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Heuberger M, Koo DH, Ahmed HI, Tiwari VK, Abrouk M, Poland J, Krattinger SG, Wicker T. Evolution of Einkorn wheat centromeres is driven by the mutualistic interplay of two LTR retrotransposons. Mob DNA 2024; 15:16. [PMID: 39103880 DOI: 10.1186/s13100-024-00326-9] [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: 05/27/2024] [Accepted: 07/25/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Centromere function is highly conserved across eukaryotes, but the underlying centromeric DNA sequences vary dramatically between species. Centromeres often contain a high proportion of repetitive DNA, such as tandem repeats and/or transposable elements (TEs). Einkorn wheat centromeres lack tandem repeat arrays and are instead composed mostly of the two long terminal repeat (LTR) retrotransposon families RLG_Cereba and RLG_Quinta which specifically insert in centromeres. However, it is poorly understood how these two TE families relate to each other and if and how they contribute to centromere function and evolution. RESULTS Based on conservation of diagnostic motifs (LTRs, integrase and primer binding site and polypurine-tract), we propose that RLG_Cereba and RLG_Quinta are a pair of autonomous and non-autonomous partners, in which the autonomous RLG_Cereba contributes all the proteins required for transposition, while the non-autonomous RLG_Quinta contributes GAG protein. Phylogenetic analysis of predicted GAG proteins showed that the RLG_Cereba lineage was present for at least 100 million years in monocotyledon plants. In contrast, RLG_Quinta evolved from RLG_Cereba between 28 and 35 million years ago in the common ancestor of oat and wheat. Interestingly, the integrase of RLG_Cereba is fused to a so-called CR-domain, which is hypothesized to guide the integrase to the functional centromere. Indeed, ChIP-seq data and TE population analysis show only the youngest subfamilies of RLG_Cereba and RLG_Quinta are found in the active centromeres. Importantly, the LTRs of RLG_Quinta and RLG_Cereba are strongly associated with the presence of the centromere-specific CENH3 histone variant. We hypothesize that the LTRs of RLG_Cereba and RLG_Quinta contribute to wheat centromere integrity by phasing and/or placing CENH3 nucleosomes, thus favoring their persistence in the competitive centromere-niche. CONCLUSION Our data show that RLG_Cereba cross-mobilizes the non-autonomous RLG_Quinta retrotransposons. New copies of both families are specifically integrated into functional centromeres presumably through direct binding of the integrase CR domain to CENH3 histone variants. The LTRs of newly inserted RLG_Cereba and RLG_Quinta elements, in turn, recruit and/or phase new CENH3 deposition. This mutualistic interplay between the two TE families and the plant host dynamically maintains wheat centromeres.
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Affiliation(s)
- Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Toulouse, France
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20724, USA
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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Merkulov P, Serganova M, Petrov G, Mityukov V, Kirov I. Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions. BMC Genomics 2024; 25:404. [PMID: 38658857 PMCID: PMC11044480 DOI: 10.1186/s12864-024-10314-1] [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: 12/18/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs can vary substantially, even in closely related species. Interspecific hybridization, a widely employed technique in tomato breeding, results in the creation of novel combinations of TEs from distinct species. The implications of this process for TE transposition activity have not been studied in modern cultivars. In this study, we used nanopore sequencing of extrachromosomal circular DNA (eccDNA) and identified two highly active Ty1/Copia LTR retrotransposon families of tomato (Solanum lycopersicum), called Salsa and Ketchup. Elements of these families produce thousands of eccDNAs under controlled conditions and epigenetic stress. EccDNA sequence analysis revealed that the major parts of eccDNA produced by Ketchup and Salsa exhibited low similarity to the S. lycopersicum genomic sequence. To trace the origin of these TEs, whole-genome nanopore sequencing and de novo genome assembly were performed. We found that these TEs occurred in a tomato breeding line via interspecific introgression from S. peruvianum. Our findings collectively show that interspecific introgressions can contribute to both genetic and phenotypic diversity not only by introducing novel genetic variants, but also by importing active transposable elements from other species.
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Affiliation(s)
- Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Melania Serganova
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Georgy Petrov
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Vladislav Mityukov
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051, Moscow, Russia
| | - Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia.
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia.
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Chen G, Yu D, Yang Y, Li X, Wang X, Sun D, Lu Y, Ke R, Zhang G, Cui J, Feng S. Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Nat Commun 2024; 15:3151. [PMID: 38605055 PMCID: PMC11009239 DOI: 10.1038/s41467-024-47501-3] [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: 09/29/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.
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Affiliation(s)
- Guangji Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- BGI Research, Wuhan, China
| | - Dan Yu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Yang
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Xiang Li
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Danyang Sun
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yanlin Lu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jie Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Institute of Infection and Health Research, Fudan University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, 200052, China.
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China.
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China.
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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4
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Cao RB, Chen R, Liao KX, Li H, Xu GB, Jiang XL. Karyotype and LTR-RTs analysis provide insights into oak genomic evolution. BMC Genomics 2024; 25:328. [PMID: 38566015 PMCID: PMC10988972 DOI: 10.1186/s12864-024-10177-6] [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: 11/23/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests. RESULTS Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes. CONCLUSION Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.
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Affiliation(s)
- Rui-Bin Cao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Ran Chen
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Ke-Xin Liao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - He Li
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Gang-Biao Xu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Xiao-Long Jiang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China.
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5
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Munasinghe M, Read A, Stitzer MC, Song B, Menard CC, Ma KY, Brandvain Y, Hirsch CN, Springer N. Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS Genet 2023; 19:e1011086. [PMID: 38134220 PMCID: PMC10773942 DOI: 10.1371/journal.pgen.1011086] [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: 04/11/2023] [Revised: 01/08/2024] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de novo genome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.
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Affiliation(s)
- Manisha Munasinghe
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Andrew Read
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Michelle C. Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Claire C. Menard
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Kristy Yubo Ma
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, Minnesota, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nathan Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
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6
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Huang Y, He J, Xu Y, Zheng W, Wang S, Chen P, Zeng B, Yang S, Jiang X, Liu Z, Wang L, Wang X, Liu S, Lu Z, Liu Z, Yu H, Yue J, Gao J, Zhou X, Long C, Zeng X, Guo YJ, Zhang WF, Xie Z, Li C, Ma Z, Jiao W, Zhang F, Larkin RM, Krueger RR, Smith MW, Ming R, Deng X, Xu Q. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nat Genet 2023; 55:1964-1975. [PMID: 37783780 DOI: 10.1038/s41588-023-01516-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide, such as sweet orange and lemon. The origin of Citrus species has long been debated and less is known about the Aurantioideae. Here, we compiled the genome sequences of 314 accessions, de novo assembled the genomes of 12 species and constructed a graph-based pangenome for Aurantioideae. Our analysis indicates that the ancient Indian Plate is the ancestral area for Citrus-related genera and that South Central China is the primary center of origin of the Citrus genus. We found substantial variations in the sequence and expression of the PH4 gene in Citrus relative to Citrus-related genera. Gene editing and biochemical experiments demonstrate a central role for PH4 in the accumulation of citric acid in citrus fruits. This study provides insights into the origin and evolution of the orange subfamily and a regulatory mechanism underpinning the evolution of fruit taste.
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Affiliation(s)
- Yue Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Jiaxian He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuantao Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Weikang Zheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shaohua Wang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Peng Chen
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Bin Zeng
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Shuizhi Yang
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Xiaolin Jiang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zishuang Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Lun Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xia Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shengjun Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhihao Lu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Ziang Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Huiwen Yu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianqiang Yue
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Junyan Gao
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Xianyan Zhou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Chunrui Long
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Xiuli Zeng
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station, Ministry of Agriculture and Rural Affairs, Lhasa, People's Republic of China
| | - Yong-Jie Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wen-Fu Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, People's Republic of China
| | - Zongzhou Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chunlong Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhaocheng Ma
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenbiao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Fei Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Robert M Larkin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Robert R Krueger
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA, USA
| | - Malcolm W Smith
- Department of Agriculture and Fisheries, Bundaberg, Queensland, Australia
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China.
