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Zou LH, Zhu B, Chen Y, Lu Y, Ramkrishnan M, Xu C, Zhou X, Ding Y, Cho J, Zhou M. Genetic and epigenetic reprogramming in response to internal and external cues by induced transposon mobilization in Moso bamboo. THE NEW PHYTOLOGIST 2024. [PMID: 39238152 DOI: 10.1111/nph.20107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/21/2024] [Indexed: 09/07/2024]
Abstract
Long terminal repeat retroelements (LTR-REs) have profound effects on DNA methylation and gene regulation. Despite the vast abundance of LTR-REs in the genome of Moso bamboo (Phyllostachys edulis), an industrial crop in underdeveloped countries, their precise implication of the LTR-RE mobility in stress response and development remains unknown. We investigated the RNA and DNA products of LTR-REs in Moso bamboo under various developmental stages and stressful conditions. Surprisingly, our analyses identified thousands of active LTR-REs, particularly those located near genes involved in stress response and developmental regulation. These genes adjacent to active LTR-REs exhibited an increased expression under stress and are associated with reduced DNA methylation that is likely affected by the induced LTR-REs. Moreover, the analyses of simultaneous mapping of insertions and DNA methylation showed that the LTR-REs effectively alter the epigenetic status of the genomic regions where they inserted, and concomitantly their transcriptional competence which might impact the stress resilience and growth of the host. Our work unveils the unusually strong LTR-RE mobility in Moso bamboo and its close association with (epi)genetic changes, which supports the co-evolution of the parasitic DNAs and host genome in attaining stress tolerance and developmental robustness.
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Affiliation(s)
- Long-Hai Zou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Bailiang Zhu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yaxin Chen
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yaping Lu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Muthusamy Ramkrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Chao Xu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Xiaohong Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yiqian Ding
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
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Horvath R, Minadakis N, Bourgeois Y, Roulin AC. The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role. eLife 2024; 12:RP93284. [PMID: 38606833 PMCID: PMC11014726 DOI: 10.7554/elife.93284] [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] [Indexed: 04/13/2024] Open
Abstract
Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.
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Affiliation(s)
- Robert Horvath
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRDMontpellierFrance
- University of PortsmouthPortsmouthUnited Kingdom
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
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3
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Gozashti L, Hartl DL, Corbett-Detig R. Universal signatures of transposable element compartmentalization across eukaryotic genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.17.562820. [PMID: 38585780 PMCID: PMC10996525 DOI: 10.1101/2023.10.17.562820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The evolutionary mechanisms that drive the emergence of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the massive accumulation of genome assemblies spanning phylogenetic diversity1,2. Transposable elements (TEs) are a rich source of large-effect mutations since they directly and indirectly drive genomic structural variation and changes in gene expression3. Here, we demonstrate universal patterns of TE compartmentalization across eukaryotic genomes spanning ~1.7 billion years of evolution, in which TEs colocalize with gene families under strong predicted selective pressure for dynamic evolution and involved in specific functions. For non-pathogenic species these genes represent families involved in defense, sensory perception and environmental interaction, whereas for pathogenic species, TE-compartmentalized genes are highly enriched for pathogenic functions. Many TE-compartmentalized gene families display signatures of positive selection at the molecular level. Furthermore, TE-compartmentalized genes exhibit an excess of high-frequency alleles for polymorphic TE insertions in fruit fly populations. We postulate that these patterns reflect selection for adaptive TE insertions as well as TE-associated structural variants. This process may drive the emergence of a shared TE-compartmentalized genome architecture across diverse eukaryotic lineages.
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Affiliation(s)
- Landen Gozashti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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4
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Kato S, Arakaki S, Nagano AJ, Kikuchi K, Hirase S. Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes. Mol Ecol 2023. [PMID: 38047388 DOI: 10.1111/mec.17216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/23/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.
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Affiliation(s)
- Shuya Kato
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Seiji Arakaki
- Amakusa Marine Biological Laboratory, Kyushu University, Amakusa, Kumamoto, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Ōtsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
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5
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Duhamel M, Hood ME, Rodríguez de la Vega RC, Giraud T. Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi. Nat Commun 2023; 14:5692. [PMID: 37709766 PMCID: PMC10502011 DOI: 10.1038/s41467-023-41413-4] [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: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
In the absence of recombination, the number of transposable elements (TEs) increases due to less efficient selection, but the dynamics of such TE accumulations are not well characterized. Leveraging a dataset of 21 independent events of recombination cessation of different ages in mating-type chromosomes of Microbotryum fungi, we show that TEs rapidly accumulated in regions lacking recombination, but that TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 million years following recombination suppression. The same TE superfamilies have expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements (Helitrons). Long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies also expanded, through transposition bursts (distinguished from gene conversion based on LTR divergence), with both non-recombining regions and autosomes affected, suggesting that non-recombining regions constitute TE reservoirs. This study improves our knowledge of genome evolution by showing that TEs can accumulate through bursts, following non-linear decelerating dynamics.
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Affiliation(s)
- Marine Duhamel
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France.
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
| | - Michael E Hood
- Department of Biology, Amherst College, 01002-5000, Amherst, MA, USA
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
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Wells JN, Chang NC, McCormick J, Coleman C, Ramos N, Jin B, Feschotte C. Transposable elements drive the evolution of metazoan zinc finger genes. Genome Res 2023; 33:1325-1339. [PMID: 37714714 PMCID: PMC10547256 DOI: 10.1101/gr.277966.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/15/2023] [Indexed: 09/17/2023]
Abstract
Cys2-His2 zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. ZNF evolution is highly dynamic and characterized by the rapid expansion and contraction of numerous subfamilies across the animal phylogeny. The forces and mechanisms underlying rapid ZNF evolution remain poorly understood, but there is growing evidence that, in tetrapods, the targeting and repression of lineage-specific transposable elements (TEs) plays a critical role in the evolution of the Krüppel-associated box ZNF (KZNF) subfamily. Currently, it is unknown whether this function and coevolutionary relationship is unique to KZNFs or is a broader feature of metazoan ZNFs. Here, we present evidence that genomic conflict with TEs has been a central driver of the diversification of ZNFs in animals. Sampling from 3221 genome assemblies, we show that the copy number of retroelements correlates with that of ZNFs across at least 750 million years of metazoan evolution. Using computational predictions, we show that ZNFs preferentially bind TEs in diverse animal species. We further investigate the largest ZNF subfamily found in cyprinid fish, which is characterized by a conserved sequence we dubbed the fish N-terminal zinc finger-associated (FiNZ) domain. Zebrafish possess approximately 700 FiNZ-ZNFs, many of which are evolving adaptively under positive selection. Like mammalian KZNFs, most zebrafish FiNZ-ZNFs are expressed at the onset of zygotic genome activation, and blocking their translation using morpholinos during early embryogenesis results in derepression of transcriptionally active TEs. Together, these data suggest that ZNF diversification has been intimately connected to TE expansion throughout animal evolution.
