeneous group of elements. We found that these elements are associated with all main superfamilies of Class II DNA transposons in plants and likely share a similar mechanism to capture new chromosomal DNA sequences. Furthermore, we report examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack-TYPE TEs in plant genome evolution. Transposable Elements (TEs) are genetic DNA sequences able to move across the genome, and their transposition activity is associated with genome plasticity and gene evolution. However, most of these elements exhibit “selfish” behaviour, meaning that they mainly transpose their own DNA sequence and only exceptionally might rearrange the DNA of coding genes. Pack-TYPE TEs, found in plants, represent an important exception, and they can efficiently capture and shuffle DNA sequences captured from the genome, accelerating the evolution of genes. We provide here the first automatic pipeline designed explicitly for the annotation of Pack-TYPE TEs. We used our approach to systematically investigate Pack-TYPE TEs in the rice and maize reference genomes, and annotated thousands of new elements in these species. We demonstrate that Pack-TYPE elements are abundant in plants and we report several examples of coding genes originated as a consequence of the mobilization of these elements.
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Affiliation(s)
- Jack S. Gisby
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (JSG); (MC)
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy
- * E-mail: (JSG); (MC)
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4
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Watson AK, Lopez P, Bapteste E. Hundreds of out-of-frame remodelled gene families in the E. coli pangenome. Mol Biol Evol 2021; 39:6430988. [PMID: 34792602 PMCID: PMC8788219 DOI: 10.1093/molbev/msab329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized to have formed de novo, from noncoding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from noncoding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodeled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodeling event. These genes with out-of-frame components represent ∼2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.
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Affiliation(s)
- Andrew K Watson
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
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5
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Stitzer MC, Anderson SN, Springer NM, Ross-Ibarra J. The genomic ecosystem of transposable elements in maize. PLoS Genet 2021; 17:e1009768. [PMID: 34648488 PMCID: PMC8547701 DOI: 10.1371/journal.pgen.1009768] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/26/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
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Affiliation(s)
- Michelle C. Stitzer
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Sarah N. Anderson
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jeffrey Ross-Ibarra
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, United States of America
- Genome Center, University of California, Davis, California, United States of America
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6
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Tan S, Ma H, Wang J, Wang M, Wang M, Yin H, Zhang Y, Zhang X, Shen J, Wang D, Banes GL, Zhang Z, Wu J, Huang X, Chen H, Ge S, Chen CL, Zhang YE. DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans. Nat Commun 2021; 12:4280. [PMID: 34257290 PMCID: PMC8277862 DOI: 10.1038/s41467-021-24585-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 06/23/2021] [Indexed: 01/06/2023] Open
Abstract
Despite long being considered as "junk", transposable elements (TEs) are now accepted as catalysts of evolution. One example is Mutator-like elements (MULEs, one type of terminal inverted repeat DNA TEs, or TIR TEs) capturing sequences as Pack-MULEs in plants. However, their origination mechanism remains perplexing, and whether TIR TEs mediate duplication in animals is almost unexplored. Here we identify 370 Pack-TIRs in 100 animal reference genomes and one Pack-TIR (Ssk-FB4) family in fly populations. We find that single-copy Pack-TIRs are mostly generated via transposition-independent gap filling, and multicopy Pack-TIRs are likely generated by transposition after replication fork switching. We show that a proportion of Pack-TIRs are transcribed and often form chimeras with hosts. We also find that Ssk-FB4s represent a young protein family, as supported by proteomics and signatures of positive selection. Thus, TIR TEs catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.
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Affiliation(s)
- Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinbo Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Man Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Mengxia Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haodong Yin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaqiong Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinying Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jieyu Shen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Danyang Wang
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China
| | - Graham L Banes
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Zhihua Zhang
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China
| | - Jianmin Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xun Huang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hua Chen
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Siqin Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun-Long Chen
- Curie Institute, PSL Research University, CNRS UMR 3244, Paris, France.
- Sorbonne University, Paris, France.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
- Chinese Institute for Brain Research, Beijing, China.
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7
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Zenda T, Liu S, Dong A, Duan H. Advances in Cereal Crop Genomics for Resilience under Climate Change. Life (Basel) 2021; 11:502. [PMID: 34072447 PMCID: PMC8228855 DOI: 10.3390/life11060502] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura P. Bag 1020, Zimbabwe
| | - Songtao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
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8
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Muyle A, Seymour D, Darzentas N, Primetis E, Gaut BS, Bousios A. Gene capture by transposable elements leads to epigenetic conflict in maize. MOLECULAR PLANT 2021; 14:237-252. [PMID: 33171302 DOI: 10.1016/j.molp.2020.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Transposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic crosstalk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which may also advantage the TEs. In this study, we examined this model by focusing on Helitrons, Pack-MULEs, and Sirevirus LTR retrotransposons in the maize genome. We documented 1263 TEs containing exon fragments from 1629 donor genes. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture. However, these patterns differed between syntelog versus translocated donor genes. Syntelogs appeared to maintain function, as measured by gene expression, consistent with moderation of silencing for functionally important genes. Epigenetic marks did not spread beyond their captured regions and 24nt crosstalk siRNAs were linked with CHH methylation. Translocated genes, in contrast, bore the signature of silencing. They were highly methylated and less expressed, but also overrepresented among donor genes and located away from chromosomal arms, which suggests a link between capture and gene movement. Splitting genes into potential functional categories based on evolutionary constraint supported the synteny-based findings. TE families captured genes in different ways, but the evidence for their advantage was generally less obvious; nevertheless, TEs with captured fragments were older, mapped fewer siRNAs, and were slightly less methylated than TEs without captured fragments. Collectively, our results argue that TE capture triggers an intragenomic conflict that may not affect the function of important genes but may lead to the pseudogenization of less-constrained genes.
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Affiliation(s)
- Aline Muyle
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA
| | - Danelle Seymour
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA; Department of Botany and Plant Sciences, UC Riverside, Riverside, CA 92521, USA
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Elias Primetis
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA.
