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Li Z, Gilbert C, Peng H, Pollet N. Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO. Nucleic Acids Res 2024:gkae679. [PMID: 39119924 DOI: 10.1093/nar/gkae679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/19/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Helitron-like elements (HLEs) are widespread eukaryotic DNA transposons employing a rolling-circle transposition mechanism. Despite their prevalence in fungi, animals, and plant genomes, identifying Helitrons remains a formidable challenge. We introduce HELIANO, a software for annotating and classifying autonomous and non-autonomous HLE sequences from whole genomes. HELIANO overcomes several limitations of existing tools in speed and accuracy, demonstrated through benchmarking and its application to the complex genomes of frogs (Xenopus tropicalis and Xenopus laevis) and rice (Oryza sativa), where it uncovered numerous previously unidentified HLEs. In an extensive analysis of 404 eukaryote genomes, we found HLEs widely distributed across phyla, with exceptions in specific taxa. HELIANO's application led to the discovery of numerous new HLEs in land plants and identified 20 protein domains captured by certain autonomous HLE families. A comprehensive phylogenetic analysis further classified HLEs into two primary clades, HLE1 and HLE2, and revealed nine subgroups, some of which are enriched within specific taxa. The future use of HELIANO promises to improve the global analysis of HLEs across genomes, significantly advancing our understanding of this fascinating transposon superfamily.
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Affiliation(s)
- Zhen Li
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Haoran Peng
- Crop Genome Dynamics Group, Agroscope, 1260 Nyon, Switzerland
| | - Nicolas Pollet
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
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2
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Hu K, Ni P, Xu M, Zou Y, Chang J, Gao X, Li Y, Ruan J, Hu B, Wang J. HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation. Nat Commun 2024; 15:5573. [PMID: 38956036 PMCID: PMC11219922 DOI: 10.1038/s41467-024-49912-8] [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: 07/09/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, HiTE has identified numerous novel transposons with well-defined structures containing protein-coding domains, some of which are directly inserted within crucial genes, leading to direct alterations in gene expression. A Nextflow version of HiTE is also available, with enhanced parallelism, reproducibility, and portability.
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Affiliation(s)
- Kang Hu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Peng Ni
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Minghua Xu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - You Zou
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Jianye Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center of Excellence on Smart Health, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yaohang Li
- Department of Computer Science, Old Dominion University, Norfolk, VA, 23529, USA
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Bin Hu
- Key Laboratory of Brain Health Intelligent Evaluation and Intervention, Ministry of Education (Beijing Institute of Technology), Beijing, P. R. China.
- School of Medical Technology, Beijing Institute of Technology, Beijing, P. R. China.
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
- Xiangjiang Laboratory, Changsha, 410205, China.
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China.
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3
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Barro-Trastoy D, Köhler C. Helitrons: genomic parasites that generate developmental novelties. Trends Genet 2024; 40:437-448. [PMID: 38429198 DOI: 10.1016/j.tig.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.
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Affiliation(s)
- Daniela Barro-Trastoy
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Claudia Köhler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden.
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4
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Cuello C, Jansen HJ, Abdallah C, Zamar Mbadinga DL, Birer Williams C, Durand M, Oudin A, Papon N, Giglioli-Guivarc'h N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism. Heliyon 2024; 10:e28078. [PMID: 38533072 PMCID: PMC10963385 DOI: 10.1016/j.heliyon.2024.e28078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Specialized metabolites possess diverse interesting biological activities and some cardenolides- and monoterpene indole alkaloids- (MIAs) derived pharmaceuticals are currently used to treat human diseases such as cancers or hypertension. While these two families of biocompounds are produced by specific subfamilies of Apocynaceae, one member of this medicinal plant family, the succulent tree Pachypodium lamerei Drake (also known as Madagascar palm), does not produce such specialized metabolites. To explore the evolutionary paths that have led to the emergence and loss of cardenolide and MIA biosynthesis in Apocynaceae, we sequenced and assembled the P. lamerei genome by combining Oxford Nanopore Technologies long-reads and Illumina short-reads. Phylogenomics revealed that, among the Apocynaceae whose genomes have been sequenced, the Madagascar palm is so far the species closest to the common ancestor between MIA producers/non-MIA producers. Transposable elements, constituting 72.48% of the genome, emerge as potential key players in shaping genomic architecture and influencing specialized metabolic pathways. The absence of crucial MIA biosynthetic genes such as strictosidine synthase in P. lamerei and non-Rauvolfioideae species hints at a transposon-mediated mechanism behind gene loss. Phylogenetic analysis not only showcases the evolutionary divergence of specialized metabolite biosynthesis within Apocynaceae but also underscores the role of transposable elements in this intricate process. Moreover, we shed light on the low conservation of enzymes involved in the final stages of MIA biosynthesis in the distinct MIA-producing plant families, inferring independent gains of these specialized enzymes along the evolution of these medicinal plant clades. Overall, this study marks a leap forward in understanding the genomic dynamics underpinning the evolution of specialized metabolites biosynthesis in the Apocynaceae family, with transposons emerging as potential architects of genomics restructuring and gene loss.
