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Lin L, Sharma A, Yu Q. Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome. BMC PLANT BIOLOGY 2021; 21:424. [PMID: 34537020 PMCID: PMC8449440 DOI: 10.1186/s12870-021-03194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. RESULTS We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. CONCLUSIONS Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.
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Affiliation(s)
- Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA.
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A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome. Genes (Basel) 2021; 12:genes12060859. [PMID: 34205210 PMCID: PMC8227079 DOI: 10.3390/genes12060859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/26/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes.
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Xin Y, Ma B, Xiang Z, He N. Amplification of miniature inverted-repeat transposable elements and the associated impact on gene regulation and alternative splicing in mulberry ( Morus notabilis). Mob DNA 2019; 10:27. [PMID: 31289464 PMCID: PMC6593561 DOI: 10.1186/s13100-019-0169-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
Background Miniature inverted-repeat transposable elements (MITEs) are common in eukaryotic genomes, and are important for genomic evolution. Results In the present study, the identification of MITEs in the mulberry genome revealed 286,122 MITE-related sequences, including 90,789 full-length elements. The amplification of mulberry MITEs and the influence of MITEs on the evolution of the mulberry genome were analyzed. The timing of MITE amplifications varied considerably among the various MITE families. Fifty-one MITE families have undergone a single round of amplification, while the other families developed from multiple amplifications. Most mulberry MITEs were inserted near genes and some could regulate gene expression through small RNAs. An analysis of transgenic plants indicated that MITE insertions can upregulate the expression of a target gene. Moreover, MITEs are frequently associated with alternative splicing events (exonizations). Conclusion The data presented herein provide insights into the generation of MITEs as well as their impact on gene regulation and evolution in mulberry. Electronic supplementary material The online version of this article (10.1186/s13100-019-0169-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youchao Xin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
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Zhou M, Tao G, Pi P, Zhu Y, Bai Y, Meng X. Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla). PLANTA 2016; 244:775-787. [PMID: 27160169 DOI: 10.1007/s00425-016-2544-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/01/2016] [Indexed: 06/05/2023]
Abstract
Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.
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Affiliation(s)
- Mingbing Zhou
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
| | - Guiyun Tao
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Peiyao Pi
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Yihang Zhu
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Youhuang Bai
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Xianwen Meng
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
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Wang L, Peng Q, Zhao J, Ren F, Zhou H, Wang W, Liao L, Owiti A, Jiang Q, Han Y. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation. PLANT MOLECULAR BIOLOGY 2016; 91:179-91. [PMID: 26941188 DOI: 10.1007/s11103-016-0454-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S-haplotype-specific F-box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus.
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Affiliation(s)
- Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Jianbo Zhao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Fei Ren
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Wei Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Albert Owiti
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Quan Jiang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China.
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
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Dai S, Hou J, Long Y, Wang J, Li C, Xiao Q, Jiang X, Zou X, Zou J, Meng J. Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae. BMC PLANT BIOLOGY 2015; 15:149. [PMID: 26084405 PMCID: PMC4471910 DOI: 10.1186/s12870-015-0490-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/07/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Miniature inverted repeat transposable elements (MITEs) are important components of eukaryotic genomes, with hundreds of families and many copies, which may play important roles in gene regulation and genome evolution. However, few studies have investigated the molecular mechanisms involved. In our previous study, a Tourist-like MITE, Monkey King, was identified from the promoter region of a flowering time gene, BnFLC.A10, in Brassica napus. Based on this MITE, the characteristics and potential roles on gene regulation of the MITE family were analyzed in Brassicaceae. RESULTS The characteristics of the Tourist-like MITE family Monkey King in Brassicaceae, including its distribution, copies and insertion sites in the genomes of major Brassicaceae species were analyzed in this study. Monkey King was actively amplified in Brassica after divergence from Arabidopsis, which was indicated by the prompt increase in copy number and by phylogenetic analysis. The genomic variations caused by Monkey King insertions, both intra- and inter-species in Brassica, were traced by PCR amplification. Genomic sequence analysis showed that most complete Monkey King elements are located in gene-rich regions, less than 3kb from genes, in both the B. rapa and A. thaliana genomes. Sixty-seven Brassica expressed sequence tags carrying Monkey King fragments were also identified from the NCBI database. Bisulfite sequencing identified specific DNA methylation of cytosine residues in the Monkey King sequence. A fragment containing putative TATA-box motifs in the MITE sequence could bind with nuclear protein(s) extracted from leaves of B. napus plants. A Monkey King-related microRNA, bna-miR6031, was identified in the microRNA database. In transgenic A. thaliana, when the Monkey King element was inserted upstream of 35S promoter, the promoter activity was weakened. CONCLUSION Monkey King, a Brassicaceae Tourist-like MITE family, has amplified relatively recently and has induced intra- and inter-species genomic variations in Brassica. Monkey King elements are most abundant in the vicinity of genes and may have a substantial effect on genome-wide gene regulation in Brassicaceae. Monkey King insertions potentially regulate gene expression and genome evolution through epigenetic modification and new regulatory motif production.