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9
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Della Coletta R, Qiu Y, Ou S, Hufford MB, Hirsch CN. How the pan-genome is changing crop genomics and improvement. Genome Biol 2021; 22:3. [PMID: 33397434 PMCID: PMC7780660 DOI: 10.1186/s13059-020-02224-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/07/2020] [Indexed: 01/13/2023] Open
Abstract
Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 USA
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10
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Della Coletta R, Qiu Y, Ou S, Hufford MB, Hirsch CN. How the pan-genome is changing crop genomics and improvement. Genome Biol 2021. [PMID: 33397434 DOI: 10.1186/s13059-020-02224-2228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
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11
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Zhang X, Zhao M, McCarty DR, Lisch D. Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes. Nucleic Acids Res 2020; 48:6685-6698. [PMID: 32442316 PMCID: PMC7337890 DOI: 10.1093/nar/gkaa370] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/27/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic genomes and by selection following integration. Here, we compare TE target site distribution in host genomes using multiple de novo transposon insertion datasets in both plants and animals and compare them in the context of genome-wide transcriptional landscapes. We showcase two distinct types of transcription-associated TE targeting strategies that suggest a process of convergent evolution among eukaryotic TE families. The integration of two precision-targeting elements are specifically associated with initiation of RNA Polymerase II transcription of highly expressed genes, suggesting the existence of novel mechanisms of precision TE targeting in addition to passive targeting of open chromatin. We also highlight two features that can facilitate TE survival and rapid proliferation: tissue-specific transposition and minimization of negative impacts on nearby gene function due to precision targeting.
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Affiliation(s)
- Xinyan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
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12
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Cerbin S, Wai CM, VanBuren R, Jiang N. GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals. Genome Biol Evol 2020; 11:3181-3193. [PMID: 31633753 PMCID: PMC6839031 DOI: 10.1093/gbe/evz230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2019] [Indexed: 02/06/2023] Open
Abstract
Transposable elements represent the largest components of many eukaryotic genomes and different genomes harbor different combinations of elements. Here, we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla. Further searching for related sequences to the conserved DDE region uncovered the presence of this superfamily of elements in fish, coral, sea anemone, and other animal species. However, this element appears restricted to Bryophytes and Lycophytes in plants. This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100-150 bp terminal inverted repeats. Analysis of transposase sequences identified the DDE motif, a catalytic domain, which shows similarity to the integrase of Gypsy-like long terminal repeat retrotransposons, the most abundant component in plant genomes. A total of 77 intact and several hundred truncated copies of GingerRoot elements were identified in S. lepidophylla. Like Gypsy retrotransposons, GingerRoots show a lack of insertion preference near genes, which contrasts to the compact genome size of about 100 Mb. Nevertheless, a considerable portion of GingerRoot elements was found to carry gene fragments, suggesting the capacity of duplicating gene sequences is unlikely attributed to the proximity to genes. Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments, indicating they are preferentially retained in gene-poor regions. This study has identified a broadly dispersed, novel DNA transposon, and the first plant DNA transposon with an integrase-related transposase, suggesting the possibility of de novo formation of Gypsy-like elements in plants.
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Affiliation(s)
- Stefan Cerbin
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
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13
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Techa-Angkoon P, Childs KL, Sun Y. GPRED-GC: a Gene PREDiction model accounting for 5 ′- 3′ GC gradient. BMC Bioinformatics 2019; 20:482. [PMID: 31874598 PMCID: PMC6929509 DOI: 10.1186/s12859-019-3047-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/21/2019] [Indexed: 11/24/2022] Open
Abstract
Background Gene is a key step in genome annotation. Ab initio gene prediction enables gene annotation of new genomes regardless of availability of homologous sequences. There exist a number of ab initio gene prediction tools and they have been widely used for gene annotation for various species. However, existing tools are not optimized for identifying genes with highly variable GC content. In addition, some genes in grass genomes exhibit a sharp 5 ′- 3′ decreasing GC content gradient, which is not carefully modeled by available gene prediction tools. Thus, there is still room to improve the sensitivity and accuracy for predicting genes with GC gradients. Results In this work, we designed and implemented a new hidden Markov model (HMM)-based ab initio gene prediction tool, which is optimized for finding genes with highly variable GC contents, such as the genes with negative GC gradients in grass genomes. We tested the tool on three datasets from Arabidopsis thaliana and Oryza sativa. The results showed that our tool can identify genes missed by existing tools due to the highly variable GC contents. Conclusions GPRED-GC can effectively predict genes with highly variable GC contents without manual intervention. It provides a useful complementary tool to existing ones such as Augustus for more sensitive gene discovery. The source code is freely available at https://sourceforge.net/projects/gpred-gc/.
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14
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Catoni M, Jonesman T, Cerruti E, Paszkowski J. Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling. Nucleic Acids Res 2019; 47:1311-1320. [PMID: 30476196 PMCID: PMC6379663 DOI: 10.1093/nar/gky1196] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/08/2018] [Accepted: 11/16/2018] [Indexed: 11/21/2022] Open
Abstract
Pack-TYPE transposons are a unique class of potentially mobile non-autonomous elements that can capture, merge and relocate fragments of chromosomal DNA. It has been postulated that their activity accelerates the evolution of host genes. However, this important presumption is based only on the sequences of currently inactive Pack-TYPE transposons and the acquisition of chromosomal DNA has not been recorded in real time. Analysing the DNA copy number variation in hypomethylated Arabidopsis lines, we have now for the first time witnessed the mobilization of novel Pack-TYPE elements related to the CACTA transposon family, over several plant generations. Remarkably, these elements can insert into genes as closely spaced direct repeats and they frequently undergo incomplete excisions, resulting in the deletion of one of the end sequences. These properties suggest a mechanism of efficient acquisition of genic DNA residing between neighbouring Pack-TYPE transposons and its subsequent mobilization. Our work documents crucial steps in the formation of in vivo novel Pack-TYPE transposons, and thus the possible mechanism of gene shuffling mediated by this type of mobile element.