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Affiliation(s)
- Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Hans J. Jansen
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Cécile Abdallah
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | | | - Ron P. Dirks
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
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5
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Xu MRX, Liao ZY, Brock JR, Du K, Li GY, Chen ZQ, Wang YH, Gao ZN, Agarwal G, Wei KHC, Shao F, Pang S, Platts AE, van de Velde J, Lin HM, Teresi SJ, Bird K, Niederhuth CE, Xu JG, Yu GH, Yang JY, Dai SF, Nelson A, Braasch I, Zhang XG, Schartl M, Edger PP, Han MJ, Zhang HH. Maternal dominance contributes to subgenome differentiation in allopolyploid fishes. Nat Commun 2023; 14:8357. [PMID: 38102128 PMCID: PMC10724154 DOI: 10.1038/s41467-023-43740-y] [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: 02/16/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.
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Affiliation(s)
- Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhen-Yang Liao
- 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, China
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Guo-Yin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | | | - Ying-Hao Wang
- 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, China
| | - Zhong-Nan Gao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University, School of Life Sciences, Chongqing, China
| | | | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Jozefien van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hong-Min Lin
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kevin Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jin-Gen Xu
- Jiujiang Academy of Agricultural Sciences, Jiujiang, China
| | - Guo-Hua Yu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Jian-Yuan Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Si-Fa Dai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | | | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bayern, Germany.
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
| | - Min-Jin Han
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China.
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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6
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Szymanski M, Maurya A, Kopec P, Karlowski WM. tRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana. BMC PLANT BIOLOGY 2023; 23:623. [PMID: 38057711 DOI: 10.1186/s12870-023-04632-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/25/2023] [Indexed: 12/08/2023]
Abstract
Although most of the genes encoding tRNAs in plants are dispersed throughout the genome, a fraction of them form tRNA gene clusters. In Arabidopsis thaliana, the smallest of tRNA clusters on chromosome 5 consists of four tRNA-Cys-GCA genes placed within repeating units of 0.4 kbp. A systematic analysis of the genomic sequences of syntenic regions from various ecotypes of A. thaliana showed that the general structure of the cluster, consisting of a tRNA-Cys pseudogene followed by repeating units containing tRNA-Cys genes, is well conserved. However, there is significant heterogeneity in the number of repeating units between different ecotypes. A unique feature of this cluster is the presence of putative transposable elements (Helitron). In addition, two further tRNA-Cys gene mini-clusters (gene pairs) in A. thaliana were identified. RNA-seq-based evaluation of expression of tRNA-Cys-GCA genes showed a positive signal for 11 out of 13 unique transcripts. An analysis of the conservation of the tRNA-Cys clusters from A. thaliana with the corresponding regions from four other Arabidopsis species suggests a sequence of events that led to the divergence of these regions.
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Affiliation(s)
- Maciej Szymanski
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Anand Maurya
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Piotr Kopec
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland.