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Affiliation(s)
- Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA;
| | - Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - John McCormick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Caitlyn Coleman
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, USA
| | - Nathalie Ramos
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Bozhou Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA;
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7
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Jiang X, Li D, Du H, Wang P, Guo L, Zhu G, Zhang C. Genomic features of meiotic crossovers in diploid potato. HORTICULTURE RESEARCH 2023; 10:uhad079. [PMID: 37323232 PMCID: PMC10261879 DOI: 10.1093/hr/uhad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/13/2023] [Indexed: 06/17/2023]
Abstract
Meiotic recombination plays an important role in genome evolution and crop improvement. Potato (Solanum tuberosum L.) is the most important tuber crop in the world, but research about meiotic recombination in potato is limited. Here, we resequenced 2163 F2 clones derived from five different genetic backgrounds and identified 41 945 meiotic crossovers. Some recombination suppression in euchromatin regions was associated with large structural variants. We also detected five shared crossover hotspots. The number of crossovers in each F2 individual from the accession Upotato 1 varied from 9 to 27, with an average of 15.5, 78.25% of which were mapped within 5 kb of their presumed location. We show that 57.1% of the crossovers occurred in gene regions, with poly-A/T, poly-AG, AT-rich, and CCN repeats enriched in the crossover intervals. The recombination rate is positively related with gene density, SNP density, Class II transposon, and negatively related with GC density, repeat sequence density and Class I transposon. This study deepens our understanding of meiotic crossovers in potato and provides useful information for diploid potato breeding.
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Affiliation(s)
- Xiuhan Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of 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, Guangdong 518120, China
| | - Dawei Li
- Shenzhen Branch, Guangdong Laboratory of 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, Guangdong 518120, China
| | - Hui Du
- Shenzhen Branch, Guangdong Laboratory of 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, Guangdong 518120, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of 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, Guangdong 518120, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangtao Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
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Palahí I Torres A, Höök L, Näsvall K, Shipilina D, Wiklund C, Vila R, Pruisscher P, Backström N. The fine-scale recombination rate variation and associations with genomic features in a butterfly. Genome Res 2023; 33:810-823. [PMID: 37308293 PMCID: PMC10317125 DOI: 10.1101/gr.277414.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/03/2023] [Indexed: 06/14/2023]
Abstract
Recombination is a key molecular mechanism that has profound implications on both micro- and macroevolutionary processes. However, the determinants of recombination rate variation in holocentric organisms are poorly understood, in particular in Lepidoptera (moths and butterflies). The wood white butterfly (Leptidea sinapis) shows considerable intraspecific variation in chromosome numbers and is a suitable system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole-genome resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed that larger chromosomes had a bimodal recombination landscape, potentially caused by interference between simultaneous chiasmata. The recombination rate was significantly lower in subtelomeric regions, with exceptions associated with segregating chromosome rearrangements, showing that fissions and fusions can have considerable effects on the recombination landscape. There was no association between the inferred recombination rate and base composition, supporting a limited influence of GC-biased gene conversion in butterflies. We found significant but variable associations between the recombination rate and the density of different classes of transposable elements, most notably a significant enrichment of short interspersed nucleotide elements in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity in recombination coldspots, potentially indicating that expression of transferases can inhibit formation of chiasmata during meiotic division. Our results provide novel information about recombination rate variation in holocentric organisms and have particular implications for forthcoming research in population genetics, molecular/genome evolution, and speciation.
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Affiliation(s)
- Aleix Palahí I Torres
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden;
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Christer Wiklund
- Department of Zoology: Division of Ecology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Roger Vila
- Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
| | - Peter Pruisscher
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
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Li G, Wu Y, Bai Y, Zhao N, Jiang Y, Li N, Lin X, Liu B, Xu C. Patterns of Chromosomal Variation, Homoeologous Exchange, and Their Relationship with Genomic Features in Early Generations of a Synthetic Rice Segmental Allotetraploid. Int J Mol Sci 2023; 24:ijms24076065. [PMID: 37047036 PMCID: PMC10094486 DOI: 10.3390/ijms24076065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Polyploidization is a driving force in plant evolution. Chromosomal variation often occurs at early generations following polyploid formation due to meiotic pairing irregularity that may compromise segregation fidelity and cause homoeologous exchange (HE). The trends of chromosomal variation and especially factors affecting HE remain to be fully deciphered. Here, by whole-genome resequencing, we performed nuanced analyses of patterns of chromosomal number variation and explored genomic features that affect HE in two early generations of a synthetic rice segmental allotetraploid. We found a wide occurrence of whole-chromosome aneuploidy and, to a lesser extent, also large segment gains/losses in both generations (S2 and S4) of the tetraploids. However, while the number of chromosome gains was similar between S2 and S4, that of losses in S4 was lower than in S2. HEs were abundant across all chromosomes in both generations and showed variable correlations with different genomic features at chromosomal and/or local scales. Contents of genes and transposable elements (TEs) were positively and negatively correlated with HE frequencies, respectively. By dissecting TEs into different classes, retrotransposons were found to be negatively correlated with HE frequency to a stronger extent than DNA transposons, whereas miniature terminal inverted elements (MITEs) showed a strong positive correlation. Local HE frequencies in the tetraploids and homologous recombination (HR) rates in diploids within 1 Mb sliding windows were significantly correlated with each other and showed similar overall distribution profiles. Nonetheless, non-concordant trends between HE and HR rates were found at distal regions in some chromosomes. At local scale, both shared and polymorphic retrotransposons between parents were negatively correlated with HE frequency; in contrast, both shared and polymorphic MITEs showed positive correlations with HE frequency. Our results shed new light on the patterns of chromosomal number variation and reveal genomic features influencing HE frequency in early generations following plant polyploidization.