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Affiliation(s)
- Marco Catoni
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.,School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Thomas Jonesman
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Elisa Cerruti
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
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15
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Zhao D, Hamilton JP, Vaillancourt B, Zhang W, Eizenga GC, Cui Y, Jiang J, Buell CR, Jiang N. The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum. Nucleic Acids Res 2019; 46:2380-2397. [PMID: 29365184 PMCID: PMC5861414 DOI: 10.1093/nar/gky025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022] Open
Abstract
Acquisition and rearrangement of host genes by transposable elements (TEs) is an important mechanism to increase gene diversity as exemplified by the ∼3000 Pack-Mutator-like TEs in the rice genome which have acquired gene sequences (Pack-MULEs), yet remain enigmatic. To identify signatures of functioning Pack-MULEs and Pack-MULE evolution, we generated transcriptome, translatome, and epigenome datasets and compared Pack-MULEs to genes and other TE families. Approximately 40% of Pack-MULEs were transcribed with 9% having translation evidence, clearly distinguishing them from other TEs. Pack-MULEs exhibited a unique expression profile associated with specificity in reproductive tissues that may be associated with seed traits. Expressed Pack-MULEs resemble regular protein-coding genes as exhibited by a low level of DNA methylation, association with active histone marks and DNase I hypersensitive sites, and an absence of repressive histone marks, suggesting that a substantial fraction of Pack-MULEs are potentially functional in vivo. Interestingly, the expression capacity of Pack-MULEs is independent of the local genomic environment, and the insertion and expression of Pack-MULEs may have altered the local chromosomal expression pattern as well as counteracted the impact of recombination on chromosomal base composition, which has profound consequences on the evolution of chromosome structure.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Wenli Zhang
- Department of Horticulture, University of Wisconsin, Madison, WI 53705, USA.,State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Georgia C Eizenga
- USDA-ARS Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR 72160, USA
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Jiming Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
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16
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Krasileva KV. The role of transposable elements and DNA damage repair mechanisms in gene duplications and gene fusions in plant genomes. CURRENT OPINION IN PLANT BIOLOGY 2019; 48:18-25. [PMID: 30849712 DOI: 10.1016/j.pbi.2019.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 05/02/2023]
Abstract
Plant genomes are shaped by structural variation. Gene-size insertions and among most prominent events and can have significant effects on amplification of gene families as well as facilitate new gene fusions. Transposable elements as well as plant DNA repair machinery have overlapping contributions to these events, and often work in synergy. Activity of transposable elements is often lineage specific and can preferentially affect specific gene families, such as disease resistance genes. Once duplicated, genes themselves can serve templates for additional variation that can arise from non-allelic homologous recombination. Non-homologous DNA repair mechanisms contribute to additional variation and diversify the mechanisms of gene movement, such as through ligation of extra-chromosomal DNA fragments. Genomic processes that generate structural variation can be induced by stress and, therefore, can provide adaptive potential. This review describes mechanisms that contribute to gene-size structural variation in plants, result in gene duplication and generation of new plant genes through gene fusion.
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Affiliation(s)
- Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States.
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17
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Abstract
Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.
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Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
- Corresponding author: E-mail:
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
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18
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Marburger S, Alexandrou MA, Taggart JB, Creer S, Carvalho G, Oliveira C, Taylor MI. Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes. Proc Biol Sci 2019; 285:rspb.2017.2732. [PMID: 29445022 PMCID: PMC5829208 DOI: 10.1098/rspb.2017.2732] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/25/2018] [Indexed: 01/12/2023] Open
Abstract
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.
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Affiliation(s)
- Sarah Marburger
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Markos A Alexandrou
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,Wildlands Conservation Science, LLC PO Box 1846, Lompoc, CA 93438, USA
| | - John B Taggart
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências/UNESP, Rua Professor Doutor Antonio Celso Wagner Zanin, s/n°18618-689 Botucatu, São Paulo, Brazil
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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19
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Liu M, Zhang C, Duan L, Luan Q, Li J, Yang A, Qi X, Ren Z. CsMYB60 is a key regulator of flavonols and proanthocyanidans that determine the colour of fruit spines in cucumber. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:69-84. [PMID: 30256979 PMCID: PMC6305189 DOI: 10.1093/jxb/ery336] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/12/2018] [Indexed: 05/08/2023]
Abstract
Spine colour is an important fruit quality trait that influences the commercial value of cucumber (Cucumis sativus). However, little is known about the metabolites and the regulatory mechanisms of their biosynthesis in black spine varieties. In this study, we determined that the pigments of black spines are flavonoids, including flavonols and proanthocyanidins (PAs). We identified CsMYB60 as the best candidate for the previously identified B (Black spine) locus. Expression levels of CsMYB60 and the key genes involved in flavonoid biosynthesis were higher in black-spine inbred lines than that in white-spine lines at different developmental stages. The insertion of a Mutator-like element (CsMULE) in the second intron of CsMYB60 decreased its expression in a white-spine line. Transient overexpression assays indicated that CsMYB60 is a key regulatory gene and Cs4CL is a key structural gene in the pigmentation of black spines. In addition, the DNA methylation level in the CsMYB60 promoter was much lower in the black-spine line compared with white-spine line. The CsMULE insert may decrease the expression level of CsMYB60, causing hindered synthesis of flavonols and PAs in cucumber fruit spines.
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Affiliation(s)
- Mengyu Liu
- State Key Laboratory of Corp Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Cunjia Zhang
- State Key Laboratory of Corp Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Lixin Duan
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Qianqian Luan
- State Key Laboratory of Corp Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Jialin Li
- State Key Laboratory of Corp Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Aigang Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Xiaoquan Qi
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun, Xiangshan, Beijing, China
| | - Zhonghai Ren
- State Key Laboratory of Corp Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
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20
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Valdes Franco JA, Wang Y, Huo N, Ponciano G, Colvin HA, McMahan CM, Gu YQ, Belknap WR. Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes. BMC Genomics 2018; 19:271. [PMID: 29673330 PMCID: PMC5907723 DOI: 10.1186/s12864-018-4653-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/10/2018] [Indexed: 12/30/2022] Open
Abstract
Background Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. Results The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50 = 22 kb), maps > 95% of the shotgun reads and is essentially complete. Approximately 40,000 transcribed, protein encoding genes were annotated on the assembly. Further characterization of this genome revealed 15 families of small, microsatellite-associated, transposable elements (TEs) with unexpected chromosomal distribution profiles. These SaTar (Satellite Targeted) elements, which are non-autonomous Mu-like elements (MULEs), were frequently observed in multimeric linear arrays of unrelated individual elements within which no individual element is interrupted by another. This uniformly non-nested TE multimer architecture has not been previously described in either eukaryotic or prokaryotic genomes. Five families of similarly distributed non-autonomous MULEs (microsatellite associated, modularly assembled) were characterized in the rice genome. Families of TEs with similar structures and distribution profiles were identified in sorghum and citrus. Conclusion The sequencing and assembly of the guayule genome provides a foundation for application of current crop improvement technologies to this plant. In addition, characterization of this genome revealed SaTar elements with distribution profiles unique among TEs. Satar targeting appears based on an alternative MULE recombination mechanism with the potential to impact gene evolution. Electronic supplementary material The online version of this article (10.1186/s12864-018-4653-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José A Valdes Franco
- Universidad Autónoma de Nuevo León, Monterrey, NL, Mexico.,Present Address: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Yi Wang
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Naxin Huo
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Grisel Ponciano
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | | | - Colleen M McMahan
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Yong Q Gu
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA.