- Hubei Hongshan Laboratory, Wuhan, People's Republic of China.
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7
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Mokhtar MM, El Allali A. MegaLTR: a web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1237426. [PMID: 37810401 PMCID: PMC10552921 DOI: 10.3389/fpls.2023.1237426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/21/2023] [Indexed: 10/10/2023]
Abstract
LTR-retrotransposons (LTR-RTs) are a class of RNA-replicating transposon elements (TEs) that can alter genome structure and function by moving positions, repositioning genes, shifting exons, and causing chromosomal rearrangements. LTR-RTs are widespread in many plant genomes and constitute a significant portion of the genome. Their movement and activity in eukaryotic genomes can provide insight into genome evolution and gene function, especially when LTR-RTs are located near or within genes. Building the redundant and non-redundant LTR-RTs libraries and their annotations for species lacking this resource requires extensive bioinformatics pipelines and expensive computing power to analyze large amounts of genomic data. This increases the need for online services that provide computational resources with minimal overhead and maximum efficiency. Here, we present MegaLTR as a web server and standalone pipeline that detects intact LTR-RTs at the whole-genome level and integrates multiple tools for structure-based, homologybased, and de novo identification, classification, annotation, insertion time determination, and LTR-RT gene chimera analysis. MegaLTR also provides statistical analysis and visualization with multiple tools and can be used to accelerate plant species discovery and assist breeding programs in their efforts to improve genomic resources. We hope that the development of online services such as MegaLTR, which can analyze large amounts of genomic data, will become increasingly important for the automated detection and annotation of LTR-RT elements.
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Affiliation(s)
- Morad M. Mokhtar
- African Genome Center, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Benguerir, Morocco
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8
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Zhang M, Qiu X. Genetic basis of genome size variation of wheat. Funct Integr Genomics 2023; 23:285. [PMID: 37648783 DOI: 10.1007/s10142-023-01194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/22/2023] [Accepted: 07/29/2023] [Indexed: 09/01/2023]
Abstract
Research on various species has revealed a connection between genome size variation and the physiological and ecological characteristics of the species, suggesting that it could be a crucial factor influencing a species' adaptability to different environments. Wheat, being one of the world's three primary grains, holds significance in this regard. Investigating the genome size of wheat and analyzing the genetic factors contributing to its variation could offer valuable insights for enhancing wheat agronomic traits. This project has developed a conservative site ratio calculation approach to determine the size of the wheat genome. Additionally, it employs flow cytometry and k-mer distribution analysis to validate this method. Furthermore, the researchers use re-sequencing data to investigate the impact of environmental selection pressure and transposon dynamics on the variation in the size of the wheat genome. The findings from this study demonstrate a strong relationship between the size of the wheat genome and several environmental factors. These results serve as a valuable reference for understanding the development of variation in the size of the hetero-hexaploid wheat genome. Moreover, they contribute to advancing fundamental research on the genetic mechanisms underlying wheat characteristics. Additionally, the study paves the way for exploring new research directions in wheat breeding, which holds promise for future advancements in this field.
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Affiliation(s)
- Ming Zhang
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuebing Qiu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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9
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Gorbenko IV, Petrushin IS, Shcherban AB, Orlov YL, Konstantinov YM. Short Interrupted Repeat Cassette (SIRC)-Novel Type of Repetitive DNA Element Found in Arabidopsis thaliana. Int J Mol Sci 2023; 24:11116. [PMID: 37446293 DOI: 10.3390/ijms241311116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Short interrupted repeat cassette (SIRC)-a novel DNA element found throughout the A. thaliana nuclear genome. SIRCs are represented by short direct repeats interrupted by diverse DNA sequences. The maxima of SIRC's distribution are located within pericentromeric regions. We suggest that originally SIRC was a special case of the complex internal structure of the miniature inverted repeat transposable element (MITE), and further MITE amplification, transposition, and loss of terminal inverted repeats gave rise to SIRC as an independent DNA element. SIRC sites were significantly enriched with several histone modifications associated with constitutive heterochromatin and mobile genetic elements. The majority of DNA-binding proteins, strongly associated with SIRC, are related to histone modifications for transcription repression. A part of SIRC was found to overlap highly inducible protein-coding genes, suggesting a possible regulatory role for these elements, yet their definitive functions need further investigation.
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Affiliation(s)
- Igor V Gorbenko
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
| | - Ivan S Petrushin
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
- Department of Business Communications and Informatics, Irkutsk State University, Irkutsk 664033, Russia
| | - Andrey B Shcherban
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Kurchatov Genomic Center ICG SB RAS, Novosibirsk 630090, Russia
| | - Yuriy L Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
- Agrarian and Technological Institute, Peoples' Friendship University of Russia, Moscow 117198, Russia
| | - Yuri M Konstantinov
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
- Biosoil Department, Irkutsk State University, Irkutsk 664003, Russia
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10
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Arvas YE, Marakli S, Kaya Y, Kalendar R. The power of retrotransposons in high-throughput genotyping and sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1174339. [PMID: 37180380 PMCID: PMC10167742 DOI: 10.3389/fpls.2023.1174339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023]
Abstract
The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant genomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented.
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Affiliation(s)
- Yunus Emre Arvas
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, Trabzon, Türkiye
| | - Sevgi Marakli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Türkiye
| | - Yılmaz Kaya
- Agricultural Biotechnology Department, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Ruslan Kalendar
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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11
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Roxo G, Brilhante M, Moura M, de Sequeira MM, Silva L, Costa JC, Vasconcelos R, Talhinhas P, Romeiras MM. Genome size variation within Crithmum maritimum: Clues on the colonization of insular environments. Ecol Evol 2023; 13:e10009. [PMID: 37091572 PMCID: PMC10116024 DOI: 10.1002/ece3.10009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Angiosperms present an astonishing diversity of genome sizes that can vary intra- or interspecifically. The remarkable new cytogenomic data shed some light on our understanding of evolution, but few studies were performed with insular and mainland populations to test possible correlations with dispersal, speciation, and adaptations to insular environments. Here, patterns of cytogenomic diversity were assessed among geographic samples (ca. 114) of Crithmum maritimum (Apiaceae), collected across the Azores and Madeira archipelagos, as well as in adjacent continental areas of Portugal. Using flow cytometry, the results indicated a significant intraspecific genome size variation, spanning from reduced sizes in the insular populations to larger ones in the mainland populations. Moreover, there was a tendency for an increase in genome size along the mainland populations, associated with lower temperatures, higher precipitation, and lower precipitation seasonality. However, this gradient might be the result of historic phylogeographical events associated with previous dispersal and extinction of local populations. Overall, our findings provided evidence that smaller genome sizes might play a critical role in the colonization of islands, corroborating other studies that argue that organisms with smaller genomes use fewer resources, having a selective advantage under insular environments. Although further studies are needed to improve our understanding of the mechanisms underlying genome size evolution on islands, conservation strategies must be promoted to protect the rich cytogenomic diversity found among C. maritimum populations, which occur in coastal areas that are particularly threatened by human activity, pollution, invasive species, and climate changes.
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Affiliation(s)
- Guilherme Roxo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - Miguel Brilhante
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Mónica Moura
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | | | - Luís Silva
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - José Carlos Costa
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Raquel Vasconcelos
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Maria M. Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de CiênciasUniversidade de LisboaLisbonPortugal
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12
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Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023; 9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.