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Affiliation(s)
- Guo Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yan Bai
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Na Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Yuhui Jiang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiuyun Lin
- Jilin Academy of Agriculture, Changchun 130033, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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Zhang F, Chen F, Schwarzacher T, Heslop-Harrison JS, Teng N. The nature and genomic landscape of repetitive DNA classes in Chrysanthemum nankingense shows recent genomic changes. ANNALS OF BOTANY 2023; 131:215-228. [PMID: 35639931 PMCID: PMC9904347 DOI: 10.1093/aob/mcac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Tandemly repeated DNA and transposable elements represent most of the DNA in higher plant genomes. High-throughput sequencing allows a survey of the DNA in a genome, but whole-genome assembly can miss a substantial fraction of highly repeated sequence motifs. Chrysanthemum nankingense (2n = 2x = 18; genome size = 3.07 Gb; Asteraceae), a diploid reference for the many auto- and allopolyploids in the genus, was considered as an ancestral species and serves as an ornamental plant and high-value food. We aimed to characterize the major repetitive DNA motifs, understand their structure and identify key features that are shaped by genome and sequence evolution. METHODS Graph-based clustering with RepeatExplorer was used to identify and classify repetitive motifs in 2.14 millions of 250-bp paired-end Illumina reads from total genomic DNA of C. nankingense. Independently, the frequency of all canonical motifs k-bases long was counted in the raw read data and abundant k-mers (16, 21, 32, 64 and 128) were extracted and assembled to generate longer contigs for repetitive motif identification. For comparison, long terminal repeat retrotransposons were checked in the published C. nankingense reference genome. Fluorescent in situ hybridization was performed to show the chromosomal distribution of the main types of repetitive motifs. KEY RESULTS Apart from rDNA (0.86 % of the total genome), a few microsatellites (0.16 %), and telomeric sequences, no highly abundant tandem repeats were identified. There were many transposable elements: 40 % of the genome had sequences with recognizable domains related to transposable elements. Long terminal repeat retrotransposons showed widespread distribution over chromosomes, although different sequence families had characteristic features such as abundance at or exclusion from centromeric or subtelomeric regions. Another group of very abundant repetitive motifs, including those most identified as low-complexity sequences (9.07 %) in the genome, showed no similarity to known sequence motifs or tandemly repeated elements. CONCLUSIONS The Chrysanthemum genome has an unusual structure with a very low proportion of tandemly repeated sequences (~1.02 %) in the genome, and a high proportion of low-complexity sequences, most likely degenerated remains of transposable elements. Identifying the presence, nature and genomic organization of major genome fractions enables inference of the evolutionary history of sequences, including degeneration and loss, critical to understanding biodiversity and diversification processes in the genomes of diploid and polyploid Chrysanthemum, Asteraceae and plants more widely.
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Affiliation(s)
- Fengjiao Zhang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Fadi Chen
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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11
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Yin L, Xu G, Yang J, Zhao M. The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments. Mol Biol Evol 2022; 39:6709529. [PMID: 36130304 PMCID: PMC9547528 DOI: 10.1093/molbev/msac198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Subgenome dominance after whole-genome duplication (WGD) has been observed in many plant species. However, the degree to which the chromatin environment affects this bias has not been explored. Here, we compared the dominant subgenome (maize1) and the recessive subgenome (maize2) with respect to patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, and accessible chromatin regions (ACRs). Our data show that the degree of bias between subgenomes for all the measured variables does not vary significantly when both of the WGD genes are located in pericentromeric regions. Our data further indicate that the location of maize1 genes in chromosomal arms is pivotal for maize1 to maintain its dominance, but location has a less effect on maize2 homoeologs. In addition to homoeologous genes, we compared ACRs, which often harbor cis-regulatory elements, between the two subgenomes and demonstrate that maize1 ACRs have a higher level of chromatin accessibility, a lower level of sequence substitution, and are enriched in chromosomal arms. Furthermore, we find that a loss of maize1 ACRs near their nearby genes is associated with a reduction in purifying selection and expression of maize1 genes relative to their maize2 homoeologs. Taken together, our data suggest that chromatin environment and cis-regulatory elements are important determinants shaping the divergence and evolution of duplicated genes.
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Affiliation(s)
- Liangwei Yin
- Department of Biology, Miami University, Oxford, OH 45056
| | - Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583
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12
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Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes. Cells 2021; 10:cells10123590. [PMID: 34944100 PMCID: PMC8700633 DOI: 10.3390/cells10123590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.
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13
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Patil AB, Vijay N. Repetitive genomic regions and the inference of demographic history. Heredity (Edinb) 2021; 127:151-166. [PMID: 34002046 PMCID: PMC8322061 DOI: 10.1038/s41437-021-00443-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Inference of demographic histories using whole-genome datasets has provided insights into diversification, adaptation, hybridization, and plant-pathogen interactions, and stimulated debate on the impact of anthropogenic interventions and past climate on species demography. However, the impact of repetitive genomic regions on these inferences has mostly been ignored by masking of repeats. We use the Populus trichocarpa genome (Pop_tri_v3) to show that masking of repeat regions leads to lower estimates of effective population size (Ne) in the distant past in contrast to an increase in Ne estimates in recent times. However, in human datasets, masking of repeats resulted in lower estimates of Ne at all time points. We demonstrate that repeats affect demographic inferences using diverse methods like PSMC, MSMC, SMC++, and the Stairway plot. Our genomic analysis revealed that the biases in Ne estimates were dependent on the repeat class type and its abundance in each atomic interval. Notably, we observed a weak, yet consistently significant negative correlation between the repeat abundance of an atomic interval and the Ne estimates for that interval, which potentially reflects the recombination rate variation within the genome. The rationale for the masking of repeats has been that variants identified within these regions are erroneous. We find that polymorphisms in some repeat classes occur in callable regions and reflect reliable coalescence histories (e.g., LTR Gypsy, LTR Copia). The current demography inference methods do not handle repeats explicitly, and hence the effect of individual repeat classes needs careful consideration in comparative analysis. Deciphering the repeat demographic histories might provide a clear understanding of the processes involved in repeat accumulation.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
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14
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Almojil D, Bourgeois Y, Falis M, Hariyani I, Wilcox J, Boissinot S. The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes. Genes (Basel) 2021; 12:genes12060918. [PMID: 34203645 PMCID: PMC8232201 DOI: 10.3390/genes12060918] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.
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Affiliation(s)
- Dareen Almojil
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Yann Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK;
| | - Marcin Falis
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Imtiyaz Hariyani
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Justin Wilcox
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Correspondence:
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15
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Rifkin JL, Beaudry FEG, Humphries Z, Choudhury BI, Barrett SCH, Wright SI. Widespread Recombination Suppression Facilitates Plant Sex Chromosome Evolution. Mol Biol Evol 2021; 38:1018-1030. [PMID: 33095227 PMCID: PMC7947811 DOI: 10.1093/molbev/msaa271] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with preexisting recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant Rumex hastatulus. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographic range. We identified the shared and neo-sex chromosomes using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosomes are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homolog indicates that low recombination rates mainly preceded sex linkage. These patterns are not unique to the sex chromosomes; all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing by repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.
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Affiliation(s)
- Joanna L Rifkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Felix E G Beaudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Zoë Humphries
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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16
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Wang Y, Dai A, Tang T. Weak Effect of Gypsy Retrotransposon Bursts on Sonneratia alba Salt Stress Gene Expression. FRONTIERS IN PLANT SCIENCE 2021; 12:830079. [PMID: 35111190 PMCID: PMC8801733 DOI: 10.3389/fpls.2021.830079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/27/2021] [Indexed: 05/07/2023]
Abstract
Transposable elements (TEs) are an important source of genetic diversity and can be co-opted for the regulation of host genes. However, to what extent the pervasive TE colonization of plant genomes has contributed to stress adaptation remains controversial. Plants inhabiting harsh environments in nature provide a unique opportunity to answer this question. We compared TE compositions and their evolutionary dynamics in the genomes of two mangrove species: the pioneer Sonneratia alba and its less salt-tolerant relative S. caseolaris. Age distribution, strength of purifying selection and the removal rate of LTR (long terminal repeat) retrotransposons were estimated. Phylogenetic analysis of LTR retrotransposons and their distribution in the genome of S. alba were surveyed. Small RNA sequencing and whole-genome bisulfite sequencing was conducted using leaves of S. alba. Expression pattern of LTR retrotransposons and their nearby genes were examined using RNA-seq data of S. alba under different salt treatments. S. alba possesses more TEs than S. caseolaris. Particularly, many more young Gypsy LTR retrotransposons have accumulated in S. alba than in S. caseolaris despite an increase in purifying selection against TE insertions. The top two most abundant Gypsy families in S. alba preferentially insert in gene-poor regions. They are under relaxed epigenetic repression, probably due to the presence of CHROMO domains in their 3'-ends. Although a considerable number of TEs in S. alba showed differential expression under salt stress, only four copies were significantly correlated with their nearby genes in expression levels. One such TE-gene pair involves Abscisic acid 8'-hydroxylase 3 functioning in abscisic acid catabolism. This study sheds light on the evolutionary dynamics and potential function of TEs in an extremophile. Our results suggest that the conclusion on co-option of TEs should be cautious even though activation of TEs by stress might be prevalent.