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Affiliation(s)
- Shutao Dai
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jinna Hou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhenzhou, Henan, 450002, China.
| | - Yan Long
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jing Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Cong Li
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Qinqin Xiao
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Xiaoxue Jiang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Xiaoxiao Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jun Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jinling Meng
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Tang Z, Zhang HH, Huang K, Zhang XG, Han MJ, Zhang Z. Repeated horizontal transfers of four DNA transposons in invertebrates and bats. Mob DNA 2015; 6:3. [PMID: 25606061 PMCID: PMC4298943 DOI: 10.1186/s13100-014-0033-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/30/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal transfer (HT) of transposable elements (TEs) into a new genome is considered as an important force to drive genome variation and biological innovation. However, most of the HT of DNA transposons previously described occurred between closely related species or insects. RESULTS In this study, we carried out a detailed analysis of four DNA transposons, which were found in the first sequenced twisted-wing parasite, Mengenilla moldrzyki. Through the homology-based strategy, these transposons were also identified in other insects, freshwater planarian, hydrozoans, and bats. The phylogenetic distribution of these transposons was discontinuous, and they showed extremely high sequence identities (>87%) over their entire length in spite of their hosts diverging more than 300 million years ago (Mya). Additionally, phylogenies and comparisons of transposons versus orthologous gene identities demonstrated that these transposons have transferred into their hosts by independent HTs. CONCLUSIONS Here, we provided the first documented example of HT of CACTA transposons, which have been so far extensively studied in plants. Our results demonstrated that bats had continuously acquired new DNA elements via HT. This implies that predation on a large quantity of insects might increase bat exposure to HT. In addition, parasite-host interaction might facilitate exchanging of their genetic materials.
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Affiliation(s)
- Zhou Tang
- School of Life Sciences, Chongqing University, Chongqing, 400044 China
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000 China
| | - Ke Huang
- College of Forestry and Life Science, Chongqing University of Sciences and Arts, Yongchuan, Chongqing, 40216 China
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000 China
| | - Min-Jin Han
- School of Life Sciences, Chongqing University, Chongqing, 400044 China
| | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, 400044 China
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Menzel G, Heitkam T, Seibt KM, Nouroz F, Müller-Stoermer M, Heslop-Harrison JS, Schmidt T. The diversification and activity of hAT transposons in Musa genomes. Chromosome Res 2014; 22:559-71. [DOI: 10.1007/s10577-014-9445-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/10/2014] [Accepted: 10/20/2014] [Indexed: 11/29/2022]
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Zhang HH, Shen YH, Xu HE, Liang HY, Han MJ, Zhang Z. A novel hAT element in Bombyx mori and Rhodnius prolixus: its relationship with miniature inverted repeat transposable elements (MITEs) and horizontal transfer. INSECT MOLECULAR BIOLOGY 2013; 22:584-596. [PMID: 23889491 DOI: 10.1111/imb.12047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Comparative analysis of transposable elements (TEs) from different species can make it possible to reconstruct their history over evolutionary time. In this study, we identified a novel hAT element in Bombyx mori and Rhodnius prolixus with characteristic GGGCGGCA repeats in its subterminal region. Meanwhile, phylogenetic analysis demonstrated that the elements in these two species might represent a separate cluster of the hAT superfamily. Strikingly, a previously identified miniature inverted repeat transposable element (MITE) shared high identity with this autonomous element across the entire length, supporting the hypothesis that MITEs are derived from the internal deletion of DNA transposons. Interestingly, identity of the consensus sequences of this novel hAT element between B. mori and R. prolixus, which diverged about 370 million years ago, was as high as 96.5% over their full length (about 3.6 kb) at the nucleotide level. The patchy distribution amongst species, coupled with overall lack of intense purifying selection acting on this element, suggest that this novel hAT element might have experienced horizontal transfer between the ancestors of B. mori and R. prolixus. Our results highlight that this novel hAT element could be used as a potential tool for germline transformation of R. prolixus to control the transmission of Trypanosoma cruzi, which causes Chagas disease.