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Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:172-192. [PMID: 35959634 PMCID: PMC9804982 DOI: 10.1111/tpj.15938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a basal eudicot plant with a unique lifestyle, physiological features, and evolutionary characteristics. Here we report the unique profile of transposable elements (TEs) in the genome, using a manually curated repeat library. TEs account for 59% of the genome, and hAT (Ac/Ds) elements alone represent 8%, more than in any other known plant genome. About 18% of the lotus genome is comprised of Copia LTR retrotransposons, and over 25% of them are associated with non-canonical termini (non-TGCA). Such high abundance of non-canonical LTR retrotransposons has not been reported for any other organism. TEs are very abundant in genic regions, with retrotransposons enriched in introns and DNA transposons primarily in flanking regions of genes. The recent insertion of TEs in introns has led to significant intron size expansion, with a total of 200 Mb in the 28 455 genes. This is accompanied by declining TE activity in intergenic regions, suggesting distinct control efficacy of TE amplification in different genomic compartments. Despite the prevalence of TEs in genic regions, some genes are associated with fewer TEs, such as those involved in fruit ripening and stress responses. Other genes are enriched with TEs, and genes in epigenetic pathways are the most associated with TEs in introns, indicating a dynamic interaction between TEs and the host surveillance machinery. The dramatic differential abundance of TEs with genes involved in different biological processes as well as the variation of target preference of different TEs suggests the composition and activity of TEs influence the path of evolution.
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Affiliation(s)
- Stefan Cerbin
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Ecology & Evolutionary BiologyUniversity of Kansas1200 Sunnyside AvenueLawrenceKS66045USA
| | - Shujun Ou
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yang Li
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Yanni Sun
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Ning Jiang
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
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14
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Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus Salvia (Lamiaceae). PLANTS 2022; 11:plants11172244. [PMID: 36079625 PMCID: PMC9460151 DOI: 10.3390/plants11172244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of S. officinalis and S. sclarea was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (S. sclarea) and twelve (S. officinalis) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of S. officinalis and S. sclarea were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in Salvia karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied Salvia species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data.
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15
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Chromosome-Level Genome Assembly of a Fragrant Japonica Rice Cultivar 'Changxianggeng 1813' Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Japonica Rice. Int J Mol Sci 2022; 23:ijms23179705. [PMID: 36077110 PMCID: PMC9456513 DOI: 10.3390/ijms23179705] [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] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
East Asia has an abundant resource of fragrant japonica rice that is gaining increasing interest among both consumers and producers. However, genomic resources and in particular complete genome sequences currently available for the breeding of fragrant japonica rice are still scarce. Here, integrating Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods, we presented a high-quality chromosome-level genome assembly (~378.78 Mb) for a new fragrant japonica cultivar ‘Changxianggeng 1813’, with 31,671 predicated protein-coding genes. Based on the annotated genome sequence, we demonstrated that it was the badh2-E2 type of deletion (a 7-bp deletion in the second exon) that caused fragrance in ‘Changxianggeng 1813’. Comparative genomic analyses revealed that multiple gene families involved in the abiotic stress response were expanded in the ‘Changxianggeng 1813’ genome, which further supported the previous finding that no generalized loss of abiotic stress tolerance associated with the fragrance phenotype. Although the ‘Changxianggeng 1813’ genome showed high genomic synteny with the genome of the non-fragrant japonica rice cultivar Nipponbare, a total of 289,970 single nucleotide polymorphisms (SNPs), 96,093 small insertion-deletion polymorphisms (InDels), and 8690 large structure variants (SVs, >1000 bp) were identified between them. Together, these genomic resources will be valuable for elucidating the mechanisms underlying economically important traits and have wide-ranging implications for genomics-assisted breeding in fragrant japonica rice.
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16
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Priest SJ, Yadav V, Roth C, Dahlmann TA, Kück U, Magwene PM, Heitman J. Uncontrolled transposition following RNAi loss causes hypermutation and antifungal drug resistance in clinical isolates of Cryptococcus neoformans. Nat Microbiol 2022; 7:1239-1251. [PMID: 35918426 PMCID: PMC10840647 DOI: 10.1038/s41564-022-01183-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 06/23/2022] [Indexed: 02/07/2023]
Abstract
Cryptococcus neoformans infections cause approximately 15% of AIDS-related deaths owing to a combination of limited antifungal therapies and drug resistance. A collection of clinical and environmental C. neoformans isolates were assayed for increased mutation rates via fluctuation analysis, and we identified two hypermutator C. neoformans clinical isolates with increased mutation rates when exposed to the combination of rapamycin and FK506. Sequencing of drug target genes found that Cnl1 transposon insertions conferred the majority of resistance to rapamycin and FK506 and could also independently cause resistance to 5-fluoroorotic acid and the clinically relevant antifungal 5-flucytosine. Whole-genome sequencing revealed both hypermutator genomes harbour a nonsense mutation in the RNA-interference component ZNF3 and hundreds of Cnl1 elements organized into massive subtelomeric arrays on each of the fourteen chromosomes. Quantitative trait locus mapping in 28 progeny derived from a cross between a hypermutator and wild-type identified a locus associated with hypermutation that included znf3. CRISPR editing of the znf3 nonsense mutation abolished hypermutation and restored small-interfering-RNA production. We conclude that hypermutation and drug resistance in these clinical isolates result from RNA-interference loss and accumulation of Cnl1 elements.
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Affiliation(s)
- Shelby J Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Cullen Roth
- Department of Biology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Tim A Dahlmann
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.
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17
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Cai X, Lin R, Liang J, King GJ, Wu J, Wang X. Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1298-1310. [PMID: 35278263 PMCID: PMC9241368 DOI: 10.1111/pbi.13807] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 05/20/2023]
Abstract
Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.
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Affiliation(s)
- Xu Cai
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Runmao Lin
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Jianli Liang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - Jian Wu
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
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18
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Yang JS, Qian ZH, Shi T, Li ZZ, Chen JM. Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness. DNA Res 2022; 29:6617837. [PMID: 35751614 PMCID: PMC9267246 DOI: 10.1093/dnares/dsac022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/24/2022] [Indexed: 11/19/2022] Open
Abstract
Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of ∼ 520 Mb. More than half of the N. indica genome consists of transposable elements (TEs), and a higher density of TEs around genes may play a significant role in response to an ever-changing environment by regulating the nearby gene. Additionally, our analysis revealed that N. indica only experienced a gamma (γ) whole-genome triplication event. Functional enrichment of the N. indica-specific and expanded gene families highlighted genes involved in the responses to hypoxia and plant–pathogen interactions, which may strengthen the ability to adapt to external challenges and improve ecological fitness. Furthermore, we identified 160 members of the nucleotide-binding site and leucine-rich repeat gene family, which may be linked to the defence response. Collectively, the high-quality N. indica genome reported here opens a novel avenue to understand the evolution and rapid invasion of Nymphoides spp.
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Affiliation(s)
- Jing-Shan Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Zhi-Hao Qian
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
| | - Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
| | - Jin-Ming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
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Amosova AV, Yurkevich OY, Bolsheva NL, Samatadze TE, Zoshchuk SA, Muravenko OV. Repeatome Analyses and Satellite DNA Chromosome Patterns in Deschampsia sukatschewii, D. cespitosa, and D. antarctica (Poaceae). Genes (Basel) 2022; 13:genes13050762. [PMID: 35627148 PMCID: PMC9141916 DOI: 10.3390/genes13050762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 02/05/2023] Open
Abstract
Subpolar and polar ecotypes of Deschampsia sukatschewii (Popl.) Roshev, D. cespitosa (L.) P. Beauv, and D. antarctica E. Desv. are well adapted to stressful environmental conditions, which make them useful model plants for genetic research and breeding. For the first time, the comparative repeatome analyses of subpolar and polar D. sukatschewii, D. cespitosa, and D. antarctica was performed using RepeatExplorer/TAREAN pipelines and FISH-based chromosomal mapping of the identified satellite DNA families (satDNAs). In the studied species, mobile genetic elements of class 1 made up the majority of their repetitive DNA; interspecific variations in the total amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were revealed; 12–18 high confident and 7–9 low confident putative satDNAs were identified. According to BLAST, most D. sukatschewii satDNAs demonstrated sequence similarity with satDNAs of D. antarctica and D. cespitosa indicating their common origin. Chromosomal mapping of 45S rDNA, 5S rDNA, and satDNAs of D. sukatschewii allowed us to construct the species karyograms and detect new molecular chromosome markers important for Deschampsia species. Our findings confirmed that genomes of D. sukatschewii and D. cespitosa were more closely related compared to D. antarctica according to repeatome composition and patterns of satDNA chromosomal distribution.