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17
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Abstract
Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic behavior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species.
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Affiliation(s)
- Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; ,
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; ,
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18
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Woodruff GC, Teterina AA. Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans. Mol Biol Evol 2020; 37:2549-2567. [PMID: 32359146 PMCID: PMC7475029 DOI: 10.1093/molbev/msaa107] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode Caenorhabditis elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated C. inopinata has experienced repetitive element expansion and reveals no association of global repeat density with chromosome position. Patterns of repeat superfamily specific distributions reveal this global pattern is driven largely by a few repeat superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate alone can generate structured repetitive genomic landscapes when insertions are weakly deleterious, whereas chromosomal heterogeneity in the fitness effects of transposon insertion can promote such landscapes across a variety of evolutionary scenarios. Thus, patterns of gene density along chromosomes likely contribute to global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.
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Affiliation(s)
- Gavin C Woodruff
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | - Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
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19
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Quesneville H. Twenty years of transposable element analysis in the Arabidopsis thaliana genome. Mob DNA 2020; 11:28. [PMID: 32742313 PMCID: PMC7385966 DOI: 10.1186/s13100-020-00223-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
Transposable elements (TEs) are mobile repetitive DNA sequences shown to be major drivers of genome evolution. As the first plant to have its genome sequenced and analyzed at the genomic scale, Arabidopsis thaliana has largely contributed to our TE knowledge. The present report describes 20 years of accumulated TE knowledge gained through the study of the Arabidopsis genome and covers the known TE families, their relative abundance, and their genomic distribution. It presents our knowledge of the different TE family activities, mobility, population and long-term evolutionary dynamics. Finally, the role of TE as substrates for new genes and their impact on gene expression is illustrated through a few selected demonstrative cases. Promising future directions for TE studies in this species conclude the review.
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20
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Kelleher ES, Barbash DA, Blumenstiel JP. Taming the Turmoil Within: New Insights on the Containment of Transposable Elements. Trends Genet 2020; 36:474-489. [PMID: 32473745 DOI: 10.1016/j.tig.2020.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are mobile genetic parasites that can exponentially increase their genomic abundance through self-propagation. Classic theoretical papers highlighted the importance of two potentially escalating forces that oppose TE spread: regulated transposition and purifying selection. Here, we review new insights into mechanisms of TE regulation and purifying selection, which reveal the remarkable foresight of these theoretical models. We further highlight emergent connections between transcriptional control enacted by small RNAs and the contribution of TE insertions to structural mutation and host-gene regulation. Finally, we call for increased comparative analysis of TE dynamics and fitness effects, as well as host control mechanisms, to reveal how interconnected forces shape the differential prevalence and distribution of TEs across the tree of life.
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21
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Sun S, Wang Y, Zeng W, Du X, Li L, Hong X, Huang X, Zhang H, Zhang M, Fan G, Liu X, Liu S. The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. Sci Rep 2020; 10:8164. [PMID: 32424221 PMCID: PMC7235238 DOI: 10.1038/s41598-020-64398-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/06/2020] [Indexed: 11/08/2022] Open
Abstract
Mekong tiger perch (Datnioides undecimradiatus) is an ornamental and vulnerable freshwater fish native to the Mekong basin in Indochina, belonging to the order Lobotiformes. Here, we generated 121X stLFR co-barcode clean reads and 18X Oxford Nanopore MinION reads and obtained a 595 Mb Mekong tiger perch genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes is more closely related to Sciaenidae than to Tetraodontiformes, resolving a long-time dispute. We depicted the genes involved in pigment development in Mekong tiger perch and results confirmed that the four rate-limiting genes of pigment synthesis had been retained after fish-specific genome duplication. We also estimated the demographic history of Mekong tiger perch, which showed that the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogenetic position of Lobotiformes and biological conservation.
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Affiliation(s)
- Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yue Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wenhong Zeng
- Jiangxi University of Traditional Chinese Medicin, Nanchang, 330004, China
| | - Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Lei Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaoning Hong
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 236009, China
| | - Xiaoyun Huang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
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22
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Diop SI, Subotic O, Giraldo-Fonseca A, Waller M, Kirbis A, Neubauer A, Potente G, Murray-Watson R, Boskovic F, Bont Z, Hock Z, Payton AC, Duijsings D, Pirovano W, Conti E, Grossniklaus U, McDaniel SF, Szövényi P. A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1378-1396. [PMID: 31692190 DOI: 10.1111/tpj.14602] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 10/28/2019] [Indexed: 05/07/2023]
Abstract
Marchantia polymorpha has recently become a prime model for cellular, evo-devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule-scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high-density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map-based cloning, feasible.
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Affiliation(s)
- Seydina I Diop
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Oliver Subotic
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Alejandro Giraldo-Fonseca
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Alexander Kirbis
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Rachel Murray-Watson
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Filip Boskovic
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, CB3 0HE, Cambridge, UK
| | - Zoe Bont
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
| | - Zsofia Hock
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Adam C Payton
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL, 32611, USA
| | | | - Walter Pirovano
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Elena Conti
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Stuart F McDaniel
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL, 32611, USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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Uzunović J, Josephs EB, Stinchcombe JR, Wright SI. Transposable Elements Are Important Contributors to Standing Variation in Gene Expression in Capsella Grandiflora. Mol Biol Evol 2020; 36:1734-1745. [PMID: 31028401 DOI: 10.1093/molbev/msz098] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) make up a significant portion of eukaryotic genomes and are important drivers of genome evolution. However, the extent to which TEs affect gene expression variation on a genome-wide scale in comparison with other types of variants is still unclear. We characterized TE insertion polymorphisms and their association with gene expression in 124 whole-genome sequences from a single population of Capsella grandiflora, and contrasted this with the effects of single nucleotide polymorphisms (SNPs). Population frequency of insertions was negatively correlated with distance to genes, as well as density of conserved noncoding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare SNPs contribute equally to up- and down-regulation, but have a weaker individual effect than TEs. An expression quantitative trait loci (eQTL) analysis shows that a greater proportion of common TEs are eQTLs as opposed to common SNPs, and a third of the genes with TE eQTLs do not have SNP eQTLs. In contrast with rare TE insertions, common insertions are more likely to increase expression, consistent with recent models of cis-regulatory evolution favoring enhancer alleles. Taken together, these results imply that TEs are a significant contributor to gene expression variation and are individually more likely than rare SNPs to cause extreme changes in gene expression.