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7
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Ouadi S, Sierro N, Kessler F, Ivanov NV. Chromosome-scale assemblies of S. malaccense, S. aqueum, S. jambos, and S. syzygioides provide insights into the evolution of Syzygium genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1248780. [PMID: 37868305 PMCID: PMC10587690 DOI: 10.3389/fpls.2023.1248780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/28/2023] [Indexed: 10/24/2023]
Abstract
Syzygium is a large and diverse tree genus in the Myrtaceae family. Genome assemblies for clove (Syzygium aromaticum, 370 Mb) and sea apple (Syzygium grande, 405 Mb) provided the first insights into the genomic features and evolution of the Syzygium genus. Here, we present additional de novo chromosome-scale genome assemblies for Syzygium malaccense, Syzygium aqueum, Syzygium jambos, and Syzygium syzygioides. Genome profiling analyses show that S. malaccense, like S. aromaticum and S. grande, is diploid (2n = 2x = 22), while the S. aqueum, S. jambos, and S. syzygioides specimens are autotetraploid (2n = 4x = 44). The genome assemblies of S. malaccense (430 Mb), S. aqueum (392 Mb), S. jambos (426 Mb), and S. syzygioides (431 Mb) are highly complete (BUSCO scores of 98%). Comparative genomics analyses showed conserved organization of the 11 chromosomes with S. aromaticum and S. grande, and revealed species-specific evolutionary dynamics of the long terminal repeat retrotransposon elements belonging to the Gypsy and Copia lineages. This set of Syzygium genomes is a valuable resource for future structural and functional comparative genomic studies on Myrtaceae species.
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Affiliation(s)
- Sonia Ouadi
- Faculty of Sciences, Laboratory of Plant Physiology, University of Neuchâtel, Neuchâtel, Switzerland
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Felix Kessler
- Faculty of Sciences, Laboratory of Plant Physiology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- Faculty of Sciences, Laboratory of Plant Physiology, University of Neuchâtel, Neuchâtel, Switzerland
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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8
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Burkes-Patton S, Cooper EA, Schlueter J. RepBox: a toolbox for the identification of repetitive elements. BMC Bioinformatics 2023; 24:317. [PMID: 37608271 PMCID: PMC10463291 DOI: 10.1186/s12859-023-05419-5] [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: 08/05/2021] [Accepted: 07/18/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are short, mobile DNA elements that are known to play important roles in the genomes of many eukaryotic species. The identification and categorization of these elements is a critical task for many genomic studies, and the continued increase in the number of de novo assembled genomes demands new tools to improve the efficiency of this process. For this reason, we developed RepBox, a suite of Python scripts that combine several pre-existing family-specific TE detection methods into a single user-friendly pipeline. RESULTS Based on comparisons of RepBox with the standard TE detection software RepeatModeler, we find that RepBox consistently classifies more elements and is also able to identify a more diverse array of TE families than the existing methods in plant genomes. CONCLUSIONS The performance of RepBox on two different plant genomes indicates that our toolbox represents a significant improvement over existing TE detection methods, and should facilitate future TE annotation efforts in additional species.
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Affiliation(s)
- Shelvasha Burkes-Patton
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Elizabeth A Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
- North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Jessica Schlueter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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9
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Samelak-Czajka A, Wojciechowski P, Marszalek-Zenczak M, Figlerowicz M, Zmienko A. Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes. Funct Integr Genomics 2023; 23:120. [PMID: 37036577 PMCID: PMC10085913 DOI: 10.1007/s10142-023-01043-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/11/2023]
Abstract
MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental and physiological processes. The roles of the nonconserved MIRs-which are MIRs restricted to one plant family, genus, or even species-are less recognized; however, many of them participate in the responses to biotic and abiotic stresses. Both over- and underproduction of miRNAs may influence various biological processes. Consequently, maintaining intracellular miRNA homeostasis seems to be crucial for the organism. Deletions and duplications in the genomic sequence may alter gene dosage and/or activity. We evaluated the extent of copy number variations (CNVs) among Arabidopsis thaliana (Arabidopsis) MIRs in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIRs were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIRs presented moderate variation. Transposon-derived MIRs displayed exceptionally high diversity. Conversely, MIRs involved in the epigenetic control of transposons reactivated during development were mostly invariable. MIR overlap with the protein-coding genes also limited their variability. At the expression level, a higher rate of nonvariable, nonconserved miRNAs was detectable in Col-0 leaves, inflorescence, and siliques compared to nonconserved variable miRNAs, although the expression of both groups was much lower than that of the conserved MIRs. Our data indicate that CNV rate of Arabidopsis MIRs is related with their age, function, and genomic localization.