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20
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On the Base Composition of Transposable Elements. Int J Mol Sci 2022; 23:ijms23094755. [PMID: 35563146 PMCID: PMC9099904 DOI: 10.3390/ijms23094755] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Transposable elements exhibit a base composition that is often different from the genomic average and from hosts’ genes. The most common compositional bias is towards Adenosine and Thymine, although this bias is not universal, and elements with drastically different base composition can coexist within the same genome. The AT-richness of transposable elements is apparently maladaptive because it results in poor transcription and sub-optimal translation of proteins encoded by the elements. The cause(s) of this unusual base composition remain unclear and have yet to be investigated. Here, I review what is known about the nucleotide content of transposable elements and how this content can affect the genome of their host as well as their own replication. The compositional bias of transposable elements could result from several non-exclusive processes including horizontal transfer, mutational bias, and selection. It appears that mutation alone cannot explain the high AT-content of transposons and that selection plays a major role in the evolution of the compositional bias. The reason why selection would favor a maladaptive nucleotide content remains however unexplained and is an area of investigation that clearly deserves attention.
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21
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Song B, Marco-Sola S, Moreto M, Johnson L, Buckler ES, Stitzer MC. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. Proc Natl Acad Sci U S A 2022; 119:e2113075119. [PMID: 34934012 PMCID: PMC8740769 DOI: 10.1073/pnas.2113075119] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/04/2022] Open
Abstract
Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication. Here, we introduce Anchored Wavefront alignment (AnchorWave), which performs whole-genome duplication-informed collinear anchor identification between genomes and performs base pair-resolved global alignment for collinear blocks using a two-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multikilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs. By contrast, other genome alignment tools showed low power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome as position matches or indels than the closest competitive approach when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor-binding sites at a rate of 1.05- to 74.85-fold higher than other tools with significantly lower false-positive alignments. AnchorWave complements available genome alignment tools by showing obvious improvement when applied to genomes with dispersed repeats, active TEs, high sequence diversity, and whole-genome duplication variation.
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Affiliation(s)
- Baoxing Song
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
| | - Santiago Marco-Sola
- Department of Computer Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain
- Departament d'Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Miquel Moreto
- Department of Computer Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain
- Departament d'Arquitectura de Computadors, Universitat Politècnica de Catalunya, Barcelona 08034, Spain
| | - Lynn Johnson
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
- Agricultural Research Service, US Department of Agriculture, Ithaca, NY 14853
| | - Michelle C Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
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22
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Oberlin S, Rajeswaran R, Trasser M, Barragán-Borrero V, Schon MA, Plotnikova A, Loncsek L, Nodine MD, Marí-Ordóñez A, Voinnet O. Innate, translation-dependent silencing of an invasive transposon in Arabidopsis. EMBO Rep 2021; 23:e53400. [PMID: 34931432 PMCID: PMC8892269 DOI: 10.15252/embr.202153400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Co‐evolution between hosts’ and parasites’ genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence degeneration, and, ultimately, loss of autonomy of most transposable elements (TEs). Recognition of newly invasive plant TEs, by contrast, involves an innate antiviral‐like silencing response. To investigate this response’s activation, we studied the single‐copy element EVADÉ (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically reactivated. In Ty1/Copia elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full‐length genomic flGAG‐POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly nuclear flGAG‐POL. During this process, an unusually intense ribosomal stalling event coincides with mRNA breakage yielding unconventional 5’OH RNA fragments that evade RNA quality control. The starting point of sRNA production by RNA‐DEPENDENT‐RNA‐POLYMERASE‐6 (RDR6), exclusively on shGAG, occurs precisely at this breakage point. This hitherto‐unrecognized “translation‐dependent silencing” (TdS) is independent of codon usage or GC content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against EVD de novo invasions that underlies its associated sRNA pattern.
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Affiliation(s)
- Stefan Oberlin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Rajendran Rajeswaran
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Marieke Trasser
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Verónica Barragán-Borrero
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.,Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Michael A Schon
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Plotnikova
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Loncsek
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Michael D Nodine
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria.,Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Arturo Marí-Ordóñez
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.,Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
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23
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Wicker T, Stritt C, Sotiropoulos AG, Poretti M, Pozniak C, Walkowiak S, Gundlach H, Stein N. Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 3:2100022. [PMID: 36619351 PMCID: PMC9744471 DOI: 10.1002/ggn2.202100022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 01/11/2023]
Abstract
Wheat has one of the largest and most repetitive genomes among major crop plants, containing over 85% transposable elements (TEs). TEs populate genomes much in the way that individuals populate ecosystems, diversifying into different lineages, sub-families and sub-populations. The recent availability of high-quality, chromosome-scale genome sequences from ten wheat lines enables a detailed analysis how TEs evolved in allohexaploid wheat, its diploids progenitors, and in various chromosomal haplotype segments. LTR retrotransposon families evolved into distinct sub-populations and sub-families that were active in waves lasting several hundred thousand years. Furthermore, It is shown that different retrotransposon sub-families were active in the three wheat sub-genomes, making them useful markers to study and date polyploidization events and chromosomal rearrangements. Additionally, haplotype-specific TE sub-families are used to characterize chromosomal introgressions in different wheat lines. Additionally, populations of non-autonomous TEs co-evolved over millions of years with their autonomous partners, leading to complex systems with multiple types of autonomous, semi-autonomous and non-autonomous elements. Phylogenetic and TE population analyses revealed the relationships between non-autonomous elements and their mobilizing autonomous partners. TE population analysis provided insights into genome evolution of allohexaploid wheat and genetic diversity of species, and may have implication for future crop breeding.
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Affiliation(s)
- Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZurichZurich8008Switzerland
| | - Christoph Stritt
- Department of Plant and Microbial BiologyUniversity of ZurichZurich8008Switzerland,Present address:
Department of Medical Parasitology and Infection BiologySwiss Tropical and Public Health InstituteBasel4123Switzerland,Present address:
University of BaselBasel4001Switzerland
| | | | - Manuel Poretti
- Department of Plant and Microbial BiologyUniversity of ZurichZurich8008Switzerland
| | - Curtis Pozniak
- Crop Development CentreUniversity of SaskatchewanSaskatoonSaskatchewanSK S7N 5A8Canada
| | - Sean Walkowiak
- Crop Development CentreUniversity of SaskatchewanSaskatoonSaskatchewanSK S7N 5A8Canada,Grain Research LaboratoryCanadian Grain CommissionWinnipegManitobaR3C 3G8Canada
| | - Heidrun Gundlach
- PGSB Plant Genome and Systems BiologyHelmholtz Center MunichGerman Research Center for Environmental HealthNeuherberg85764Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Seeland06466Germany,Center of Integrated Breeding Research (CiBreed)Department of Crop SciencesGeorg‐August‐UniversityGöttingen37075Germany
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24
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Roquis D, Robertson M, Yu L, Thieme M, Julkowska M, Bucher E. Genomic impact of stress-induced transposable element mobility in Arabidopsis. Nucleic Acids Res 2021; 49:10431-10447. [PMID: 34551439 PMCID: PMC8501995 DOI: 10.1093/nar/gkab828] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.