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Affiliation(s)
- Jasmina Uzunović
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Koffler Scientific Reserve, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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Shi J, Liang C. Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection. PLANT PHYSIOLOGY 2019; 180:1803-1815. [PMID: 31152127 PMCID: PMC6670090 DOI: 10.1104/pp.19.00386] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/17/2019] [Indexed: 05/25/2023]
Abstract
Comprehensive and accurate annotation of the repeatome, including transposons, is critical for deepening our understanding of repeat origins, biogenesis, regulatory mechanisms, and roles. Here, we developed Generic Repeat Finder (GRF), a tool for genome-wide repeat detection based on fast, exhaustive numerical calculation algorithms integrated with optimized dynamic programming strategies. GRF sensitively identifies terminal inverted repeats (TIRs), terminal direct repeats (TDRs), and interspersed repeats that bear both inverted and direct repeats. GRF also detects DNA or RNA transposable elements characterized by these repeats in plant and animal genomes. For TIRs and TDRs, GRF identifies spacers in the middle and mismatches/insertions or deletions in terminal repeats, showing their alignment or base-pairing information. GRF helps improve the annotation for various DNA transposons and retrotransposons, such as miniature inverted-repeat transposable elements (MITEs), long terminal repeat (LTR) retrotransposons, and non-LTR retrotransposons, including long interspersed nuclear elements and short interspersed nuclear elements in plants. We used GRF to perform TIR/TDR, interspersed-repeat, and MITE detection in several species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and mouse (Mus musculus). As a generic bioinformatics tool in repeat finding implemented as a parallelized C++ program, GRF was faster and more sensitive than the existing inverted repeat/MITE detection tools based on numerical approaches (i.e. detectIR and detectMITE) in Arabidopsis and mouse. GRF is more sensitive than Inverted Repeat Finder in TIR detection, LTR_FINDER in short TDR detection (≤1,000 nt), and phRAIDER in interspersed repeat detection in Arabidopsis and rice. GRF is an open source available from Github.
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Affiliation(s)
- Jieming Shi
- Department of Biology, Miami University, Oxford, Ohio 45056
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio 45056
- Department of Computer Science and Software Engineering, Miami University, Oxford, Ohio 45056
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25
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Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination. Chromosoma 2019; 128:279-296. [PMID: 31332531 DOI: 10.1007/s00412-019-00718-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023]
Abstract
During meiosis, DNA double-strand breaks are initiated by the topoisomerase-like enzyme SPO11 and are repaired by inter-sister chromatid and inter-homologue DNA repair pathways. Genome-wide maps of initiating DNA double-strand breaks and inter-homologue repair events are now available for a number of mammalian, fungal and plant species. In mammals, PRDM9 specifies the location of meiotic recombination initiation via recognition of specific DNA sequence motifs by its C2H2 zinc finger array. In fungi and plants, meiotic recombination appears to be initiated less discriminately in accessible chromatin, including at gene promoters. Generally, meiotic crossover is suppressed in highly repetitive genomic regions that are made up of transposable elements (TEs), to prevent deleterious non-allelic homologous recombination events. However, recent and older studies have revealed intriguing relationships between meiotic recombination initiation and repair, and transposable elements. For instance, gene conversion events have been detected in maize centromeric retroelements, mouse MULE-MuDR DNA transposons undergo substantial meiotic recombination initiation, Arabidopsis Helitron TEs are among the hottest of recombination initiation hotspots, and human TE sequences can modify the crossover rate at adjacent PRDM9 motifs in cis. Here, we summarize the relationship between meiotic recombination and TEs, discuss recent insights from highly divergent eukaryotes and highlight outstanding questions in the field.
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26
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Legrand S, Caron T, Maumus F, Schvartzman S, Quadrana L, Durand E, Gallina S, Pauwels M, Mazoyer C, Huyghe L, Colot V, Hanikenne M, Castric V. Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes. Mob DNA 2019; 10:30. [PMID: 31346350 PMCID: PMC6636163 DOI: 10.1186/s13100-019-0171-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
Background Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Results Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. Conclusion Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.
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Affiliation(s)
- Sylvain Legrand
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Thibault Caron
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Florian Maumus
- 2URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Sol Schvartzman
- 3InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Leandro Quadrana
- 4IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Eléonore Durand
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Sophie Gallina
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Maxime Pauwels
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Clément Mazoyer
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Lucie Huyghe
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Vincent Colot
- 4IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Marc Hanikenne
- 3InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Vincent Castric
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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Hu K, Xu K, Wen J, Yi B, Shen J, Ma C, Fu T, Ouyang Y, Tu J. Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species. BMC Bioinformatics 2019; 20:354. [PMID: 31234777 PMCID: PMC6591975 DOI: 10.1186/s12859-019-2945-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 06/11/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated. RESULTS We developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined Helitron density (abundance/Mb) and visualized and examined Helitron distribution patterns. We identified more than 104,653 Helitrons, including many new Helitrons not predicted by other software. Whole genome Helitron density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into Arabidopsis thaliana groups. For most Brassicaceae species, Helitron density negatively correlated with gene density, and Helitron distribution patterns were similar to those of A. thaliana. They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13 Helitron polymorphism loci with flowering-time phenotypes in 18 A. thaliana ecotypes. CONCLUSION EAHelitron is a fast and efficient tool to identify new Helitrons. Whole genome Helitron density can be an informative character for plant classification. Helitron insertion polymorphism could be used in association analysis.
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Affiliation(s)
- Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Kai Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Ma B, Xin Y, Kuang L, He N. Distribution and Characteristics of Transposable Elements in the Mulberry Genome. THE PLANT GENOME 2019; 12:180094. [PMID: 31290922 DOI: 10.3835/plantgenome2018.12.0094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mulberry ( C. K. Schneid) leaves have been used as the food for the domesticated silkworm, , for more than 5000 yr, and the mulberry-silkworm relationship is one of the best-known and oldest models of plant defense-insect adaptation. The availability of a genome assembly of mulberry provides us with an opportunity to mine the characteristics and distribution of transposable elements (TEs) in this species and to examine their relationship to genes and gene expression. In this study, a significantly correlated inverse relationship between the percentage coverage of genes and TEs was observed. The TE-rich regions appeared to have a lower percentage of putatively expressed genes. Distribution patterns between different TE superfamilies were detected in the mulberry genome. The elements (the TE making up the greatest proportion of the mulberry genome) were significantly overrepresented within genes in the mulberry genome, and they may have a dominant influence on evolution of the mulberry genome. Approximately 96.93% (330/344) of the TE-containing genes assigned to pathways were assigned to metabolism-related pathways. The TE-related alternative splicing events accounted for 7.58% (402/5,302) of all alternative splicing types in the mulberry genome, suggesting that TEs are one of the driving forces in the formation of the alternatively spliced genes. The results will be valuable in improving our understanding of the important roles of TEs in mulberry genome evolution.