| | - William R Belknap
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
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21
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Cerbin S, Jiang N. Duplication of host genes by transposable elements. Curr Opin Genet Dev 2018; 49:63-69. [PMID: 29571044 DOI: 10.1016/j.gde.2018.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/12/2022]
Abstract
The availability of large amounts of genomic and transcriptome sequences have allowed systematic surveys about the host gene sequences that have been duplicated by transposable elements. It is now clear that all super-families of transposons are capable of duplicating genes or gene fragments, and such incidents have been detected in a wide spectrum of organisms. Emerging evidence suggests that a considerable portion of them function as coding or non-coding sequences, driving innovations at molecular and phenotypic levels. Interestingly, the duplication events not only have to occur in the reproductive tissues to become heritable, but the duplicated copies are also preferentially expressed in those tissues. As a result, reproductive tissues may serve as the 'incubator' for genes generated by transposable elements.
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Affiliation(s)
- Stefan Cerbin
- Department of Horticulture, 1066 Bogue Street, Michigan State University, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, 1066 Bogue Street, Michigan State University, East Lansing, MI 48824, USA.
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22
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Abstract
LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. These elements can fall inside or close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene regulation and evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes. The presence of retrotransposon remnants in genes that are necessary for normal gene function, demonstrates the importance of exaptation and co-option, and is also a consequence of the abundance of these elements in plant genomes. Furthermore, insertions of LTR retrotransposons in and around genes provide potential for alternative splicing, epigenetic control, transduction, duplication and recombination. These characteristics can become an active part of the evolution of gene families as in the case of resistance genes (R-genes). The character of TEs as exclusively selfish is now being re-evaluated. Since genome-wide reprogramming via TEs is a long evolutionary process, the changes we can examine are case-specific and their fitness advantage may not be evident until TE-derived motifs and domains have been completely co-opted and fixed. Nevertheless, the presence of LTR retrotransposons inside genes and as part of gene promoter regions is consistent with their roles as engines of plant genome evolution.
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23
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Song X, Cao X. Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:111-118. [PMID: 28273484 DOI: 10.1016/j.pbi.2017.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 05/19/2023]
Abstract
Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Moraes AP, Koehler S, Cabral JS, Gomes SSL, Viccini LF, Barros F, Felix LP, Guerra M, Forni-Martins ER. Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:298-308. [PMID: 27917576 DOI: 10.1111/plb.12527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
Orchidaceae is a widely distributed plant family with very diverse vegetative and floral morphology, and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariinea to detect how much chromosome and GS variation there is in these groups and to evaluate which genome rearrangements are involved in the species evolution. To do so, the GS (14 species), the karyotype - based on chromosome number, heterochromatic banding and 5S and 45S rDNA localisation (18 species) - was characterised and analysed along with published data using phylogenetic approaches. The GS presented a high phylogenetic correlation and it was related to morphological groups in Bifrenaria (larger plants - higher GS). The two largest GS found among genera were caused by different mechanisms: polyploidy in Bifrenaria tyrianthina and accumulation of repetitive DNA in Scuticaria hadwenii. The chromosome number variability was caused mainly through descending dysploidy, and x=20 was estimated as the base chromosome number. Combining GS and karyotype data with molecular phylogeny, our data provide a more complete scenario of the karyotype evolution in Maxillariinae orchids, allowing us to suggest, besides dysploidy, that inversions and transposable elements as two mechanisms involved in the karyotype evolution. Such karyotype modifications could be associated with niche changes that occurred during species evolution.
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Affiliation(s)
- A P Moraes
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, Brazil
- Instituto de Ciências e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, Brazil
| | - S Koehler
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
| | - J S Cabral
- Departamento de Botânica, Centro de Ciências Biológicas, Cidade Universitária, Universidade Federal de Pernambuco, Recife, Brazil
- Synthesis Centre, German Centre for Integrative Biodiversity Research, Leipzig, Germany
- Center for Computational and Theoretical Biology, Ecosystem Modeling, University of Würzburg, Würzburg, Germany
| | - S S L Gomes
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - L F Viccini
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - F Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado de São Paulo, São Paulo, Brazil
| | - L P Felix
- Departamento de Ciências Biológicas, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Rodovia, Areias, Brazil
| | - M Guerra
- Departamento de Botânica, Centro de Ciências Biológicas, Cidade Universitária, Universidade Federal de Pernambuco, Recife, Brazil
| | - E R Forni-Martins
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
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Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation. G3-GENES GENOMES GENETICS 2017; 7:203-219. [PMID: 27852012 PMCID: PMC5217110 DOI: 10.1534/g3.116.036020] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5′ untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.