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Affiliation(s)
- David Roquis
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
| | - Marta Robertson
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
| | - Liang Yu
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Michael Thieme
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | | | - Etienne Bucher
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
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25
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Senderowicz M, Nowak T, Rojek-Jelonek M, Bisaga M, Papp L, Weiss-Schneeweiss H, Kolano B. Descending Dysploidy and Bidirectional Changes in Genome Size Accompanied Crepis (Asteraceae) Evolution. Genes (Basel) 2021; 12:1436. [PMID: 34573417 PMCID: PMC8472258 DOI: 10.3390/genes12091436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 02/05/2023] Open
Abstract
The evolution of the karyotype and genome size was examined in species of Crepis sensu lato. The phylogenetic relationships, inferred from the plastid and nrITS DNA sequences, were used as a framework to infer the patterns of karyotype evolution. Five different base chromosome numbers (x = 3, 4, 5, 6, and 11) were observed. A phylogenetic analysis of the evolution of the chromosome numbers allowed the inference of x = 6 as the ancestral state and the descending dysploidy as the major direction of the chromosome base number evolution. The derived base chromosome numbers (x = 5, 4, and 3) were found to have originated independently and recurrently in the different lineages of the genus. A few independent events of increases in karyotype asymmetry were inferred to have accompanied the karyotype evolution in Crepis. The genome sizes of 33 Crepis species differed seven-fold and the ancestral genome size was reconstructed to be 1C = 3.44 pg. Both decreases and increases in the genome size were inferred to have occurred within and between the lineages. The data suggest that, in addition to dysploidy, the amplification/elimination of various repetitive DNAs was likely involved in the genome and taxa differentiation in the genus.
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Affiliation(s)
- Magdalena Senderowicz
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
| | - Teresa Nowak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
| | - Magdalena Rojek-Jelonek
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
| | - Maciej Bisaga
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
| | - Laszlo Papp
- Eötvös Loránd University Botanical Garden, Illés u. 25, 1083 Budapest, Hungary;
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria;
| | - Bozena Kolano
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
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26
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Haas M, Kono T, Macchietto M, Millas R, McGilp L, Shao M, Duquette J, Qiu Y, Hirsch CN, Kimball J. Whole-genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole-genome duplication in the Zizania genus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1802-1818. [PMID: 34310794 DOI: 10.1111/tpj.15419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/16/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Zizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. Using long- and short-range sequencing, Hi-C scaffolding and RNA-seq data from eight tissues, we generated an annotated whole-genome de novo assembly of NWR. The assembly was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania-Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26-30 million years ago (26-30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6-8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR-Z. latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.
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Affiliation(s)
- Matthew Haas
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Thomas Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marissa Macchietto
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Reneth Millas
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lillian McGilp
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Mingqin Shao
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jacques Duquette
- North Central Research and Outreach Center, University of Minnesota, Grand Rapids, MN, 55744, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jennifer Kimball
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
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27
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Boutanaev AM. Components of Intrageneric Genome Size Dynamics in Plants and Animals. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421080032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Aubin E, El Baidouri M, Panaud O. Horizontal Gene Transfers in Plants. Life (Basel) 2021; 11:life11080857. [PMID: 34440601 PMCID: PMC8401529 DOI: 10.3390/life11080857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
In plants, as in all eukaryotes, the vertical transmission of genetic information through reproduction ensures the maintenance of the integrity of species. However, many reports over the past few years have clearly shown that horizontal gene transfers, referred to as HGTs (the interspecific transmission of genetic information across reproductive barriers) are very common in nature and concern all living organisms including plants. The advent of next-generation sequencing technologies (NGS) has opened new perspectives for the study of HGTs through comparative genomic approaches. In this review, we provide an up-to-date view of our current knowledge of HGTs in plants.
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29
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Ebrahimzadegan R, Orooji F, Ma P, Mirzaghaderi G. Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes. FRONTIERS IN PLANT SCIENCE 2021; 12:716750. [PMID: 34490015 PMCID: PMC8417419 DOI: 10.3389/fpls.2021.716750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn't detect differences between subspecies, although (GAA)10 signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Fatemeh Orooji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, China
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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30
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Neumann P, Oliveira L, Čížková J, Jang TS, Klemme S, Novák P, Stelmach K, Koblížková A, Doležel J, Macas J. Impact of parasitic lifestyle and different types of centromere organization on chromosome and genome evolution in the plant genus Cuscuta. THE NEW PHYTOLOGIST 2021; 229:2365-2377. [PMID: 33090498 DOI: 10.1111/nph.17003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/01/2020] [Indexed: 05/06/2023]
Abstract
The parasitic genus Cuscuta (Convolvulaceae) is exceptional among plants with respect to centromere organization, including both monocentric and holocentric chromosomes, and substantial variation in genome size and chromosome number. We investigated 12 species representing the diversity of the genus in a phylogenetic context to reveal the molecular and evolutionary processes leading to diversification of their genomes. We measured genome sizes and investigated karyotypes and centromere organization using molecular cytogenetic techniques. We also performed low-pass whole genome sequencing and comparative analysis of repetitive DNA composition. A remarkable 102-fold variation in genome sizes (342-34 734 Mbp/1C) was detected for monocentric Cuscuta species, while genomes of holocentric species were of moderate sizes (533-1545 Mbp/1C). The genome size variation was primarily driven by the differential accumulation of LTR-retrotransposons and satellite DNA. The transition to holocentric chromosomes in the subgenus Cuscuta was associated with loss of histone H2A phosphorylation and elimination of centromeric retrotransposons. In addition, basic chromosome number of holocentric species (x = 7) was smaller than in monocentrics (x = 15 or 16). We demonstrated that the transition to holocentricity in Cuscuta was accompanied by significant changes in epigenetic marks, chromosome number and the repetitive DNA sequence composition.
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Affiliation(s)
- Pavel Neumann
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Ludmila Oliveira
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-779 00, Czech Republic
| | - Tae-Soo Jang
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sonja Klemme
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Katarzyna Stelmach
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
- Department of Plant Biology and Biotechnology, University of Agriculture in Krakow, 29 Listopada 54, Krakow, 31-425, Poland
| | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-779 00, Czech Republic
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
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31
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Penin AA, Kasianov AS, Klepikova AV, Kirov IV, Gerasimov ES, Fesenko AN, Logacheva MD. High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum. FRONTIERS IN PLANT SCIENCE 2021; 12:612382. [PMID: 33815435 PMCID: PMC8010679 DOI: 10.3389/fpls.2021.612382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/03/2021] [Indexed: 05/06/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5-1 Mya) multiplied TEs ("transposon burst") and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size of F. esculentum compared with its sister species F. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspecies F. esculentum ssp. ancestrale and buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA: http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.
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Affiliation(s)
- Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
- *Correspondence: Maria D. Logacheva,
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Maiwald S, Weber B, Seibt KM, Schmidt T, Heitkam T. The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability. ANNALS OF BOTANY 2021; 127:91-109. [PMID: 33009553 PMCID: PMC7750724 DOI: 10.1093/aob/mcaa176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS Plant genomes contain many retrotransposons and their derivatives, which are subject to rapid sequence turnover. As non-autonomous retrotransposons do not encode any proteins, they experience reduced selective constraints leading to their diversification into multiple families, usually limited to a few closely related species. In contrast, the non-coding Cassandra terminal repeat retrotransposons in miniature (TRIMs) are widespread in many plants. Their hallmark is a conserved 5S rDNA-derived promoter in their long terminal repeats (LTRs). As sugar beet (Beta vulgaris) has a well-described LTR retrotransposon landscape, we aim to characterize TRIMs in beet and related genomes. METHODS We identified Cassandra retrotransposons in the sugar beet reference genome and characterized their structural relationships. Genomic organization, chromosomal localization, and distribution of Cassandra-TRIMs across the Amaranthaceae were verified by Southern and fluorescent in situ hybridization. KEY RESULTS All 638 Cassandra sequences in the sugar beet genome contain conserved LTRs and thus constitute a single family. Nevertheless, variable internal regions required a subdivision into two Cassandra subfamilies within B. vulgaris. The related Chenopodium quinoa harbours a third subfamily. These subfamilies vary in their distribution within Amaranthaceae genomes, their insertion times and the degree of silencing by small RNAs. Cassandra retrotransposons gave rise to many structural variants, such as solo LTRs or tandemly arranged Cassandra retrotransposons. These Cassandra derivatives point to an interplay of template switch and recombination processes - mechanisms that likely caused Cassandra's subfamily formation and diversification. CONCLUSIONS We traced the evolution of Cassandra in the Amaranthaceae and detected a considerable variability within the short internal regions, whereas the LTRs are strongly conserved in sequence and length. Presumably these hallmarks make Cassandra a prime target for unequal recombination, resulting in the observed structural diversity, an example of the impact of LTR-mediated evolutionary mechanisms on the host genome.