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Affiliation(s)
- Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, 60-965, Poznan, Poland
| | | | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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10
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Li C, Cong C, Liu F, Yu Q, Zhan Y, Zhu L, Li Y. Abundance of Transgene Transcript Variants Associated with Somatically Active Transgenic Helitrons from Multiple T-DNA Integration Sites in Maize. Int J Mol Sci 2023; 24:ijms24076574. [PMID: 37047545 PMCID: PMC10095026 DOI: 10.3390/ijms24076574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Helitrons, a novel type of mysterious DNA transposons discovered computationally prior to bench work confirmation, are components ubiquitous in most sequenced genomes of various eukaryotes, including plants, animals, and fungi. There is a paucity of empirical evidence to elucidate the mechanism of Helitrons transposition in plants. Here, by constructing several artificial defective Helitron (dHel) reporter systems, we aim to identify the autonomous Helitrons (aHel) in maize genetically and to demonstrate the transposition and repair mechanisms of Helitrons upon the dHel-GFP excision in maize. When crossing with various inbred lines, several transgenic lines produced progeny of segregated, purple-blotched kernels, resulting from a leaky expression of the C1 gene driven by the dHel-interrupted promoter. Transcription analysis indicated that the insertion of different dHels into the C1 promoter or exon would lead to multiple distinct mRNA transcripts corresponding to transgenes in the host genome. Simple excision products and circular intermediates of dHel-GFP transposition have been detected from the leaf tissue of the seedlings in F1 hybrids of transgenic lines with corresponding c1 tester, although they failed to be detected in all primary transgenic lines. These results revealed the transposition and repair mechanism of Helitrons in maize. It is strongly suggested that this reporter system can detect the genetic activity of autonomic Helitron at the molecular level. Sequence features of dHel itself, together with the flanking regions, impact the excision activity of dHel and the regulation of the dHel on the transcription level of the host gene.
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Affiliation(s)
- Chuxi Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunsheng Cong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fangyuan Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qian Yu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yuan Zhan
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yubin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
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11
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Takeuchi T, Suzuki Y, Watabe S, Nagai K, Masaoka T, Fujie M, Kawamitsu M, Satoh N, Myers EW. A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. DNA Res 2022; 29:dsac035. [PMID: 36351462 PMCID: PMC9646362 DOI: 10.1093/dnares/dsac035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 07/30/2023] Open
Abstract
Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.
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Affiliation(s)
| | - Yoshihiko Suzuki
- Present address: Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Sagamihara, Kanagawa, Japan
| | - Kiyohito Nagai
- Pearl Research Institute, K. MIKIMOTO & CO., LTD, Shima, Mie, Japan
| | - Tetsuji Masaoka
- Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Tamaki, Mie, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Eugene W Myers
- Algorithms for Eco and Evo Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
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12
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Martin SL, Lujan Toro B, James T, Sauder CA, Laforest M. Insights from the genomes of 4 diploid Camelina spp. G3 (BETHESDA, MD.) 2022; 12:jkac182. [PMID: 35976116 PMCID: PMC9713399 DOI: 10.1093/g3journal/jkac182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 06/12/2022] [Indexed: 11/12/2022]
Abstract
Plant evolution has been a complex process involving hybridization and polyploidization making understanding the origin and evolution of a plant's genome challenging even once a published genome is available. The oilseed crop, Camelina sativa (Brassicaceae), has a fully sequenced allohexaploid genome with 3 unknown ancestors. To better understand which extant species best represent the ancestral genomes that contributed to C. sativa's formation, we sequenced and assembled chromosome level draft genomes for 4 diploid members of Camelina: C. neglecta C. hispida var. hispida, C. hispida var. grandiflora, and C. laxa using long and short read data scaffolded with proximity data. We then conducted phylogenetic analyses on regions of synteny and on genes described for Arabidopsis thaliana, from across each nuclear genome and the chloroplasts to examine evolutionary relationships within Camelina and Camelineae. We conclude that C. neglecta is closely related to C. sativa's sub-genome 1 and that C. hispida var. hispida and C. hispida var. grandiflora are most closely related to C. sativa's sub-genome 3. Further, the abundance and density of transposable elements, specifically Helitrons, suggest that the progenitor genome that contributed C. sativa's sub-genome 3 maybe more similar to the genome of C. hispida var. hispida than that of C. hispida var. grandiflora. These diploid genomes show few structural differences when compared to C. sativa's genome indicating little change to chromosome structure following allopolyploidization. This work also indicates that C. neglecta and C. hispida are important resources for understanding the genetics of C. sativa and potential resources for crop improvement.