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Affiliation(s)
- H-H Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
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Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes. BMC Genomics 2013; 14:71. [PMID: 23369001 PMCID: PMC3579700 DOI: 10.1186/1471-2164-14-71] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Class 2 transposable elements (TEs) are the predominant elements in and around plant genes where they generate significant allelic diversity. Using the complete sequences of four grasses, we have performed a novel comparative analysis of class 2 TEs. To ensure consistent comparative analyses, we re-annotated class 2 TEs in Brachypodium distachyon, Oryza sativa (rice), Sorghum bicolor and Zea mays and assigned them to one of the five cut-and-paste superfamilies found in plant genomes (Tc1/mariner, PIF/Harbinger, hAT, Mutator, CACTA). We have focused on noncoding elements because of their abundance, and compared superfamily copy number, size and genomic distribution as well as correlation with the level of nearby gene expression. RESULTS Our comparison revealed both unique and conserved features. First, the average length or size distribution of elements in each superfamily is largely conserved, with the shortest always being Tc1/mariner elements, followed by PIF/Harbinger, hAT, Mutator and CACTA. This order also holds for the ratio of the copy numbers of noncoding to coding elements. Second, with the exception of CACTAs, noncoding TEs are enriched within and flanking genes, where they display conserved distribution patterns, having the highest peak in the promoter region. Finally, our analysis of microarray data revealed that genes associated with Tc1/mariner and PIF/Harbinger noncoding elements have significantly higher expression levels than genes without class 2 TEs. In contrast, genes with CACTA elements have significantly lower expression than genes without class 2 TEs. CONCLUSIONS We have achieved the most comprehensive annotation of class 2 TEs to date in these four grass genomes. Comparative analysis of this robust dataset led to the identification of several previously unknown features of each superfamily related to copy number, element size, genomic distribution and correlation with the expression levels of nearby genes. These results highlight the importance of distinguishing TE superfamilies when assessing their impact on gene and genome evolution.
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msechBari, a new MITE-like element in Drosophila sechellia related to the Bari transposon. Genet Res (Camb) 2012; 93:381-5. [PMID: 22189603 DOI: 10.1017/s0016672311000371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A few occurrences of miniature inverted-repeat transposable elements (MITEs) have been reported in species of the genus Drosophila. Here, we describe msechBari, a MITE-like element in Drosophila sechellia. The element is short, approximately 90 bp in length, AT-rich and occurs in association with, or close to, genes, characteristics that are typical for MITEs. The identification was performed in silico using the sequenced genome of D. sechellia and confirmed in a laboratory strain. This short element is related to the Bari_DM transposon of Drosophila melanogaster, having terminal inverted repeats (TIRs) of a similar length and a high identity with the full-length Bari_DM element. The estimated recent origin of the element and the homogeneity observed between copies found in the genome suggests that msechBari could be active in D. sechellia.