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Affiliation(s)
- Sophie Maiwald
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kathrin M Seibt
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Tony Heitkam
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
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Retrotransposons and the Evolution of Genome Size in Pisum. BIOTECH 2020; 9:biotech9040024. [PMID: 35822827 PMCID: PMC9258317 DOI: 10.3390/biotech9040024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of pea LTR-containing retrotransposons have the frequency and age distributions consistent with the behavior of neutral alleles and whether these parameters can explain the rate of change of genome size in legumes. (2) We used the recently assembled v1a pea genome sequence to obtain data on LTR-LTR divergence from which their age can be estimated. We coupled these data to prior information on the distribution of insertion site alleles. (3) We found that the age and frequency distribution data are consistent with the neutral theory. (4) We concluded that demographic processes are the underlying cause of genome size variation in legumes.
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Hsu CC, Chen SY, Lai PH, Hsiao YY, Tsai WC, Liu ZJ, Chung MC, Panaud O, Chen HH. Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids. BMC Genomics 2020; 21:807. [PMID: 33213366 PMCID: PMC7678294 DOI: 10.1186/s12864-020-07221-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilitates understanding the transpositional activity of TEs with their effects on the orchid genome structure. RESULTS We combined the draft whole-genome sequences of Phalaenopsis equestris with BAC end sequences, Roche 454, and Illumina/Solexa, and identified long terminal repeat (LTR) retrotransposons in these genome sequences by using LTRfinder and classified by using Gepard software. Among the 10 families Gypsy-like retrotransposons, three families Gypsy1, Gypsy2, and Gypsy3, contained the most copies among these predicted elements. In addition, six high-copy retrotransposons were identified according to their reads in the sequenced raw data. The 12-kb Orchid-rt1 contains 18,000 copies representing 220 Mbp of the P. equestris genome. Southern blot and slot blot assays showed that these four retrotransposons Gypsy1, Gypsy2, Gypsy3, and Orchid-rt1 contained high copies in the large-genome-size/large-chromosome species P. violacea and P. bellina. Both Orchid-rt1 and Gypsy1 displayed various ratios of copy number for the LTR sequences versus coding sequences among four Phalaenopsis species, including P. violacea and P. bellina and small-genome-size/small-chromosome P. equestris and P. ahprodite subsp. formosana, which suggests that Orchid-rt1 and Gypsy1 have been through various mutations and homologous recombination events. FISH results showed amplification of Orchid-rt1 in the euchromatin regions among the four Phalaenopsis species. The expression levels of Peq018599 encoding copper transporter 1 is highly upregulated with the insertion of Orchid-rt1, while it is down regulated for Peq009948 and Peq014239 encoding for a 26S proteasome non-ATP regulatory subunit 4 homolog and auxin-responsive factor AUX/IAA-related. In addition, insertion of Orchid-rt1 in these three genes are all in their intron regions. CONCLUSION Orchid-rt1 and Gypsy1-3 have amplified within Phalaenopsis orchids concomitant with the expanded genome sizes, and Orchid-rt1 and Gypsy1 may have gone through various mutations and homologous recombination events. Insertion of Orchid-rt1 is in the introns and affects gene expression levels.
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Affiliation(s)
- Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Yun Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Han Lai
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mei-Chu Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Olivier Panaud
- Institute of Plant Genome and Development, University of Perpignan, Perpignan, France
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. .,Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan.
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Lanciano S, Cristofari G. Measuring and interpreting transposable element expression. Nat Rev Genet 2020; 21:721-736. [PMID: 32576954 DOI: 10.1038/s41576-020-0251-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA sequencing include transposon-derived transcripts, most computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from chimeric gene-TE transcripts or pervasive transcription. Here we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.
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Boutanaev AM, Nemchinov LG. Genome Size Dynamics within Multiple Genera of Diploid Seed Plants. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Akakpo R, Carpentier MC, Ie Hsing Y, Panaud O. The impact of transposable elements on the structure, evolution and function of the rice genome. THE NEW PHYTOLOGIST 2020; 226:44-49. [PMID: 31797393 DOI: 10.1111/nph.16356] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Transposable elements (TEs) are ubiquitous in plants and are the primary genomic component of the majority of taxa. Knowledge of their impact on the structure, function and evolution of plant genomes is therefore a priority in the field of genomics. Rice, as one of the most prevalent crops for food security worldwide, has been subjected to intense research efforts over recent decades. Consequently, a considerable amount of genomic resources has been generated and made freely available to the scientific community. These can be exploited both to improve our understanding of some basic aspects of genome biology of this species and to develop new concepts for crop improvement. In this review, we describe the current knowledge on how TEs have shaped rice chromosomes and propose a new strategy based on a genome-wide association study (GWAS) to address the important question of their functional impact on this crop.
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Affiliation(s)
- Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Yue Ie Hsing
- Institute of Plant and Microbial Biology, Acadeia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- Institut Universitaire de France, 1 Rue Descartes, 75231, Paris Cedex 05, France
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Li MY, Feng K, Hou XL, Jiang Q, Xu ZS, Wang GL, Liu JX, Wang F, Xiong AS. The genome sequence of celery ( Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae family. HORTICULTURE RESEARCH 2020; 7:9. [PMID: 31934340 PMCID: PMC6944684 DOI: 10.1038/s41438-019-0235-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 11/02/2019] [Accepted: 12/05/2019] [Indexed: 05/02/2023]
Abstract
Celery (Apium graveolens L.) is a vegetable crop in the Apiaceae family that is widely cultivated and consumed because it contains necessary nutrients and multiple biologically active ingredients, such as apigenin and terpenoids. Here, we report the genome sequence of celery based on the use of HiSeq 2000 sequencing technology to obtain 600.8 Gb of data, achieving ~189-fold genome coverage, from 68 sequencing libraries with different insert sizes ranging from 180 bp to 10 kb in length. The assembled genome has a total sequence length of 2.21 Gb and consists of 34,277 predicted genes. Repetitive DNA sequences represent 68.88% of the genome sequences, and LTR retrotransposons are the main components of the repetitive sequences. Evolutionary analysis showed that a recent whole-genome duplication event may have occurred in celery, which could have contributed to its large genome size. The genome sequence of celery allowed us to identify agronomically important genes involved in disease resistance, flavonoid biosynthesis, terpenoid metabolism, and other important cellular processes. The comparative analysis of apigenin biosynthesis genes among species might explain the high apigenin content of celery. The whole-genome sequences of celery have been deposited at CeleryDB (http://apiaceae.njau.edu.cn/celerydb). The availability of the celery genome data advances our knowledge of the genetic evolution of celery and will contribute to further biological research and breeding in celery as well as other Apiaceae plants.
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Affiliation(s)
- Meng-Yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Qian Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
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Jedlicka P, Lexa M, Kejnovsky E. What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination? FRONTIERS IN PLANT SCIENCE 2020; 11:644. [PMID: 32508870 PMCID: PMC7251063 DOI: 10.3389/fpls.2020.00644] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/27/2020] [Indexed: 05/10/2023]
Abstract
LTR retrotransposons constitute a significant part of plant genomes and their evolutionary dynamics play an important role in genome size changes. Current methods of LTR retrotransposon age estimation are based only on LTR (long terminal repeat) divergence. This has prompted us to analyze sequence similarity of LTRs in 25,144 LTR retrotransposons from fifteen plant species as well as formation of solo LTRs. We found that approximately one fourth of nested retrotransposons showed a higher LTR divergence than the pre-existing retrotransposons into which they had been inserted. Moreover, LTR similarity was correlated with LTR length. We propose that gene conversion can contribute to this phenomenon. Gene conversion prediction in LTRs showed potential converted regions in 25% of LTR pairs. Gene conversion was higher in species with smaller genomes while the proportion of solo LTRs did not change with genome size in analyzed species. The negative correlation between the extent of gene conversion and the abundance of solo LTRs suggests interference between gene conversion and ectopic recombination. Since such phenomena limit the traditional methods of LTR retrotransposon age estimation, we recommend an improved approach based on the exclusion of regions affected by gene conversion.