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Affiliation(s)
- Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0CA, Canada
| | - Beatriz Lujan Toro
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0CA, Canada
| | - Tracey James
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0CA, Canada
| | - Connie A Sauder
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0CA, Canada
| | - Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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13
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Yim WC, Swain ML, Ma D, An H, Bird KA, Curdie DD, Wang S, Ham HD, Luzuriaga-Neira A, Kirkwood JS, Hur M, Solomon JKQ, Harper JF, Kosma DK, Alvarez-Ponce D, Cushman JC, Edger PP, Mason AS, Pires JC, Tang H, Zhang X. The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome. THE PLANT CELL 2022; 34:4143-4172. [PMID: 35961044 PMCID: PMC9614464 DOI: 10.1093/plcell/koac249] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/24/2022] [Indexed: 05/05/2023]
Abstract
Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.
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Affiliation(s)
| | | | - Dongna Ma
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - David D Curdie
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Samuel Wang
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Hyun Don Ham
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Juan K Q Solomon
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada, Reno, Nevada 89557, USA
| | - Jeffrey F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Annaliese S Mason
- Plant Breeding Department, INRES, The University of Bonn, Bonn 53115, Germany
| | - J Chris Pires
- Division of Biological Sciences, Bond Life Sciences Center, , University of Missouri, Columbia, Missouri 65211, USA
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
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14
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Depotter JRL, Ökmen B, Ebert MK, Beckers J, Kruse J, Thines M, Doehlemann G. High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens. Microbiol Spectr 2022; 10:e0034922. [PMID: 35972267 PMCID: PMC9603552 DOI: 10.1128/spectrum.00349-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated with the mating-type locus sizes, which is up to ~560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results in substitutions that often lead to amino acid alterations. IMPORTANCE Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. They also impact genome evolution as their repetitive nature facilitates nonhomologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, Ustilago hordei. This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. We hypothesize that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.
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Affiliation(s)
- J. R. L. Depotter
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - B. Ökmen
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - M. K. Ebert
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Beckers
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Kruse
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - G. Doehlemann
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
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15
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Yu L, Huang T, Qi X, Yu J, Wu T, Luo Z, Zhou L, Li Y. Genome-Wide Analysis of Long Non-coding RNAs Involved in Nodule Senescence in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:917840. [PMID: 35707611 PMCID: PMC9189404 DOI: 10.3389/fpls.2022.917840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Plant long non-coding RNAs (lncRNAs) are widely accepted to play crucial roles during diverse biological processes. In recent years, thousands of lncRNAs related to the establishment of symbiosis, root nodule organogenesis and nodule development have been identified in legumes. However, lncRNAs involved in nodule senescence have not been reported. In this study, senescence-related lncRNAs were investigated in Medicago truncatula nodules by high-throughput strand-specific RNA-seq. A total of 4576 lncRNAs and 126 differentially expressed lncRNAs (DElncRNAs) were identified. We found that more than 60% lncRNAs were associated with transposable elements, especially TIR/Mutator and Helitron DNA transposons families. In addition, 49 DElncRNAs were predicted to be the targets of micro RNAs. Functional analysis showed that the largest sub-set of differently expressed target genes of DElncRNAs were associated with the membrane component. Of these, nearly half genes were related to material transport, suggesting that an important function of DElncRNAs during nodule senescence is the regulation of substance transport across membranes. Our findings will be helpful for understanding the functions of lncRNAs in nodule senescence and provide candidate lncRNAs for further research.