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Tatarinova TV, Chekalin E, Nikolsky Y, Bruskin S, Chebotarov D, McNally KL, Alexandrov N. Nucleotide diversity analysis highlights functionally important genomic regions. Sci Rep 2016; 6:35730. [PMID: 27774999 PMCID: PMC5075931 DOI: 10.1038/srep35730] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/30/2016] [Indexed: 12/15/2022] Open
Abstract
We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (http://snp-seek.irri.org), the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions. In general, the observed profound patterns of nucleotide variability reveal functionally important genomic regions. As expected, nucleotide diversity is much higher in intergenic regions than within gene bodies (regions spanning gene models), and protein-coding sequences are more conserved than untranslated gene regions. We have observed a sharp decline in nucleotide diversity that begins at about 250 nucleotides upstream of the transcription start and reaches minimal diversity exactly at the transcription start. We found the transcription termination sites to have remarkably symmetrical patterns of SNP density, implying presence of functional sites near transcription termination. Also, nucleotide diversity was significantly lower near 3′ UTRs, the area rich with regulatory regions.
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Affiliation(s)
- Tatiana V Tatarinova
- Center for Personalized Medicine and Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Yuri Nikolsky
- Vavilov Institute of General Genetics, Moscow, Russia.,F1 Genomics, San Diego, CA, USA.,School of Systems Biology, George Mason University, VA, USA
| | | | - Dmitry Chebotarov
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Kenneth L McNally
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
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Lehti-Shiu MD, Panchy N, Wang P, Uygun S, Shiu SH. Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:3-20. [PMID: 27522016 DOI: 10.1016/j.bbagrm.2016.08.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/21/2016] [Accepted: 08/06/2016] [Indexed: 12/19/2022]
Abstract
Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
| | - Nicholas Panchy
- The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Peipei Wang
- Department of Plant Biology, East Lansing, MI 48824, USA
| | - Sahra Uygun
- The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, East Lansing, MI 48824, USA; The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA.
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28
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Panchy N, Lehti-Shiu M, Shiu SH. Evolution of Gene Duplication in Plants. PLANT PHYSIOLOGY 2016; 171:2294-316. [PMID: 27288366 PMCID: PMC4972278 DOI: 10.1104/pp.16.00523] [Citation(s) in RCA: 760] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/17/2016] [Indexed: 05/18/2023]
Abstract
Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.
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Affiliation(s)
- Nicholas Panchy
- Genetics Program (N.P., S.-H.S.) and Department of Plant Biology (M.L.-S., S.-H.S.), Michigan State University, East Lansing, Michigan 48824
| | - Melissa Lehti-Shiu
- Genetics Program (N.P., S.-H.S.) and Department of Plant Biology (M.L.-S., S.-H.S.), Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Genetics Program (N.P., S.-H.S.) and Department of Plant Biology (M.L.-S., S.-H.S.), Michigan State University, East Lansing, Michigan 48824
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29
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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30
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Wang J, Yu Y, Tao F, Zhang J, Copetti D, Kudrna D, Talag J, Lee S, Wing RA, Fan C. DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biol 2016; 17:92. [PMID: 27154274 PMCID: PMC4858842 DOI: 10.1186/s13059-016-0954-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/14/2016] [Indexed: 01/17/2023] Open
Abstract
Background Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. These elements can capture ectopic genomic sequences that lead to the formation of new gene structures. Here, based on whole-genome comparative analyses, we comprehensively investigated processes and mechanisms of the evolution of putative genes derived from Mutator-like transposable elements in ten Oryza species and the outgroup Leersia perieri, bridging ~20 million years of evolutionary history. Results Our analysis identified thousands of putative genes in each of the Oryza species, a large proportion of which have evidence of expression and contain chimeric structures. Consistent with previous reports, we observe that the putative Mutator-like transposable element-derived genes are generally GC-rich and mainly derive from GC-rich parental sequences. Furthermore, we determine that Mutator-like transposable elements capture parental sequences preferentially from genomic regions with low methylation levels and high recombination rates. We explicitly show that methylation levels in the internal and terminated inverted repeat regions of these elements, which might be directed by the 24-nucleotide small RNA-mediated pathway, are different and change dynamically over evolutionary time. Lastly, we demonstrate that putative genes derived from Mutator-like transposable elements tend to be expressed in mature pollen, which have undergone de-methylation programming, thereby providing a permissive expression environment for newly formed/transposable element-derived genes. Conclusions Our results suggest that DNA methylation may be a primary mechanism to facilitate the origination, survival, and regulation of genes derived from Mutator-like transposable elements, thus contributing to the evolution of gene innovation and novelty in plant genomes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0954-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Wang
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Feng Tao
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Dave Kudrna
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Seunghee Lee
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,T.T. Chang Genetics Resources Center, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.
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31
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Abstract
The Mutator system of transposable elements (TEs) is a highly mutagenic family of transposons in maize. Because they transpose at high rates and target genic regions, these transposons can rapidly generate large numbers of new mutants, which has made the Mutator system a favored tool for both forward and reverse mutagenesis in maize. Low copy number versions of this system have also proved to be excellent models for understanding the regulation and behavior of Class II transposons in plants. Notably, the availability of a naturally occurring locus that can heritably silence autonomous Mutator elements has provided insights into the means by which otherwise active transposons are recognized and silenced. This chapter will provide a review of the biology, regulation, evolution and uses of this remarkable transposon system, with an emphasis on recent developments in our understanding of the ways in which this TE system is recognized and epigenetically silenced as well as recent evidence that Mu-like elements (MULEs) have had a significant impact on the evolution of plant genomes.
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32
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Zhao D, Ferguson AA, Jiang N. What makes up plant genomes: The vanishing line between transposable elements and genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:366-80. [PMID: 26709091 DOI: 10.1016/j.bbagrm.2015.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023]
Abstract
The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ann A Ferguson
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA.