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Affiliation(s)
- Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Brno, Czechia
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- *Correspondence: Eduard Kejnovsky,
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Ebrahimzadegan R, Houben A, Mirzaghaderi G. Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds. Sci Rep 2019; 9:19989. [PMID: 31882680 PMCID: PMC6934454 DOI: 10.1038/s41598-019-56383-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 11/09/2022] Open
Abstract
Here, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (-B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, 6617715175, Sanandaj, Iran
| | - Andreas Houben
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, 6617715175, Sanandaj, Iran.
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Majka J, Bzdęga K, Janiak A, Ćwiek-Kupczyńska H, Krajewski P, Książczyk T, Zwierzykowski Z. Cytogenetic and molecular genotyping in the allotetraploid Festuca pratensis × Lolium perenne hybrids. BMC Genomics 2019; 20:367. [PMID: 31088367 PMCID: PMC6518686 DOI: 10.1186/s12864-019-5766-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/03/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids can merge in their genomes agronomically important characteristics. However, in polyploid plants, especially in allopolyploids, the hybridization of divergent genomes could contribute to various abnormalities, such as variability in chromosome number, structural rearrangements, and/or disorders in inheritance patterns. Here we studied these issues in allotetraploid Festuca pratensis × Lolium perenne hybrids. RESULTS Cytogenetic procedures, including fluorescent in situ hybridization, genomic in situ hybridization, and molecular markers - inter-simple sequence repeats (ISSR) were exploited. This cytogenetic approach indicated the dynamics in the number and distribution of ribosomal RNA genes and structural rearrangements for both parental genomes (Festuca and Lolium) in hybrid karyotypes. The separate analysis of F. pratensis and L. perenne chromosomes in hybrid plants (F2-F3 generations of F. pratensis × L. perenne) revealed the asymmetrical level of rearrangements. Recognized structural changes were mainly located in the distal part of chromosome arms, and in chromosomes bearing ribosomal DNA, they were more frequently mapped in arms without this sequence. Based on the ISSR markers distribution, we found that the tetrasomic type of inheritance was characteristic for the majority of ISSR loci, but the disomic type was also observed. Nonetheless, no preference in the transmission of either Festuca or Lolium alleles to the following generations of allotetraploid F. pratensis × L. perenne hybrid was observed. CONCLUSION Our study reports cytogenetic and molecular genotyping of the F. pratensis × L. perenne hybrid and its following F2-F3 progenies. The analysis of 137 allotetraploid F. pratensis × L. perenne hybrids revealed the higher level of recombination in chromosomes derived from F. pratensis genome. The results of ISSR markers indicated a mixed model of inheritance, which may be characteristic for these hybrids.
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Affiliation(s)
- Joanna Majka
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Katarzyna Bzdęga
- Department of Botany and Nature Protection, University of Silesia in Katowice, Katowice, Poland
| | - Agnieszka Janiak
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Hanna Ćwiek-Kupczyńska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Tomasz Książczyk
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Neumann P, Novák P, Hoštáková N, Macas J. Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mob DNA 2019; 10:1. [PMID: 30622655 PMCID: PMC6317226 DOI: 10.1186/s13100-018-0144-1] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/20/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related species. Previous attempts to group these families into broader categories reflecting their phylogenetic relationships were limited either to analyzing a narrow range of plant species or to analyzing a small numbers of elements. Furthermore, there is no reference database that allows for similarity based classification of LTR-retrotransposons. RESULTS We have assembled a database of retrotransposon encoded polyprotein domains sequences extracted from 5410 Ty1/copia elements and 8453 Ty3/gypsy elements sampled from 80 species representing major groups of green plants (Viridiplantae). Phylogenetic analysis of the three most conserved polyprotein domains (RT, RH and INT) led to dividing Ty1/copia and Ty3/gypsy retrotransposons into 16 and 14 lineages respectively. We also characterized various features of LTR-retrotransposon sequences including additional polyprotein domains, extra open reading frames and primer binding sites, and found that the occurrence and/or type of these features correlates with phylogenies inferred from the three protein domains. CONCLUSIONS We have established an improved classification system applicable to LTR-retrotransposons from a wide range of plant species. This system reflects phylogenetic relationships as well as distinct sequence and structural features of the elements. A comprehensive database of retrotransposon protein domains (REXdb) that reflects this classification provides a reference for efficient and unified annotation of LTR-retrotransposons in plant genomes. Access to REXdb related tools is implemented in the RepeatExplorer web server (https://repeatexplorer-elixir.cerit-sc.cz/) or using a standalone version of REXdb that can be downloaded seaparately from RepeatExplorer web page (http://repeatexplorer.org/).
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Affiliation(s)
- Pavel Neumann
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 České Budějovice, Czech Republic
| | - Petr Novák
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 České Budějovice, Czech Republic
| | - Nina Hoštáková
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 České Budějovice, Czech Republic
| | - Jiří Macas
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 České Budějovice, Czech Republic
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Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nat Commun 2019; 10:24. [PMID: 30604755 PMCID: PMC6318337 DOI: 10.1038/s41467-018-07974-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
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Affiliation(s)
- Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Ernandes Manfroi
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, 305-8687, Ibaraki, Japan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Emilie Debladis
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France.
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France.
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Kelleher ES, Jaweria J, Akoma U, Ortega L, Tang W. QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline. PLoS Biol 2018; 16:e2006040. [PMID: 30376574 PMCID: PMC6207299 DOI: 10.1371/journal.pbio.2006040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/26/2018] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) are obligate genetic parasites that propagate in host genomes by replicating in germline nuclei, thereby ensuring transmission to offspring. This selfish replication not only produces deleterious mutations—in extreme cases, TE mobilization induces genotoxic stress that prohibits the production of viable gametes. Host genomes could reduce these fitness effects in two ways: resistance and tolerance. Resistance to TE propagation is enacted by germline-specific small-RNA-mediated silencing pathways, such as the Piwi-interacting RNA (piRNA) pathway, and is studied extensively. However, it remains entirely unknown whether host genomes may also evolve tolerance by desensitizing gametogenesis to the harmful effects of TEs. In part, the absence of research on tolerance reflects a lack of opportunity, as small-RNA-mediated silencing evolves rapidly after a new TE invades, thereby masking existing variation in tolerance. We have exploited the recent historical invasion of the Drosophila melanogaster genome by P-element DNA transposons in order to study tolerance of TE activity. In the absence of piRNA-mediated silencing, the genotoxic stress imposed by P-elements disrupts oogenesis and, in extreme cases, leads to atrophied ovaries that completely lack germline cells. By performing quantitative trait locus (QTL) mapping on a panel of recombinant inbred lines (RILs) that lack piRNA-mediated silencing of P-elements, we uncovered multiple QTL that are associated with differences in tolerance of oogenesis to P-element transposition. We localized the most significant QTL to a small 230-kb euchromatic region, with the logarithm of the odds (LOD) peak occurring in the bruno locus, which codes for a critical and well-studied developmental regulator of oogenesis. Genetic, cytological, and expression analyses suggest that bruno dosage modulates germline stem cell (GSC) loss in the presence of P-element activity. Our observations reveal segregating variation in TE tolerance for the first time, and implicate gametogenic regulators as a source of tolerant variants in natural populations. Transposable elements (TEs), or “jumping genes,” are mobile fragments of selfish DNA that leave deleterious mutations and DNA damage in their wake as they spread through host genomes. Their harmful effects are known to select for resistance by the host, in which the propagation of TEs is regulated and reduced. Here, we study for the first time whether host cells might also exhibit tolerance to TEs, by reducing their harmful effects without directly controlling their movement. By taking advantage of a panel of wild-type Drosophila melanogaster that lack resistance to P-element DNA transposons, we identified a small region of the genome that influences tolerance of P-element activity. We further demonstrate that a gene within that region, bruno, strongly influences the negative effects of P-element mobilization on the fly. When bruno dosage is reduced, the fertility of females carrying mobile P-elements is enhanced. The bruno locus encodes a protein with no known role in TE regulation but multiple well-characterized functions in oogenesis. We propose that bruno function reduces tolerance of the developing oocyte to DNA damage that is caused by P-elements.
