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Gao D. Introduction of Plant Transposon Annotation for Beginners. BIOLOGY 2023; 12:1468. [PMID: 38132293 PMCID: PMC10741241 DOI: 10.3390/biology12121468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for beginners, as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detection including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes transposon classification and explains why the terms 'autonomous' and 'non-autonomous' cannot be used to classify the superfamilies of transposons. Lastly, this review also discusses how to identify misannotated transposons and improve the quality of the transposon database. This review provides helpful information about plant transposons and a beginner's guide on annotating these repetitive sequences.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210, USA
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Mokhtar MM, Alsamman AM, El Allali A. PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons. FRONTIERS IN PLANT SCIENCE 2023; 14:1134627. [PMID: 36950350 PMCID: PMC10025401 DOI: 10.3389/fpls.2023.1134627] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/16/2023] [Indexed: 05/29/2023]
Abstract
LTR-retrotransposons (LTR-RTs) are a large group of transposable elements that replicate through an RNA intermediate and alter genome structure. The activities of LTR-RTs in plant genomes provide helpful information about genome evolution and gene function. LTR-RTs near or within genes can directly alter gene function. This work introduces PlantLTRdb, an intact LTR-RT database for 195 plant species. Using homology- and de novo structure-based methods, a total of 150.18 Gbp representing 3,079,469 pseudomolecules/scaffolds were analyzed to identify, characterize, annotate LTR-RTs, estimate insertion ages, detect LTR-RT-gene chimeras, and determine nearby genes. Accordingly, 520,194 intact LTR-RTs were discovered, including 29,462 autonomous and 490,732 nonautonomous LTR-RTs. The autonomous LTR-RTs included 10,286 Gypsy and 19,176 Copia, while the nonautonomous were divided into 224,906 Gypsy, 218,414 Copia, 1,768 BARE-2, 3,147 TR-GAG and 4,2497 unknown. Analysis of the identified LTR-RTs located within genes showed that a total of 36,236 LTR-RTs were LTR-RT-gene chimeras and 11,619 LTR-RTs were within pseudo-genes. In addition, 50,026 genes are within 1 kbp of LTR-RTs, and 250,587 had a distance of 1 to 10 kbp from LTR-RTs. PlantLTRdb allows researchers to search, visualize, BLAST and analyze plant LTR-RTs. PlantLTRdb can contribute to the understanding of structural variations, genome organization, functional genomics, and the development of LTR-RT target markers for molecular plant breeding. PlantLTRdb is available at https://bioinformatics.um6p.ma/PlantLTRdb.
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Puzakov MV, Puzakova LV, Ulupova YN. Differential Activity of Genes with IS630/TC1/MARINER Transposon Fragments in the Genome of the Ctenophore Mnemiopsis leidyi. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2022. [DOI: 10.3103/s089141682204005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
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4
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Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis). Sci Rep 2022; 12:16233. [PMID: 36171247 PMCID: PMC9519581 DOI: 10.1038/s41598-022-20400-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Marker-assisted breeding and tagging of important quantitative trait loci for beneficial traits are two important strategies for the genetic improvement of plants. However, the scarcity of diverse and informative genetic markers covering the entire tea genome limits our ability to achieve such goals. In the present study, we used a comparative genomic approach to mine the tea genomes of Camellia sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS) to identify the markers to differentiate tea genotypes. In our study, 43 and 60 Camellia sinensis miniature inverted-repeat transposable element (CsMITE) families were identified in these two sequenced tea genomes, with 23,170 and 37,958 putative CsMITE sequences, respectively. In addition, we identified 4912 non-redundant, Camellia sinensis intron length polymorphic (CsILP) markers, 85.8% of which were shared by both the CSS and CSA genomes. To validate, a subset of randomly chosen 10 CsMITE markers and 15 CsILP markers were tested and found to be polymorphic among the 36 highly diverse tea genotypes. These genome-wide markers, which were identified for the first time in tea plants, will be a valuable resource for genetic diversity analysis as well as marker-assisted breeding of tea genotypes for quality improvement.