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33
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Yao W, Li G, Zhao H, Wang G, Lian X, Xie W. Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol 2015; 16:187. [PMID: 26403182 PMCID: PMC4583175 DOI: 10.1186/s13059-015-0757-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The dispensable genome of a species, consisting of the dispensable sequences present only in a subset of individuals, is believed to play important roles in phenotypic variation and genome evolution. However, construction of the dispensable genome is costly and labor-intensive at present, and so the influence of the dispensable genome in genetic and functional genomic studies has not been fully explored. RESULTS We construct the dispensable genome of rice through a metagenome-like de novo assembly strategy based on low-coverage (1-3×) sequencing data of 1483 cultivated rice (Oryza sativa L.) accessions. Thousands of protein-coding genes are successfully assembled, including most of the known agronomically important genes absent from the Nipponbare rice reference genome. We develop an integration approach based on alignment and linkage disequilibrium, which is able to assign genomic positions relative to the reference genome for more than 78.2 % of the dispensable sequences. We carry out association mapping studies for rice grain width and 840 metabolic traits using 0.46 million polymorphisms between the dispensable sequences of different rice accessions. About 23.5 % of metabolic traits have more significant association signals with polymorphisms from dispensable sequences than with SNPs from the reference genome, and 41.6 % of trait-associated SNPs have concordant genomic locations with associated dispensable sequences. CONCLUSIONS Our results suggest the feasibility of building a species' dispensable genome using low-coverage population sequencing data. The constructed sequences will be helpful for understanding the rice dispensable genome and are complementary to the reference genome for identifying candidate genes associated with phenotypic variation.
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Affiliation(s)
- Wen Yao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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Guérillot R, Siguier P, Gourbeyre E, Chandler M, Glaser P. The diversity of prokaryotic DDE transposases of the mutator superfamily, insertion specificity, and association with conjugation machineries. Genome Biol Evol 2015; 6:260-72. [PMID: 24418649 PMCID: PMC3942029 DOI: 10.1093/gbe/evu010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are major components of both prokaryotic and eukaryotic genomes and play a significant role in their evolution. In this study, we have identified new prokaryotic DDE transposase families related to the eukaryotic Mutator-like transposases. These genes were retrieved by cascade PSI-Blast using as initial query the transposase of the streptococcal integrative and conjugative element (ICE) TnGBS2. By combining secondary structure predictions and protein sequence alignments, we predicted the DDE catalytic triad and the DNA-binding domain recognizing the terminal inverted repeats. Furthermore, we systematically characterized the organization and the insertion specificity of the TEs relying on these prokaryotic Mutator-like transposases (p-MULT) for their mobility. Strikingly, two distant TE families target their integration upstream σA dependent promoters. This allowed us to identify a transposase sequence signature associated with this unique insertion specificity and to show that the dissymmetry between the two inverted repeats is responsible for the orientation of the insertion. Surprisingly, while DDE transposases are generally associated with small and simple transposons such as insertion sequences (ISs), p-MULT encoding TEs show an unprecedented diversity with several families of IS, transposons, and ICEs ranging in size from 1.1 to 52 kb.
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Affiliation(s)
- Romain Guérillot
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, Paris, France
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35
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Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. PLANT PHYSIOLOGY 2015; 167:25-39. [PMID: 25384563 PMCID: PMC4280997 DOI: 10.1104/pp.114.245027] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/02/2014] [Indexed: 05/18/2023]
Abstract
The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes.
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Affiliation(s)
- MeiYee Law
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Kevin L Childs
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Michael S Campbell
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Joshua C Stein
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Andrew J Olson
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Carson Holt
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Nicholas Panchy
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Jikai Lei
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Dian Jiao
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Carson M Andorf
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Carolyn J Lawrence
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Doreen Ware
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Shin-Han Shiu
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Yanni Sun
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Ning Jiang
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
| | - Mark Yandell
- The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)
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Zhao D, Ferguson A, Jiang N. Transposition of a rice Mutator-like element in the yeast Saccharomyces cerevisiae. THE PLANT CELL 2015; 27:132-148. [PMID: 25587002 PMCID: PMC4330571 DOI: 10.1105/tpc.114.128488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/30/2014] [Accepted: 12/24/2014] [Indexed: 06/04/2023]
Abstract
Mutator-like transposable elements (MULEs) are widespread in plants and are well known for their high transposition activity as well as their ability to duplicate and amplify host gene fragments. Despite their abundance and importance, few active MULEs have been identified. In this study, we demonstrated that a rice (Oryza sativa) MULE, Os3378, is capable of excising and reinserting in yeast (Saccharomyces cerevisiae), suggesting that yeast harbors all the host factors for the transposition of MULEs. The transposition activity induced by the wild-type transposase is low but can be altered by modification of the transposase sequence, including deletion, fusion, and substitution. Particularly, fusion of a fluorescent protein to the transposase enhanced the transposition activity, representing another approach to manipulate transposases. Moreover, we identified a critical region in the transposase where the net charge of the amino acids seems to be important for activity. Finally, transposition efficiency is also influenced by the element and its flanking sequences (i.e., small elements are more competent than their large counterparts). Perfect target site duplication is favorable, but not required, for precise excision. In addition to the potential application in functional genomics, this study provides the foundation for further studies of the transposition mechanism of MULEs.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Ann Ferguson
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
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37
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Belyayev A. Bursts of transposable elements as an evolutionary driving force. J Evol Biol 2014; 27:2573-84. [PMID: 25290698 DOI: 10.1111/jeb.12513] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 12/25/2022]
Abstract
A burst of transposable elements (TEs) is a massive outbreak that may cause radical genomic rebuilding. This phenomenon has been reported in connection with the formation of taxonomic groups and species and has therefore been associated with major evolutionary events in the past. Over the past few years, several research groups have discovered recent stress-induced bursts of different TEs. The events for which bursts of TEs have been recorded include domestication, polyploidy, changes in mating systems, interspecific and intergeneric hybridization and abiotic stress. Cases involving abiotic stress, particularly bursts of TEs in natural populations driven by environmental change, are of special interest because this phenomenon may underlie micro- and macro-evolutionary events and ultimately support the maintenance and generation of biological diversity. This study reviews the known cases of bursts of TEs and their possible consequences, with particular emphasis on the speciation process.