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Affiliation(s)
- Erin S. Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- * E-mail:
| | - Jaweria Jaweria
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Uchechukwu Akoma
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lily Ortega
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Wenpei Tang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
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45
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Ren L, Huang W, Cannon EKS, Bertioli DJ, Cannon SB. A Mechanism for Genome Size Reduction Following Genomic Rearrangements. Front Genet 2018; 9:454. [PMID: 30356760 PMCID: PMC6189423 DOI: 10.3389/fgene.2018.00454] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
The factors behind genome size evolution have been of great interest, considering that eukaryotic genomes vary in size by more than three orders of magnitude. Using a model of two wild peanut relatives, Arachis duranensis and Arachis ipaensis, in which one genome experienced large rearrangements, we find that the main determinant in genome size reduction is a set of inversions that occurred in A. duranensis, and subsequent net sequence removal in the inverted regions. We observe a general pattern in which sequence is lost more rapidly at newly distal (telomeric) regions than it is gained at newly proximal (pericentromeric) regions - resulting in net sequence loss in the inverted regions. The major driver of this process is recombination, determined by the chromosomal location. Any type of genomic rearrangement that exposes proximal regions to higher recombination rates can cause genome size reduction by this mechanism. In comparisons between A. duranensis and A. ipaensis, we find that the inversions all occurred in A. duranensis. Sequence loss in those regions was primarily due to removal of transposable elements. Illegitimate recombination is likely the major mechanism responsible for the sequence removal, rather than unequal intrastrand recombination. We also measure the relative rate of genome size reduction in these two Arachis diploids. We also test our model in other plant species and find that it applies in all cases examined, suggesting our model is widely applicable.
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Affiliation(s)
- Longhui Ren
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, United States
| | - Wei Huang
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, United States.,Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Ethalinda K S Cannon
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, United States.,Department of Computer Science, Iowa State University, Ames, IA, United States
| | - David J Bertioli
- Institute of Biological Sciences, University of Brasiìlia, Brasiìlia, Brazil.,Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Ames, IA, United States
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Wicker T, Gundlach H, Spannagl M, Uauy C, Borrill P, Ramírez-González RH, De Oliveira R, Mayer KFX, Paux E, Choulet F. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol 2018; 19:103. [PMID: 30115100 PMCID: PMC6097303 DOI: 10.1186/s13059-018-1479-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/11/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. RESULTS The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid. CONCLUSIONS Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.
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Affiliation(s)
- Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Philippa Borrill
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | | | - Romain De Oliveira
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France
| | - Klaus F X Mayer
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, Munich, Germany
| | - Etienne Paux
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France
| | - Frédéric Choulet
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France.
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47
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Yuan Z, Fang Y, Zhang T, Fei Z, Han F, Liu C, Liu M, Xiao W, Zhang W, Wu S, Zhang M, Ju Y, Xu H, Dai H, Liu Y, Chen Y, Wang L, Zhou J, Guan D, Yan M, Xia Y, Huang X, Liu D, Wei H, Zheng H. The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1363-1374. [PMID: 29271050 PMCID: PMC5999313 DOI: 10.1111/pbi.12875] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/26/2017] [Accepted: 12/18/2017] [Indexed: 05/18/2023]
Abstract
Pomegranate (Punica granatum L.) has an ancient cultivation history and has become an emerging profitable fruit crop due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the limited genomic resources have restricted further elucidation of genetics and evolution of these interesting traits. Here, we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336-Mb genome, consists of 2177 scaffolds with an N50 size of 1.7 Mb and contains 30 903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis share the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the colour formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence provides an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding.
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Affiliation(s)
- Zhaohe Yuan
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | - Yanming Fang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Taikui Zhang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
- USDA Robert W. Holley Center for Agriculture and HealthIthacaNYUSA
| | | | - Cuiyu Liu
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | - Min Liu
- Biomarker Technologies CorporationBeijingChina
| | - Wei Xiao
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | | | - Shan Wu
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Mengwei Zhang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | - Youhui Ju
- Biomarker Technologies CorporationBeijingChina
| | - Huili Xu
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | - He Dai
- Biomarker Technologies CorporationBeijingChina
| | - Yujun Liu
- College of Biological Sciences and BiotechnologyBeijing Forestry UniversityBeijingChina
| | - Yanhui Chen
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Lili Wang
- Biomarker Technologies CorporationBeijingChina
| | - Jianqing Zhou
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | - Dian Guan
- Biomarker Technologies CorporationBeijingChina
| | - Ming Yan
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | - Yanhua Xia
- Biomarker Technologies CorporationBeijingChina
| | - Xianbin Huang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
| | | | - Hongmin Wei
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- College of ForestryNanjing Forestry UniversityNanjingChina
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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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49
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Abstract
The “centromere paradox” refers to rapidly evolving and highly diverse centromere DNA sequences even in closely related eukaryotes. However, factors contributing to this rapid divergence are largely unknown. Here, we identified large regional, LTR retrotransposon-rich centromeres in a group of human fungal pathogens belonging to the Cryptococcus species complex. We provide evidence that loss-of-functional RNAi machinery and possibly cytosine DNA methylation trigger instability of the genome by activation of centromeric retrotransposons presumably suppressed by RNAi. We propose that RNAi, together with cytosine DNA methylation, serves as a critical determinant that maintains repetitive transposon-rich centromere structures. This study explores the direct link between RNAi and centromere structure evolution. The centromere DNA locus on a eukaryotic chromosome facilitates faithful chromosome segregation. Despite performing such a conserved function, centromere DNA sequence as well as the organization of sequence elements is rapidly evolving in all forms of eukaryotes. The driving force that facilitates centromere evolution remains an enigma. Here, we studied the evolution of centromeres in closely related species in the fungal phylum of Basidiomycota. Using ChIP-seq analysis of conserved inner kinetochore proteins, we identified centromeres in three closely related Cryptococcus species: two of which are RNAi-proficient, while the other lost functional RNAi. We find that the centromeres in the RNAi-deficient species are significantly shorter than those of the two RNAi-proficient species. While centromeres are LTR retrotransposon-rich in all cases, the RNAi-deficient species lost all full-length retroelements from its centromeres. In addition, centromeres in RNAi-proficient species are associated with a significantly higher level of cytosine DNA modifications compared with those of RNAi-deficient species. Furthermore, when an RNAi-proficient Cryptococcus species and its RNAi-deficient mutants were passaged under similar conditions, the centromere length was found to be occasionally shortened in RNAi mutants. In silico analysis of predicted centromeres in a group of closely related Ustilago species, also belonging to the Basidiomycota, were found to have undergone a similar transition in the centromere length in an RNAi-dependent fashion. Based on the correlation found in two independent basidiomycetous species complexes, we present evidence suggesting that the loss of RNAi and cytosine DNA methylation triggered transposon attrition, which resulted in shortening of centromere length during evolution.
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50
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Domb K, Keidar D, Yaakov B, Khasdan V, Kashkush K. Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides). BMC PLANT BIOLOGY 2017; 17:175. [PMID: 29078757 PMCID: PMC5659041 DOI: 10.1186/s12870-017-1134-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 10/17/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes. RESULTS We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat. CONCLUSIONS For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.
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Affiliation(s)
- Katherine Domb
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Danielle Keidar
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Beery Yaakov
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Vadim Khasdan
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
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