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16
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Cho A, Jang H, Baek S, Kim MJ, Yim B, Huh S, Kwon SH, Yu HJ, Mun JH. An improved Raphanus sativus cv. WK10039 genome localizes centromeres, uncovers variation of DNA methylation and resolves arrangement of the ancestral Brassica genome blocks in radish chromosomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1731-1750. [PMID: 35249126 DOI: 10.1007/s00122-022-04066-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
This study presents an improved genome of Raphanus sativus cv. WK10039 uncovering centromeres and differentially methylated regions of radish chromosomes. Comprehensive genome comparison of radish and diploid Brassica species of U's triangle reveals that R. sativus arose from the Brassica B genome lineage and is a sibling species of B. nigra. Radish (Raphanus sativus L.) is a key root vegetable crop closely related to the Brassica crop species of the family Brassicaceae. We reported a draft genome of R. sativus cv. WK10039 (Rs1.0), which had 54.6 Mb gaps. To study the radish genome and explore previously unknown regions, we generated an improved genome assembly (Rs2.0) by long-read sequencing and high-resolution genome-wide mapping of chromatin interactions. Rs2.0 was 434.9 Mb in size with 0.27 Mb gaps, and the N50 scaffold length was 37.3 Mb (40-fold larger assembly compared to Rs1.0). Approximately 38% of Rs2.0 was comprised of repetitive sequences, and 52,768 protein-coding genes and 4845 non-protein-coding genes were predicted and annotated. The improved contiguity and coverage of Rs2.0, along with the detection of highly methylated regions, enabled localization of centromeres where R. sativus-specific centromere-associated repeats, full-length OTA and CRM LTR-Gypsy retrotransposons, hAT-Ac, CMC-EnSpm and Helitron DNA transposons, and sequences highly homologous to B. nigra centromere-specific CENH3-associated CL sequences were enriched. Whole-genome bisulfite sequencing combined with mRNA sequencing identified differential epigenetic marks in the radish genome related to tissue development. Synteny comparison and genomic distance analysis of radish and three diploid Brassica species of U's triangle suggested that the radish genome arose from the Brassica B genome lineage through unique rearrangement of the triplicated ancestral Brassica genome after splitting of the Brassica A/C and B genomes.
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Affiliation(s)
- Ara Cho
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Hoyeol Jang
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Seunghoon Baek
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Moon-Jin Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Bomi Yim
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Sunmi Huh
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Song-Hwa Kwon
- Department of Mathematics, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Hee-Ju Yu
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, Korea.
| | - Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea.
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17
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Storer JM, Hubley R, Rosen J, Smit AFA. Methodologies for the De novo Discovery of Transposable Element Families. Genes (Basel) 2022; 13:709. [PMID: 35456515 PMCID: PMC9025800 DOI: 10.3390/genes13040709] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023] Open
Abstract
The discovery and characterization of transposable element (TE) families are crucial tasks in the process of genome annotation. Careful curation of TE libraries for each organism is necessary as each has been exposed to a unique and often complex set of TE families. De novo methods have been developed; however, a fully automated and accurate approach to the development of complete libraries remains elusive. In this review, we cover established methods and recent developments in de novo TE analysis. We also present various methodologies used to assess these tools and discuss opportunities for further advancement of the field.
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Affiliation(s)
| | | | | | - Arian F. A. Smit
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.M.S.); (R.H.); (J.R.)
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18
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Finding and Characterizing Repeats in Plant Genomes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2443:327-385. [PMID: 35037215 DOI: 10.1007/978-1-0716-2067-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Plant genomes contain a particularly high proportion of repeated structures of various types. This chapter proposes a guided tour of the available software that can help biologists to scan automatically for these repeats in sequence data or check hypothetical models intended to characterize their structures. Since transposable elements (TEs) are a major source of repeats in plants, many methods have been used or developed for this broad class of sequences. They are representative of the range of tools available for other classes of repeats and we have provided two sections on this topic (for the analysis of genomes or directly of sequenced reads), as well as a selection of the main existing software. It may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of an efficient search for repeats and more complex patterns. We first introduce the key concepts of the art of indexing and mapping or querying sequences. We end the chapter with the more prospective issue of building models of repeat families. We present the Machine Learning approach first, seeking to build predictors automatically for some families of ET, from a set of sequences known to belong to this family. A second approach, the linguistic (or syntactic) approach, allows biologists to describe themselves and check the validity of models of their favorite repeat family.