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Affiliation(s)
- A Belyayev
- Institute of Botany, Czech Academy of Sciences, Pruhonice near Prague, Czech Republic
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38
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Liu Y, Yang G. Tc1-like transposable elements in plant genomes. Mob DNA 2014; 5:17. [PMID: 24926322 PMCID: PMC4054914 DOI: 10.1186/1759-8753-5-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Tc1/mariner superfamily of transposable elements (TEs) is widespread in animal genomes. Mariner-like elements, which bear a DDD triad catalytic motif, have been identified in a wide range of flowering plant species. However, as the founding member of the superfamily, Tc1-like elements that bear a DD34E triad catalytic motif are only known to unikonts (animals, fungi, and Entamoeba). RESULTS Here we report the identification of Tc1-like elements (TLEs) in plant genomes. These elements bear the four terminal nucleotides and the characteristic DD34E triad motif of Tc1 element. The two TLE families (PpTc1, PpTc2) identified in the moss (Physcomitrella patens) genome contain highly similar copies. Multiple copies of PpTc1 are actively transcribed and the transcripts encode intact full length transposase coding sequences. TLEs are also found in angiosperm genome sequence databases of rice (Oryza sativa), dwarf birch (Betula nana), cabbage (Brassica rapa), hemp (Cannabis sativa), barley (Hordium valgare), lettuce (Lactuta sativa), poplar (Populus trichocarpa), pear (Pyrus x bretschneideri), and wheat (Triticum urartu). CONCLUSIONS This study extends the occurrence of TLEs to the plant phylum. The elements in the moss genome have amplified recently and may still be capable of transposition. The TLEs are also present in angiosperm genomes, but apparently much less abundant than in moss.
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Affiliation(s)
- Yuan Liu
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6 Mississauga, ON, Canada ; Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Guojun Yang
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6 Mississauga, ON, Canada ; Cell and Systems Biology, University of Toronto, Toronto, Canada
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Oliver KR, McComb JA, Greene WK. Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol 2014; 5:1886-901. [PMID: 24065734 PMCID: PMC3814199 DOI: 10.1093/gbe/evt141] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin's "abominable mystery": the spectacular success of the angiosperms.
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Affiliation(s)
- Keith R Oliver
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
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40
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Yang G, Fattash I, Lee CN, Liu K, Cavinder B. Birth of three stowaway-like MITE families via microhomology-mediated miniaturization of a Tc1/Mariner element in the yellow fever mosquito. Genome Biol Evol 2014; 5:1937-48. [PMID: 24068652 PMCID: PMC3814204 DOI: 10.1093/gbe/evt146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic genomes contain numerous DNA transposons that move by a cut-and-paste mechanism. The majority of these elements are self-insufficient and dependent on their autonomous relatives to transpose. Miniature inverted repeat transposable elements (MITEs) are often the most numerous nonautonomous DNA elements in a higher eukaryotic genome. Little is known about the origin of these MITE families as few of them are accompanied by their direct ancestral elements in a genome. Analyses of MITEs in the yellow fever mosquito identified its youngest MITE family, designated as Gnome, that contains at least 116 identical copies. Genome-wide search for direct ancestral autonomous elements of Gnome revealed an elusive single copy Tc1/Mariner-like element, named as Ozma, that encodes a transposase with a DD37E triad motif. Strikingly, Ozma also gave rise to two additional MITE families, designated as Elf and Goblin. These three MITE families were derived at different times during evolution and bear internal sequences originated from different regions of Ozma. Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6–8 bp). These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology. Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes.
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Affiliation(s)
- Guojun Yang
- Department of Biology, University of Toronto Mississauga, Ontario, Canada
- *Corresponding author: E-mail:
| | - Isam Fattash
- Department of Biology, University of Toronto Mississauga, Ontario, Canada
| | - Chia-Ni Lee
- Department of Biology, University of Toronto Mississauga, Ontario, Canada
| | - Kun Liu
- Department of Botany and Plant Sciences, University of California Riverside
| | - Brad Cavinder
- Department of Plant Pathology and Microbiology, University of California Riverside
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Abstract
The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology; University of Chicago; Chicago, IL USA
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Tang HM, Liu S, Hill-Skinner S, Wu W, Reed D, Yeh CT, Nettleton D, Schnable PS. The maize brown midrib2 (bm2) gene encodes a methylenetetrahydrofolate reductase that contributes to lignin accumulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:380-92. [PMID: 24286468 PMCID: PMC4282534 DOI: 10.1111/tpj.12394] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 10/31/2013] [Accepted: 11/20/2013] [Indexed: 05/02/2023]
Abstract
The midribs of maize brown midrib (bm) mutants exhibit a reddish-brown color associated with reductions in lignin concentration and alterations in lignin composition. Here, we report the mapping, cloning, and functional and biochemical analyses of the bm2 gene. The bm2 gene was mapped to a small region of chromosome 1 that contains a putative methylenetetrahydrofolate reductase (MTHFR) gene, which is down-regulated in bm2 mutant plants. Analyses of multiple Mu-induced bm2-Mu mutant alleles confirmed that this constitutively expressed gene is bm2. Yeast complementation experiments and a previously published biochemical characterization show that the bm2 gene encodes a functional MTHFR. Quantitative RT-PCR analyses demonstrated that the bm2 mutants accumulate substantially reduced levels of bm2 transcript. Alteration of MTHFR function is expected to influence accumulation of the methyl donor S-adenosyl-L-methionine (SAM). Because SAM is consumed by two methyltransferases in the lignin pathway (Ye et al., ), the finding that bm2 encodes a functional MTHFR is consistent with its lignin phenotype. Consistent with this functional assignment of bm2, the expression patterns of genes in a variety of SAM-dependent or -related pathways, including lignin biosynthesis, are altered in the bm2 mutant. Biochemical assays confirmed that bm2 mutants accumulate reduced levels of lignin with altered composition compared to wild-type. Hence, this study demonstrates a role for MTHFR in lignin biosynthesis.