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Menzel G, Krebs C, Diez M, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T. Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives. PLANT MOLECULAR BIOLOGY 2012; 78:393-405. [PMID: 22246381 DOI: 10.1007/s11103-011-9872-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/20/2011] [Indexed: 05/03/2023]
Abstract
Genome-wide analyses of repetitive DNA suggest a significant impact particularly of transposable elements on genome size and evolution of virtually all eukaryotic organisms. In this study, we analyzed the abundance and diversity of the hAT transposon superfamily of the sugar beet (B. vulgaris) genome, using molecular, bioinformatic and cytogenetic approaches. We identified 81 transposase-coding sequences, three of which are part of structurally intact but nonfunctional hAT transposons (BvhAT), in a B. vulgaris BAC library as well as in whole genome sequencing-derived data sets. Additionally, 116 complete and 497 truncated non-autonomous BvhAT derivatives lacking the transposase gene were in silico-detected. The 116 complete derivatives were subdivided into four BvhATpin groups each characterized by a distinct terminal inverted repeat motif. Both BvhAT and BvhATpin transposons are specific for species of the genus Beta and closely related species, showing a localization on B. vulgaris chromosomes predominantely in euchromatic regions. The lack of any BvhAT transposase function together with the high degree of degeneration observed for the BvhAT and the BvhATpin genomic fraction contrasts with the abundance and activity of autonomous and non-autonomous hAT transposons revealed in other plant species. This indicates a possible genus-specific structural and functional repression of the hAT transposon superfamily during Beta diversification and evolution.
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Affiliation(s)
- Gerhard Menzel
- Institute of Botany, Dresden University of Technology, 01062 Dresden, Germany
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Sarilar V, Marmagne A, Brabant P, Joets J, Alix K. BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space. PLANT MOLECULAR BIOLOGY 2011; 77:59-75. [PMID: 21626236 DOI: 10.1007/s11103-011-9794-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 05/12/2011] [Indexed: 05/02/2023]
Abstract
We characterized a Brassica miniature inverted repeat transposable element (MITE) from the Stowaway superfamily, designated BraSto (Bra ssica Sto waway). BraSto copy number was assessed using real-time quantitative PCR in the two diploid species B. rapa (genome A) and B. oleracea (genome C) and the corresponding allotetraploid species B. napus (genome AC). Phylogenetic relationships among a set of 131 BraSto copies were then analyzed. BraSto appears to have been only moderately amplified in the Brassica genome and was still active recently with marks of proliferation in both diploid Brassica species, which diverged 3.75 million years ago, but also in the allotetraploid species after reuniting of the two differentiated genomes. We characterized insertion sites for low-divergence BraSto copies among the gene space of the B. rapa genome using bioinformatics approaches. For BraSto copies localized nearby or within genes, we observed frequent associations of BraSto with putative promoters and regulatory regions of genes, but exclusion from coding regions. In addition, BraSto was significantly similar to several Brassica expressed sequence tags (ESTs), including stress-induced ESTs. We also demonstrated the enrichment of BraSto sequences in binding sites for transcription factors and other regulatory elements. Our results lead to the question of a role for BraSto in the regulation of gene expression: this putative role, if further confirmed experimentally, would help to obtain a new insight into the significance of MITEs in the functional plant genome.
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Affiliation(s)
- Véronique Sarilar
- AgroParisTech/CNRS, UMR 0320/UMR 8120 Génétique Végétale INRA/Univ. Paris-Sud/CNRS/AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France
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Han Y, Wessler SR. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res 2010; 38:e199. [PMID: 20880995 PMCID: PMC3001096 DOI: 10.1093/nar/gkq862] [Citation(s) in RCA: 367] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are a special type of Class 2 non-autonomous transposable element (TE) that are abundant in the non-coding regions of the genes of many plant and animal species. The accurate identification of MITEs has been a challenge for existing programs because they lack coding sequences and, as such, evolve very rapidly. Because of their importance to gene and genome evolution, we developed MITE-Hunter, a program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets. The output of MITE-Hunter is composed of consensus TE sequences grouped into families that can be used as a library file for homology-based TE detection programs such as RepeatMasker. MITE-Hunter was evaluated by searching the rice genomic database and comparing the output with known rice TEs. It discovered most of the previously reported rice MITEs (97.6%), and found sixteen new elements. MITE-Hunter was also compared with two other MITE discovery programs, FINDMITE and MUST. Unlike MITE-Hunter, neither of these programs can search large genomic data sets including whole genome sequences. More importantly, MITE-Hunter is significantly more accurate than either FINDMITE or MUST as the vast majority of their outputs are false-positives.