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29
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Choudhury RR, Rogivue A, Gugerli F, Parisod C. Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes. Mol Ecol 2019; 28:1550-1562. [DOI: 10.1111/mec.15014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/26/2018] [Indexed: 01/03/2023]
Affiliation(s)
| | - Aude Rogivue
- WSL Swiss Federal Research Institute Birmensdorf Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Birmensdorf Switzerland
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30
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Ma B, Kuang L, Xin Y, He N. New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species. Genes (Basel) 2019; 10:genes10040285. [PMID: 30970574 PMCID: PMC6523491 DOI: 10.3390/genes10040285] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/27/2019] [Accepted: 04/04/2019] [Indexed: 11/16/2022] Open
Abstract
The evolutionary dynamics of long terminal repeat (LTR) retrotransposons in tree genomes has remained largely unknown. The availability of the complete genome sequences of the mulberry tree (Morus notabilis) has offered an unprecedented opportunity for us to characterize these retrotransposon elements. We investigated 202 and 114 families of Copia and Gypsy superfamilies, respectively, comprising 2916 intact elements in the mulberry genome. The tRNAMet was the most frequently used type of tRNA in both superfamilies. Phylogenetic analysis suggested that Copia and Gypsy from mulberry can be grouped into eight and six lineages, respectively. All previously characterized families of such elements could also be found in the mulberry genome. About 95% of the identified Copia and Gypsy full elements were estimated to have been inserted into the mulberry genome within the past 2–3 million years. Meanwhile, the estimated insertion times of members of the three most abundant families of the Copia superfamily (908 members from the three most abundant families) and Gypsy superfamily (783 members from the three most abundant families) revealed divergent life histories. Compared with the situation in Gypsy elements, three families of Copia elements are under positive selection pressure, which suggested that Copia elements may have a dominant influence in the evolution of mulberry genes. Analysis of insertion and deletion dynamics suggested that Copia and Gypsy elements exhibited a very long half-life in the mulberry genome. The present work provides new insights into the insertion and deletion dynamics of LTR retrotransposons, and it will greatly improve our understanding of the important roles transposable elements play in the architecture of the mulberry genome.
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Affiliation(s)
- Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.
| | - Lulu Kuang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.
| | - Youchao Xin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.
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31
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Choi JY, Purugganan MD. Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice. Mol Biol Evol 2019; 35:365-382. [PMID: 29126199 PMCID: PMC5850837 DOI: 10.1093/molbev/msx284] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on five factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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32
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Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW. Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol 2019; 28:1491-1505. [DOI: 10.1111/mec.14969] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/15/2018] [Accepted: 10/23/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Stefan Dennenmoser
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
| | | | - Michael C. Schatz
- Cold Spring Harbor Laboratory Cold Spring Harbor New York
- Departments of Computer Science and Biology Johns Hopkins University Baltimore Maryland
| | - Janine Altmüller
- Cologne Center for Genomics, and Institute of Human Genetics University of Cologne Cologne Germany
| | | | - Arne W. Nolte
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
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33
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Ha J, Shim S, Lee T, Kang YJ, Hwang WJ, Jeong H, Laosatit K, Lee J, Kim SK, Satyawan D, Lestari P, Yoon MY, Kim MY, Chitikineni A, Tanya P, Somta P, Srinives P, Varshney RK, Lee S. Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:517-530. [PMID: 30059608 PMCID: PMC6335072 DOI: 10.1111/pbi.12995] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/26/2018] [Indexed: 05/02/2023]
Abstract
Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.
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Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Sangrea Shim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Yang J. Kang
- Division of Applied Life Science (BK21 plus program) DepartmentGyeongsang National UniversityPMBBRCJinju‐siKorea
- Division of Life Science DepartmentGyeongsang National UniversityJinju‐siKorea
| | | | - Haneul Jeong
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Kularb Laosatit
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Jayern Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sue K. Kim
- Department of ChemistryCollege of Natural ScienceDankook UniversityCheonanSouth Korea
| | - Dani Satyawan
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Puji Lestari
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Min Y. Yoon
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Moon Y. Kim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Patcharin Tanya
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Prakit Somta
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Peerasak Srinives
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Suk‐Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
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34
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Grativol C, Thiebaut F, Sangi S, Montessoro P, Santos WDS, Hemerly AS, Ferreira PC. A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses. PeerJ 2019; 7:e6080. [PMID: 30648010 PMCID: PMC6331000 DOI: 10.7717/peerj.6080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 11/07/2018] [Indexed: 11/25/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
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Affiliation(s)
- Clicia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Flavia Thiebaut
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Sangi
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Patricia Montessoro
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Walaci da Silva Santos
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo C.G. Ferreira
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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Stritt C, Gordon SP, Wicker T, Vogel JP, Roulin AC. Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon. Genome Biol Evol 2018; 10:304-318. [PMID: 29281015 PMCID: PMC5786231 DOI: 10.1093/gbe/evx276] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 01/05/2023] Open
Abstract
Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Our study shows that while TEs in B. distachyon are “well-behaved” compared with TEs in other species with larger genomes, they are an abundant source of lineage-specific genetic variation and may play an important role in population divergence and adaptation.
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Affiliation(s)
- Christoph Stritt
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, California
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, California
| | - Anne C Roulin
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
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Horvath R, Slotte T. The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora. Genome Biol Evol 2018; 9:2911-2920. [PMID: 29036316 PMCID: PMC5737465 DOI: 10.1093/gbe/evx206] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/13/2022] Open
Abstract
To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population. To explore how effects of TE silencing on gene regulation shapes purifying selection on TEs, we analyzed whole genome sequencing data from 166 individuals of a large population of the outcrossing species Capsella grandiflora. We found that most TEs are rare, and in chromosome arms, silenced TEs are exposed to stronger purifying selection than those that are not silenced by 24-nucleotide small RNAs, especially with increasing proximity to genes. An age-of-allele test of neutrality on a subset of TEs supports our inference of purifying selection on silenced TEs, suggesting that our results are robust to varying transposition rates. Our results provide new insights into the processes affecting the accumulation of TEs in an outcrossing species and support the view that epigenetic silencing of TEs results in a trade-off between preventing TE proliferation and interference with nearby gene regulation. We also suggest that in the centromeric and pericentromeric regions, the negative aspects of epigenetic TE silencing are missing.