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Affiliation(s)
- Ho Man Tang
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, 50011, USA
- †Center for Cell Dynamics, Department of Biological Chemistry, Johns Hopkins University School of MedicineBaltimore, MD, 21205, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- *For correspondence (e-mails (SL) or (PSS))
| | - Sarah Hill-Skinner
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
| | - Wei Wu
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- Center for Plant Genomics, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- §Pioneer Hi-Bred International Inc.Johnston, IA, 50131, USA
| | - Danielle Reed
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, 50011, USA
- §Pioneer Hi-Bred International Inc.Johnston, IA, 50131, USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
| | - Dan Nettleton
- Center for Plant Genomics, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- Department of Statistics, Iowa State University2115 Snedecor, Ames, IA, 50011, USA
| | - Patrick S Schnable
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, 50011, USA
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- Center for Plant Genomics, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- *For correspondence (e-mails (SL) or (PSS))
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New insights into helitron transposable elements in the mesopolyploid species Brassica rapa. Gene 2013; 532:236-45. [DOI: 10.1016/j.gene.2013.09.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 11/19/2022]
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Ferguson AA, Zhao D, Jiang N. Selective acquisition and retention of genomic sequences by Pack-Mutator-like elements based on guanine-cytosine content and the breadth of expression. PLANT PHYSIOLOGY 2013; 163:1419-32. [PMID: 24028844 PMCID: PMC3813661 DOI: 10.1104/pp.113.223271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The process of gene duplication followed by sequence and functional divergence is important for the generation of new genes. Pack-MULEs, nonautonomous Mutator-like elements (MULEs) that carry genic sequence(s), are potentially involved in generating new open reading frames and regulating parental gene expression. These elements are identified in many plant genomes and are most abundant in rice (Oryza sativa). Despite the abundance of Pack-MULEs, the mechanism by which parental genes are captured by Pack-MULEs remains largely unknown. In this study, we identified all MULEs in rice and examined factors likely important for sequence acquisition. Terminal inverted repeat MULEs are the predominant MULE type and account for the majority of the Pack-MULEs. In addition to genic sequences, rice MULEs capture guanine-cytosine (GC)-rich intergenic sequences, albeit at a much lower frequency. MULEs carrying nontransposon sequences have longer terminal inverted repeats and higher GC content in terminal and subterminal regions. An overrepresentation of genes with known functions and genes with orthologs among parental genes of Pack-MULEs is observed in rice, maize (Zea mays), and Arabidopsis (Arabidopsis thaliana), suggesting preferential acquisition for bona fide genes by these elements. Pack-MULEs selectively acquire/retain parental sequences through a combined effect of GC content and breadth of expression, with GC content playing a stronger role. Increased GC content and number of tissues with detectable expression result in higher chances of a gene being acquired by Pack-MULEs. Such selective acquisition/retention provides these elements greater chances of carrying functional sequences that may provide new genetic resources for the evolution of new genes or the modification of existing genes.
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Schulman AH. Retrotransposon replication in plants. Curr Opin Virol 2013; 3:604-14. [PMID: 24035277 DOI: 10.1016/j.coviro.2013.08.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/31/2022]
Abstract
Retrotransposons comprise the bulk of large plant genomes, replicating via an RNA intermediate whereby the original, integrated element remains in place. Of the two main orders, the LTR retrotransposons considerably outnumber the LINEs. LINEs integrate into target sites simultaneously with the RNA transcript being copied into cDNA by target-primed reverse transcription. LTR retrotransposon replication is basically equivalent to the intracellular phase of retroviral life cycles. The envelope gene giving extracellular mobility to retroviruses is in fact widespread in plants and their retrotransposons. Evolutionary analyses of the retrotransposons and retroviruses suggest that both form an ancient monophyletic group. The particular adaptations of LTR retrotransposons to plant life cycles enabling their success remain to be clarified.
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Affiliation(s)
- Alan H Schulman
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland; Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen FIN-31600, Finland.
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Shapiro JA. Implications of the Read-Write Genome view. Phys Life Rev 2013; 10:347-50. [PMID: 23988879 DOI: 10.1016/j.plrev.2013.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 07/16/2013] [Indexed: 10/26/2022]
Affiliation(s)
- James A Shapiro
- Dept. of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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Ahmad T, Sablok G, Tatarinova TV, Xu Q, Deng XX, Guo WW. Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags. DNA Res 2013; 20:135-50. [PMID: 23315666 PMCID: PMC3628444 DOI: 10.1093/dnares/dss039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid.
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Affiliation(s)
- Touqeer Ahmad
- Key Laboratory of Horticultural Plant Biology MOE, Huazhong Agricultural University, Wuhan 430070, China
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Abstract
The initial identification of transposable elements (TEs) was attributed to the activity of DNA transposable elements, which are prevalent in plants. Unlike RNA elements, which accumulate in the gene-poor heterochromatic regions, most DNA elements are located in the gene rich regions and many of them carry genes or gene fragments. As such, DNA elements have a more intimate relationship with genes and may have an immediate impact on gene expression and gene function. DNA elements are structurally distinct from RNA elements and most of them have terminal inverted repeats (TIRs). Such structural features have been used to identify the relevant elements from genomic sequences. Among the DNA elements in plants, the most abundant type is the miniature inverted repeat transposable elements (MITEs). This chapter discusses the methods to identify MITEs, Helitrons, and other DNA transposable elements.
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Affiliation(s)
- Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
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Affiliation(s)
- Nina V Fedoroff
- King Abdullah University of Science and Technology, Saudi Arabia.
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McCue AD, Slotkin RK. Transposable element small RNAs as regulators of gene expression. Trends Genet 2012; 28:616-23. [PMID: 23040327 DOI: 10.1016/j.tig.2012.09.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/31/2012] [Accepted: 09/05/2012] [Indexed: 11/30/2022]
Abstract
Transposable elements (TEs) are a source of endogenous small RNAs in animals and plants. These TE-derived small RNAs have been traditionally treated as functionally distinct from gene-regulating small RNAs, such as miRNAs. Two recent reports in Drosophila and Arabidopsis have blurred the lines of this distinction. In both examples, epigenetically and developmentally regulated bursts in TE expression produce gene-regulating small RNAs. In the Drosophila early embryo, maternally deposited TE-derived PIWI-interacting small RNAs (piRNAs) play a role in regulating the nanos mRNA through small RNA binding sites in the nanos 3' untranslated region (UTR). In Arabidopsis, when Athila retrotransposons are epigenetically activated, their transcripts are processed into small RNAs, which directly target the 3'UTR of the genic oligouridylate binding protein 1B (UBP1b) mRNA. Based on these two examples, we suggest that other TE-derived small RNAs regulate additional genes and propose that, through small RNAs, the epigenetic status of TEs could widely influence the genic transcriptome.
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Affiliation(s)
- Andrea D McCue
- Department of Molecular Genetics & Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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