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Affiliation(s)
- Yujun Han
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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Renault S, Demattéi MV, Lahouassa H, Bigot Y, Augé-Gouillou C. In vitro recombination and inverted terminal repeat binding activities of the Mcmar1 transposase. Biochemistry 2010; 49:3534-44. [PMID: 20359246 DOI: 10.1021/bi901957p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Mcmar1 mariner element (MLE) presents some intriguing features with two large, perfectly conserved, 355 bp inverted terminal repeats (ITRs) containing two 28 bp direct repeats (DRs). The presence of a complete ORF in Mcmar1 makes it possible to explore the transposition of this unusual MLE. Mcmar1 transposase (MCMAR1) was purified, and in vitro transposition assays showed that it is able to promote ITR-dependent DNA cleavages and recombination events, which correspond to plasmid fusions and transpositions with imprecise ends. Further analyses indicated that MCMAR1 is able to interact with the 355 bp ITR through two DRs: the EDR (external DR) is a high-affinity binding site for MCMAR1, whereas the IDR (internal DR) is a low-affinity binding site. The main complex detected within the EDR contained a transposase dimer and only one DNA molecule. We hypothesize that the inability of MCMAR1 to promote precise in vitro transposition events could be due to mutations in its ORF sequence or to the specific features of transposase binding to the ITR. Indeed, the ITR region spanning from EDR to IDR resembles a MITE and could be bent by specific host factors. This suggests that the assembly of the transposition complex is more complex than that of those involved in the mobility of the Mos1 and Himar1 mariner elements.
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Affiliation(s)
- Sylvaine Renault
- Université François Rabelais de Tours, GICC, CNRS, UMR 6239, UFR des Sciences & Techniques, Parc de Grandmont, 37200 Tours, France.
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Benjak A, Boué S, Forneck A, Casacuberta JM. Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.). Genome Biol Evol 2009; 1:75-84. [PMID: 20333179 PMCID: PMC2817404 DOI: 10.1093/gbe/evp009] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2009] [Indexed: 01/07/2023] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II transposons present in genomes as highly homogeneous populations of small elements. Their high copy number and close association to genes make their potential impact on gene evolution particularly relevant. Here, we present a detailed analysis of the MITE families directly related to grapevine "cut-and-paste" transposons. Our results show that grapevine MITEs have transduplicated and amplified genomic sequences, including gene sequences and fragments of other mobile elements. Our results also show that although some of the MITE families were already present in the ancestor of the European and American Vitis wild species, they have been amplified and have been actively transposing accompanying grapevine domestication and breeding. We show that MITEs are abundant in grapevine and some of them are frequently inserted within the untranslated regions of grapevine genes. MITE insertions are highly polymorphic among grapevine cultivars, which frequently generate transcript variability. The data presented here show that MITEs have greatly contributed to the grapevine genetic diversity which has been used for grapevine domestication and breeding.
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Affiliation(s)
- Andrej Benjak
- Department of Plant Molecular Genetics, Center for Research in Agricultural Genomics (Consejo Superior Investigaciones Científicas-Institut de Recerca I Tecnologia Agrícola-Universitat Autònoma de Barcelona), Barcelona, Spain
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Fujino K, Sekiguchi H. Site specific cytosine methylation in rice nonautonomous transposable element nDart. PLANT MOLECULAR BIOLOGY 2008; 67:511-8. [PMID: 18409027 DOI: 10.1007/s11103-008-9335-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 04/03/2008] [Indexed: 05/15/2023]
Abstract
The mobile nonautonomous element nDart, which is active in intact rice plants, exhibits locus specific transposition. Due to the high homogeneity of nDart elements, the locus specificity of nDart transposition might be controlled by factors other than genetic differences. In this study, we elucidated the regulation of the locus specificity of nDart transposition. The difference of transpositional activities in 10 nDart elements among rice varieties exhibiting nDart transposition was clearly correlated with the methylation state of nDart elements. Both hyper- and hypo-methylated nDart elements were inactive, while site specific methylation in both subterminal regions was identified in active nDart loci. The specific methylation sites contain the pentamer motif GCC/ACG. The repeated motifs in the subterminal region of nDart elements may contribute to the stable secondary structure of nDart elements with low free energy. Our results suggested that site specific cytosine methylation may loosen the stable secondary structure of the nDart element to allow it to bind TPase, which then perform the excision of nDart elements from genomic loci.
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Affiliation(s)
- Kenji Fujino
- Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Higashi-5, Kita-15, Naganuma 0691317, Hokkaido, Japan.
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