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Affiliation(s)
- Robert Horvath
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Tanja Slotte
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
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Genome-Wide Survey and Comparative Analysis of Long Terminal Repeat (LTR) Retrotransposon Families in Four Gossypium Species. Sci Rep 2018; 8:9399. [PMID: 29925876 PMCID: PMC6010443 DOI: 10.1038/s41598-018-27589-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/06/2018] [Indexed: 11/08/2022] Open
Abstract
Long terminal repeat (LTR) retrotransposon is the most abundant DNA component and is largely responsible for plant genome size variation. Although it has been studied in plant species, very limited data is available for cotton, the most important fiber and texture crop. In this study, we performed a comprehensive analysis of LTR retrotransposon families across four cotton species. In tetraploid Gossypium species, LTR retrotransposon families from the progenitor D genome had more copies in D-subgenome, and families from the progenitor A genome had more copies in A-subgenome. Some LTR retrotransposon families that insert after polyploid formation may still distribute the majority of its copies in one of the subgenomes. The data also shows that families of 10~200 copies are abundant and they have a great influence on the Gossypium genome size; on the contrary, a small number of high copy LTR retrotransposon families have less contribution to the genome size. Kimura distance distribution indicates that high copy number family is not a recent outbreak, and there is no obvious relationship between family copy number and the period of evolution. Further analysis reveals that each LTR retrotransposon family may have their own distribution characteristics in cotton.
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38
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Kent TV, Uzunović J, Wright SI. Coevolution between transposable elements and recombination. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0458. [PMID: 29109221 DOI: 10.1098/rstb.2016.0458] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 12/24/2022] Open
Abstract
One of the most striking patterns of genome structure is the tight, typically negative, association between transposable elements (TEs) and meiotic recombination rates. While this is a highly recurring feature of eukaryotic genomes, the mechanisms driving correlations between TEs and recombination remain poorly understood, and distinguishing cause versus effect is challenging. Here, we review the evidence for a relation between TEs and recombination, and discuss the underlying evolutionary forces. Evidence to date suggests that overall TE densities correlate negatively with recombination, but the strength of this correlation varies across element types, and the pattern can be reversed. Results suggest that heterogeneity in the strength of selection against ectopic recombination and gene disruption can drive TE accumulation in regions of low recombination, but there is also strong evidence that the regulation of TEs can influence local recombination rates. We hypothesize that TE insertion polymorphism may be important in driving within-species variation in recombination rates in surrounding genomic regions. Furthermore, the interaction between TEs and recombination may create positive feedback, whereby TE accumulation in non-recombining regions contributes to the spread of recombination suppression. Further investigation of the coevolution between recombination and TEs has important implications for our understanding of the evolution of recombination rates and genome structure.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Tyler V Kent
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, Canada M5S3B2
| | - Jasmina Uzunović
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, Canada M5S3B2
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, Canada M5S3B2
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Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GKS, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:515-533. [PMID: 29237241 DOI: 10.1111/tpj.13801] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Florent Murat
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D-06466, Stadt Seeland, Germany
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Mathieu Piednoel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Cristina Vives
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | | | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Omar Saleh
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Daniel S Rokshar
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Shengqiang Shu
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Fritz Thümmler
- Vertis Biotechnologie AG, Lise-Meitner-Str. 30, 85354, Freising, Germany
| | - Michael Tillich
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Thomas Widiez
- Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH-1211, Switzerland
- Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ann Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yong Zhang
- Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- WZW, Technical University Munich, Munich, Germany
| | | | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Jérome Salse
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
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40
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Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive variation. Proc Biol Sci 2017; 284:rspb.2016.2864. [PMID: 28566483 DOI: 10.1098/rspb.2016.2864] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/04/2017] [Indexed: 12/16/2022] Open
Abstract
The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Nicholas H Barton
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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Marand AP, Jansky SH, Zhao H, Leisner CP, Zhu X, Zeng Z, Crisovan E, Newton L, Hamernik AJ, Veilleux RE, Buell CR, Jiang J. Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato. Genome Biol 2017; 18:203. [PMID: 29084572 PMCID: PMC5663088 DOI: 10.1186/s13059-017-1326-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022] Open
Abstract
Background Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few of these maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic crossovers. Results Using a whole genome sequencing-based approach, we developed two high-density reference-based haplotype maps using diploid potato clones as parents. The vast majority (81%) of meiotic crossovers were mapped to less than 5 kb. The fine-scale accuracy of crossover detection was validated by Sanger sequencing for a subset of ten crossover events. We demonstrate that crossovers reside in genomic regions of “open chromatin”, which were identified based on hypersensitivity to DNase I digestion and association with H3K4me3-modified nucleosomes. The genomic regions spanning crossovers were significantly enriched with the Stowaway family of miniature inverted-repeat transposable elements (MITEs). The occupancy of Stowaway elements in gene promoters is concomitant with an increase in recombination rate. A generalized linear model identified the presence of Stowaway elements as the third most important genomic or chromatin feature behind genes and open chromatin for predicting crossover formation over 10-kb windows. Conclusions Collectively, our results suggest that meiotic crossovers in potato are largely determined by the local chromatin status, marked by accessible chromatin, H3K4me3-modified nucleosomes, and the presence of Stowaway transposons. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1326-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandre P Marand
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Shelley H Jansky
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA. .,USDA-ARS, Vegetable Crops Research Unit, Madison, Wisconsin, 53706, USA.
| | - Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Courtney P Leisner
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Xiaobiao Zhu
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Emily Crisovan
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Andy J Hamernik
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,USDA-ARS, Vegetable Crops Research Unit, Madison, Wisconsin, 53706, USA
| | | | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA. .,Current address: Departments of Plant Biology and Horticulture, Michigan State University, East Lansing, Michigan, 48824, USA.
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42
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Jiang X, Tang H, Ye Z, Lynch M. Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex. Genome Biol Evol 2017; 9:362-374. [PMID: 28057730 PMCID: PMC5381639 DOI: 10.1093/gbe/evw302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2016] [Indexed: 12/20/2022] Open
Abstract
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread and elimination of TEs. We identified nine asexual-specific fixed TE insertions, eight long terminal repeat retrotransposons, and one DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except one TE insertion located on a contig from chromosome 7, the other eight asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all nine asexual-specific fixed TE insertions can also be detected in some Daphnia pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals.
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Affiliation(s)
- Xiaoqian Jiang
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, Indiana
| | - Zhiqiang Ye
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana
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43
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Guo C, Spinelli M, Ye C, Li QQ, Liang C. Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. Sci Rep 2017; 7:2634. [PMID: 28572566 PMCID: PMC5454002 DOI: 10.1038/s41598-017-02855-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes. They are known to critically influence the process of genome evolution and play a role in gene regulation. As the first study concentrated in the transposition activities of MITEs among different ecotype accessions within a species, we conducted a genome-wide comparative analysis by characterizing and comparing MITEs in 19 Arabidopsis thaliana accessions. A total of 343485 MITE putative sequences, including canonical, diverse and partial ones, were delineated from all 19 accessions. Within the entire population of MITEs sequences, 80.7% of them were previously unclassified MITEs, demonstrating a different genomic distribution and functionality compared to the classified MITEs. The interactions between MITEs and homologous genes across 19 accessions provided a fine source for analyzing MITE transposition activities and their impacts on genome evolution. Moreover, a significant proportion of MITEs were found located in the last exon of genes besides the ordinary intron locality, thus potentially modifying the end of genes. Finally, analysis of the impact of MITEs on gene expression suggests that migrations of MITEs have no detectable effect on the expression level for host genes across accessions.