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5
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Puzakov MV, Puzakova LV, Cheresiz SV, Sang Y. The IS630/Tc1/mariner transposons in three ctenophore genomes. Mol Phylogenet Evol 2021; 163:107231. [PMID: 34133948 DOI: 10.1016/j.ympev.2021.107231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Transposable elements (TEs) exert a significant effect on the structure and functioning of the genomes and also serve as a source of the new genes. The study of the TE diversity and evolution in different taxa is indispensable for the fundamental understanding of their roles in the genomes. IS630/Tc1/mariner (ITm) transposable elements represent the most prevalent and diverse group of DNA transposons. In this work, we studied the diversity, evolutionary dynamics and the phylogenetic relationships of the ITm transposons found in three ctenophore species: Mnemiopsis leidyi, Pleurobrachia bachei, Beroe ovata. We identified 29 ITm transposons, seven of which possess the terminal inverted repeats (TIRs) and an intact transposase, and, thus, are, presumably, active. Four other ITm transposons have the features of domesticated TEs. According to the results of the phylogenetic analysis, the ITm transposons of the ctenophores represent five groups - MLE/DD34D, TLE/DD34-38E, mosquito/DD37E, Visiror/DD41D and pogo/DDxD. Pogo/DDxD superfamily turnes out to be the most diverse and prevalent, since it accounts for more than 40% of the TEs identified. The data obtained in this research will fill the gap of knowledge of the diversity and evolution of the ITm transposons in the multicellular genomes and will lay the ground for the study of the TE effects on the evolution of the ctenophores.
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Affiliation(s)
- Mikhail V Puzakov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia.
| | - Ludmila V Puzakova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia
| | - Sergey V Cheresiz
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogova st., 1, Novosibirsk 630090, Russia; State Scientific Research Institute of Physiology and Basic Medicine, P.O. Box 237, Novosibirsk 630117, Russia
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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Chen S, Wang Y, Yu L, Zheng T, Wang S, Yue Z, Jiang J, Kumari S, Zheng C, Tang H, Li J, Li Y, Chen J, Zhang W, Kuang H, Robertson JS, Zhao PX, Li H, Shu S, Yordanov YS, Huang H, Goodstein DM, Gai Y, Qi Q, Min J, Xu C, Wang S, Qu GZ, Paterson AH, Sankoff D, Wei H, Liu G, Yang C. Genome sequence and evolution of Betula platyphylla. HORTICULTURE RESEARCH 2021; 8:37. [PMID: 33574224 PMCID: PMC7878895 DOI: 10.1038/s41438-021-00481-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/08/2020] [Accepted: 12/13/2020] [Indexed: 05/07/2023]
Abstract
Betula L. (birch) is a pioneer hardwood tree species with ecological, economic, and evolutionary importance in the Northern Hemisphere. We sequenced the Betula platyphylla genome and assembled the sequences into 14 chromosomes. The Betula genome lacks evidence of recent whole-genome duplication and has the same paleoploidy level as Vitis vinifera and Prunus mume. Phylogenetic analysis of lignin pathway genes coupled with tissue-specific expression patterns provided clues for understanding the formation of higher ratios of syringyl to guaiacyl lignin observed in Betula species. Our transcriptome analysis of leaf tissues under a time-series cold stress experiment revealed the presence of the MEKK1-MKK2-MPK4 cascade and six additional mitogen-activated protein kinases that can be linked to a gene regulatory network involving many transcription factors and cold tolerance genes. Our genomic and transcriptome analyses provide insight into the structures, features, and evolution of the B. platyphylla genome. The chromosome-level genome and gene resources of B. platyphylla obtained in this study will facilitate the identification of important and essential genes governing important traits of trees and genetic improvement of B. platyphylla.