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19
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Bayer PE, Scheben A, Golicz AA, Yuan Y, Faure S, Lee H, Chawla HS, Anderson R, Bancroft I, Raman H, Lim YP, Robbens S, Jiang L, Liu S, Barker MS, Schranz ME, Wang X, King GJ, Pires JC, Chalhoub B, Snowdon RJ, Batley J, Edwards D. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2488-2500. [PMID: 34310022 PMCID: PMC8633514 DOI: 10.1111/pbi.13674] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/11/2021] [Accepted: 07/20/2021] [Indexed: 05/26/2023]
Abstract
Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Armin Scheben
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVICAustralia
| | - Yuxuan Yuan
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - HueyTyng Lee
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Harmeet Singh Chawla
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Robyn Anderson
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural Institute, PMBWagga WaggaNSWAustralia
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeonSouth Korea
| | | | - Lixi Jiang
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Shengyi Liu
- Chinese Academy of Agricultural SciencesOil Crops Research InstituteWuhanChina
| | - Michael S. Barker
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - M. Eric Schranz
- Biosystematics GroupWageningen University and Research CenterWageningenThe Netherlands
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences (IVF, CAAS)BeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - J. Chris Pires
- Division of Biological SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Boulos Chalhoub
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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20
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Dash L, McEwan RE, Montes C, Mejia L, Walley JW, Dilkes BP, Kelley DR. slim shady is a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201. PLANT DIRECT 2021; 5:e00326. [PMID: 34136747 PMCID: PMC8197431 DOI: 10.1002/pld3.326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/22/2021] [Indexed: 05/06/2023]
Abstract
Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin, rapid changes in transcript and protein abundance occur in hypocotyls, and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin-regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we called slim shady, in an annotated insertion line in IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR). Overexpression of the IRR gene failed to rescue the slim shady phenotype and characterization of a second T-DNA allele of IRR found that it had a wild-type (WT) hypocotyl length. The slim shady mutant has an elevated expression of numerous genes associated with the brassinosteroid-auxin-phytochrome (BAP) regulatory module compared to WT, including transcription factors that regulate brassinosteroid, auxin, and phytochrome pathways. Additionally, slim shady seedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence data and genetic complementation analysis with SALK_015201C, we determined that a novel single nucleotide polymorphism in PHYTOCHROME B was responsible for the slim shady phenotype. This is predicted to induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase-related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses with phyb-9 confirmed that slim shady is a mutant allele of PHYB. This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin-dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-DNA stocks.
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Affiliation(s)
- Linkan Dash
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
| | - Robert E. McEwan
- Center for Plant BiologyPurdue UniversityWest LafayettINUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayettINUSA
| | - Christian Montes
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Ludvin Mejia
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
| | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Brian P. Dilkes
- Center for Plant BiologyPurdue UniversityWest LafayettINUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayettINUSA
- Department of BiochemistryPurdue UniversityWest LafayettINUSA
| | - Dior R. Kelley
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
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Qi H, Li L, Zhang G. Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas. Mol Ecol Resour 2021; 21:1670-1685. [PMID: 33655634 DOI: 10.1111/1755-0998.13368] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022]
Abstract
The Pacific oyster (Crassostrea gigas) is a widely distributed marine bivalve of great ecological and economic importance. In this study, we provide a high-quality chromosome-level genome assembled using Pacific Bioscience long reads and Hi-C-based and linkage-map-based scaffolding technologies and a high-resolution variation map constructed using large-scale resequencing analysis. The 586.8 Mb genome consists of 10 pseudochromosome sequences ranging from 38.6 to 78.9 Mb, containing 301 contigs with an N50 size of 3.1 Mb. A total of 30,078 protein-coding genes were predicted, of which 22,757 (75.7%) were high-reliability annotations supported by a homologous match to a curated protein in the SWISS-PROT database or transcript expression. Although a medium level of repeat components (57.2%) was detected, the genomic content of the segmental duplications reached 26.2%, which is the highest among the reported genomes. By whole genome resequencing analysis of 495 Pacific oysters, a comprehensive variation map was built, comprised of 4.78 million single nucleotide polymorphisms, 0.60 million short insertions and deletions, and 49,333 copy number variation regions. The structural variations can lead to an average interindividual genomic divergence of 0.21, indicating their crucial role in shaping the Pacific oyster genome diversity. The large amount of mosaic distributed repeat elements, small variations, and copy number variations indicate that the Pacific oyster is a diploid organism with an extremely high genomic complexity at the intra- and interindividual level. The genome and variation maps can improve our understanding of oyster genome diversity and enrich the resources for oyster molecular evolution, comparative genomics, and genetic research.