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Affiliation(s)
- Cheng Guo
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | | | - Congting Ye
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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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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Complexity of genetic mechanisms conferring nonuniformity of recombination in maize. Sci Rep 2017; 7:1205. [PMID: 28446764 PMCID: PMC5430679 DOI: 10.1038/s41598-017-01240-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/28/2017] [Indexed: 11/10/2022] Open
Abstract
Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs. Compared to recombination variation in whole genome, more QTLs were mapped for variations in recombination hot regions. The majority QTLs for recombination hot regions are trans-QTLs and co-localized with genes from the recombination pathway. We also found that recombination variation was positively associated with the presence of genes and DNA transposons, but negatively related to the presence of long terminal repeat retrotransposons. Additionally, 41 recombination hot regions were fine-mapped. The high-resolution genotyping of five randomly selected regions in two F2 populations verified that they indeed have ultra-high recombination frequency, which is even higher than that of the well-known recombination hot regions sh1-bz and a1-sh2. Taken together, our results further our understanding of recombination variation in plants.
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Useful parasites: the evolutionary biology and biotechnology applications of transposable elements. J Genet 2017; 95:1039-1052. [PMID: 27994207 DOI: 10.1007/s12041-016-0702-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as 'parasitic' or 'selfish'. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of their hosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of 'selfish' DNA, play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobile fraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.
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Coates BS, Abel CA, Perera OP. Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools. Genome 2016; 60:310-324. [PMID: 28177843 DOI: 10.1139/gen-2016-0067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size. Assembly of Illumina HiSeq 2000 reads generated from 14 pools that encompassed all BAC clones resulted in 165 485 genomic contigs (N50 = 3262 bp; 324.6 Mbp total). Long terminal repeat (LTR) protein coding regions annotated from 181 contigs included 30 Ty1/copia, 78 Ty3/gypsy, and 73 BEL/Pao elements, of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. Approximately 14% of LTR elements are distributed non-randomly across pools of BAC clones.
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Affiliation(s)
- Brad S Coates
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.,b Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Craig A Abel
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Omaththage P Perera
- c USDA-ARS, Southern Insect Management Research Unit, 141 Experiment Station Road, P.O. Box 346, Stoneville, MS 38776, USA
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Gion JM, Hudson CJ, Lesur I, Vaillancourt RE, Potts BM, Freeman JS. Genome-wide variation in recombination rate in Eucalyptus. BMC Genomics 2016; 17:590. [PMID: 27507140 PMCID: PMC4979139 DOI: 10.1186/s12864-016-2884-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 07/06/2016] [Indexed: 11/25/2022] Open
Abstract
Background Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation. Results Recombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = −0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = −0.75). Conclusions The correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus.
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Affiliation(s)
| | - Corey J Hudson
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.,Present address: Tasmanian Alkaloids, P.O. Box 130, Westbury, TAS, 7303, Australia
| | | | - René E Vaillancourt
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Brad M Potts
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Jules S Freeman
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
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Campos-Sánchez R, Cremona MA, Pini A, Chiaromonte F, Makova KD. Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PLoS Comput Biol 2016; 12:e1004956. [PMID: 27309962 PMCID: PMC4911145 DOI: 10.1371/journal.pcbi.1004956] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/29/2016] [Indexed: 01/24/2023] Open
Abstract
Endogenous retroviruses (ERVs), the remnants of retroviral infections in the germ line, occupy ~8% and ~10% of the human and mouse genomes, respectively, and affect their structure, evolution, and function. Yet we still have a limited understanding of how the genomic landscape influences integration and fixation of ERVs. Here we conducted a genome-wide study of the most recently active ERVs in the human and mouse genome. We investigated 826 fixed and 1,065 in vitro HERV-Ks in human, and 1,624 fixed and 242 polymorphic ETns, as well as 3,964 fixed and 1,986 polymorphic IAPs, in mouse. We quantitated >40 human and mouse genomic features (e.g., non-B DNA structure, recombination rates, and histone modifications) in ±32 kb of these ERVs' integration sites and in control regions, and analyzed them using Functional Data Analysis (FDA) methodology. In one of the first applications of FDA in genomics, we identified genomic scales and locations at which these features display their influence, and how they work in concert, to provide signals essential for integration and fixation of ERVs. The investigation of ERVs of different evolutionary ages (young in vitro and polymorphic ERVs, older fixed ERVs) allowed us to disentangle integration vs. fixation preferences. As a result of these analyses, we built a comprehensive model explaining the uneven distribution of ERVs along the genome. We found that ERVs integrate in late-replicating AT-rich regions with abundant microsatellites, mirror repeats, and repressive histone marks. Regions favoring fixation are depleted of genes and evolutionarily conserved elements, and have low recombination rates, reflecting the effects of purifying selection and ectopic recombination removing ERVs from the genome. In addition to providing these biological insights, our study demonstrates the power of exploiting multiple scales and localization with FDA. These powerful techniques are expected to be applicable to many other genomic investigations.
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Affiliation(s)
- Rebeca Campos-Sánchez
- Genetics Graduate Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
| | - Marzia A. Cremona
- MOX—Modeling and Scientific Computing, Department of Mathematics, Politecnico di Milano, Milano, Italy
- Department of Statistics, Penn State University, University Park, Pennsylvania, United States of America
| | - Alessia Pini
- MOX—Modeling and Scientific Computing, Department of Mathematics, Politecnico di Milano, Milano, Italy
| | - Francesca Chiaromonte
- Department of Statistics, Penn State University, University Park, Pennsylvania, United States of America
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
| | - Kateryna D. Makova
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
- Department of Biology, Penn State University, University Park, Pennsylvania, United States of America
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50
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Moreno-Romero J, Jiang H, Santos-González J, Köhler C. Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm. EMBO J 2016; 35:1298-311. [PMID: 27113256 DOI: 10.15252/embj.201593534] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/17/2016] [Indexed: 12/11/2022] Open
Abstract
Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited differential DNA methylation affects de novo targeting of chromatin modifiers in the early endosperm. Our data reveal that polycomb-mediated H3 lysine 27 trimethylation (H3K27me3) is preferentially localized to regions that are targeted by the DNA glycosylase DEMETER (DME), mechanistically linking DNA hypomethylation to imprinted gene expression. Our data furthermore suggest an absence of de novo DNA methylation in the early endosperm, providing an explanation how DME-mediated hypomethylation of the maternal genome is maintained after fertilization. Lastly, we show that paternal-specific H3K27me3-marked regions are located at pericentromeric regions, suggesting that H3K27me3 and DNA methylation are not necessarily exclusive marks at pericentromeric regions in the endosperm.
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Affiliation(s)
- Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Hua Jiang
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
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