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Affiliation(s)
- Su Chen
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Lili Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Tao Zheng
- BGI-Tech, BGI-Shenzhen, Shenzhen, China
| | - Sui Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Zhen Yue
- BGI-Tech, BGI-Shenzhen, Shenzhen, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Sapna Kumari
- College of Forest Resources and Environmental Science, Institute of Computing and Cybersystems, Michigan Technological University, Houghton, MI, USA
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Jun Li
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, USA
| | - Yuqi Li
- BGI-Tech, BGI-Shenzhen, Shenzhen, China
| | - Jiongjiong Chen
- Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P.R. China
| | - Wenbo Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Hanhui Kuang
- Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jon S Robertson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia
| | - Patrick X Zhao
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, USA
| | - Huiyu Li
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Yordan S Yordanov
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, USA
| | - Haijiao Huang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, P. R. China
| | - Qi Qi
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, P. R. China
| | | | | | | | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Institute of Computing and Cybersystems, Michigan Technological University, Houghton, MI, USA
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China.
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China.
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Gao B, Zong W, Miskey C, Ullah N, Diaby M, Chen C, Wang X, Ivics Z, Song C. Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals. Mob DNA 2020; 11:32. [PMID: 33303022 PMCID: PMC7731502 DOI: 10.1186/s13100-020-00227-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain largely unknown. RESULTS Here, we comprehensively investigated the evolutionary profiles of ITs, and evaluated their cut-and-paste activities in cells. ITs exhibited a narrow taxonomic distribution pattern in the animal kingdom, with invasions into two invertebrate phyla (Arthropoda and Cnidaria) and three vertebrate lineages (Actinopterygii, Agnatha, and Anura): very similar to that of the DD36E/IC family. Some animal orders and species seem to be more hospitable to Tc1/mariner transposons, one order of Amphibia and seven Actinopterygian orders are the most common orders with horizontal transfer events and have been invaded by all four families (DD38E/IT, DD35E/TR, DD36E/IC and DD37E/TRT) of Tc1/mariner transposons, and eight Actinopterygii species were identified as the major hosts of these families. Intact ITs have a total length of 1.5-1.7 kb containing a transposase gene flanked by terminal inverted repeats (TIRs). The phylogenetic tree and sequence identity showed that IT transposases were most closely related to DD34E/Tc1. ITs have been involved in multiple events of horizontal transfer in vertebrates and have invaded most lineages recently (< 5 million years ago) based on insertion age analysis. Accordingly, ITs presented high average sequence identity (86-95%) across most vertebrate species, suggesting that some are putatively active. ITs can transpose in human HeLa cells, and the transposition efficiency of consensus TIRs was higher than that of the TIRs of natural isolates. CONCLUSIONS We conclude that DD38E/IT originated from DD34E/Tc1 and can be detected in two invertebrate phyla (Arthropoda and Cnidaria), and in three vertebrate lineages (Actinopterygii, Agnatha and Anura). IT has experienced multiple HT events in animals, dominated by recent amplifications in most species and has high identity among vertebrate taxa. Our reconstructed IT transposon vector designed according to the sequence from the "cat" genome showed high cut-and-paste activity. The data suggest that IT has been acquired recently and is active in many species. This study is meaningful for understanding the evolution of the Tc1/mariner superfamily members and their hosts.
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Affiliation(s)
- Bo Gao
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China.,Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Numan Ullah
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Mohamed Diaby
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China.
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Vendrell-Mir P, López-Obando M, Nogué F, Casacuberta JM. Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium ( Physcomitrella) patens. FRONTIERS IN PLANT SCIENCE 2020; 11:1274. [PMID: 32973835 PMCID: PMC7466625 DOI: 10.3389/fpls.2020.01274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/05/2020] [Indexed: 05/07/2023]
Abstract
Similarly to other plant genomes of similar size, more than half of the genome of P. patens is covered by Transposable Elements (TEs). However, the composition and distribution of P. patens TEs is quite peculiar, with Long Terminal Repeat (LTR)-retrotransposons, which form patches of TE-rich regions interleaved with gene-rich regions, accounting for the vast majority of the TE space. We have already shown that RLG1, the most abundant TE in P. patens, is expressed in non-stressed protonema tissue. Here we present a non-targeted analysis of the TE expression based on RNA-Seq data and confirmed by qRT-PCR analyses that shows that, at least four LTR-RTs (RLG1, RLG2, RLC4 and tRLC5) and one DNA transposon (PpTc2) are expressed in P. patens. These TEs are expressed during development or under stresses that P. patens frequently faces, such as dehydratation/rehydratation stresses, suggesting that TEs have ample possibilities to transpose during P. patens life cycle. Indeed, an analysis of the TE polymorphisms among four different P. patens accessions shows that different TE families have recently transposed in this species and have generated genetic variability that may have phenotypic consequences, as a fraction of the TE polymorphisms are within or close to genes. Among the transcribed and mobile TEs, tRLC5 is particularly interesting as it concentrates in a single position per chromosome that could coincide with the centromere, and its expression is specifically induced in young sporophyte, where meiosis takes place.