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Affiliation(s)
- Haigang Qi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
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22
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Nowak MD, Birkeland S, Mandáková T, Roy Choudhury R, Guo X, Gustafsson ALS, Gizaw A, Schrøder‐Nielsen A, Fracassetti M, Brysting AK, Rieseberg L, Slotte T, Parisod C, Lysak MA, Brochmann C. The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. Mol Ecol Resour 2021; 21:661-676. [PMID: 33058468 PMCID: PMC7983928 DOI: 10.1111/1755-0998.13280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/26/2020] [Accepted: 10/09/2020] [Indexed: 01/04/2023]
Abstract
The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
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Affiliation(s)
| | | | | | | | - Xinyi Guo
- CEITECMasaryk UniversityBrnoCzech Republic
| | | | - Abel Gizaw
- Natural History MuseumUniversity of OsloOsloNorway
| | | | - Marco Fracassetti
- Science for Life Laboratory and Department of EcologyEnvironment and Plant ScienceStockholm UniversityStockholmSweden
| | - Anne K. Brysting
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | - Loren Rieseberg
- Department of BotanyThe University of British ColumbiaVancouverBCCanada
| | - Tanja Slotte
- Science for Life Laboratory and Department of EcologyEnvironment and Plant ScienceStockholm UniversityStockholmSweden
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23
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Peñaloza C, Gutierrez AP, Eöry L, Wang S, Guo X, Archibald AL, Bean TP, Houston RD. A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas. Gigascience 2021; 10:6187865. [PMID: 33764468 PMCID: PMC7992393 DOI: 10.1093/gigascience/giab020] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/10/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
Background The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas. Findings High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome. Conclusions This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture.
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Affiliation(s)
- Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Alejandro P Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Lél Eöry
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Shan Wang
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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24
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Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs. Biochem Soc Trans 2021; 48:1005-1017. [PMID: 32573687 PMCID: PMC7329337 DOI: 10.1042/bst20190937] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) constitute major fractions of plant genomes. Their potential to be mobile provides them with the capacity to cause major genome rearrangements. Those effects are potentially deleterious and enforced the evolution of epigenetic suppressive mechanisms controlling TE activity. However, beyond their deleterious effects, TE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. Indeed, TEs are increasingly recognized as major drivers of evolutionary novelties by regulating the expression of nearby genes. TEs frequently contain binding motifs for transcription factors and capture binding motifs during transposition, which they spread through the genome by transposition. Thus, TEs drive the evolution and diversification of gene regulatory networks by recruiting lineage-specific targets under the regulatory control of specific transcription factors. This process can explain the rapid and repeated evolution of developmental novelties, such as C4 photosynthesis and a wide spectrum of stress responses in plants. It also underpins the convergent evolution of embryo nourishing tissues, the placenta in mammals and the endosperm in flowering plants. Furthermore, the gene regulatory network underlying flower development has also been largely reshaped by TE-mediated recruitment of regulatory elements; some of them being preserved across long evolutionary timescales. In this review, we highlight the potential role of TEs as evolutionary toolkits in plants by showcasing examples of TE-mediated evolutionary novelties.
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