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Affiliation(s)
- Pol Vendrell-Mir
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain
| | - Mauricio López-Obando
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre of Plant Biology in Uppsala, Uppsala, Sweden
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- *Correspondence: Fabien Nogué, ; Josep M. Casacuberta,
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain
- *Correspondence: Fabien Nogué, ; Josep M. Casacuberta,
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Lantican DV, Strickler SR, Canama AO, Gardoce RR, Mueller LA, Galvez HF. De Novo Genome Sequence Assembly of Dwarf Coconut ( Cocos nucifera L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species. G3 (BETHESDA, MD.) 2019; 9:2377-2393. [PMID: 31167834 PMCID: PMC6686914 DOI: 10.1534/g3.119.400215] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/31/2019] [Indexed: 11/23/2022]
Abstract
We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. The draft genome was improved through Chicago sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality.
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Affiliation(s)
- Darlon V Lantican
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | | | - Alma O Canama
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | - Roanne R Gardoce
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | | | - Hayde F Galvez
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
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10
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Puzakov MV, Puzakova LV. leidyi Is a New Group of DD41D Transposons in Mnemiopsis leidyi Genome. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Palazzo A, Lorusso P, Miskey C, Walisko O, Gerbino A, Marobbio CMT, Ivics Z, Marsano RM. Transcriptionally promiscuous "blurry" promoters in Tc1/ mariner transposons allow transcription in distantly related genomes. Mob DNA 2019; 10:13. [PMID: 30988701 PMCID: PMC6446368 DOI: 10.1186/s13100-019-0155-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/26/2019] [Indexed: 12/04/2022] Open
Abstract
Background We have recently described a peculiar feature of the promoters in two Drosophila Tc1-like elements, Bari1 and Bari3. The AT-richness and the presence of weak core-promoter motifs make these promoters, that we have defined “blurry”, able to activate transcription of a reporter gene in cellular systems as diverse as fly, human, yeast and bacteria. In order to clarify whether the blurry promoter is a specific feature of the Bari transposon family, we have extended this study to promoters isolated from three additional DNA transposon and from two additional LTR retrotransposons. Results Here we show that the blurry promoter is also a feature of two vertebrate transposable elements, Sleeping Beauty and Hsmar1, belonging to the Tc1/mariner superfamily. In contrast, this feature is not shared by the promoter of the hobo transposon, which belongs to the hAT superfamily, nor by LTR retrotransposon-derived promoters, which, in general, do not activate transcription when introduced into non-related genomes. Conclusions Our results suggest that the blurry promoter could be a shared feature of the members of the Tc1/mariner superfamily with possible evolutionary and biotechnological implications. Electronic supplementary material The online version of this article (10.1186/s13100-019-0155-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonio Palazzo
- 1Department of Biology, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy.,Present address: Laboratory of Translational Nanotechnology, "Istituto Tumori Giovanni Paolo II" I.R.C.C.S, Viale Orazio Flacco 65, 70125 Bari, Italy
| | - Patrizio Lorusso
- 1Department of Biology, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
| | - Csaba Miskey
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Oliver Walisko
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Andrea Gerbino
- 3Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | | | - Zoltán Ivics
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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12
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An Analysis of IS630/Tc1/mariner Transposons in the Genome of a Pacific Oyster, Crassostrea gigas. J Mol Evol 2018; 86:566-580. [PMID: 30283979 DOI: 10.1007/s00239-018-9868-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
Transposable elements represent the DNA fragments capable of increasing their copy number and moving within the genome. Class II mobile elements represents the DNA transposons, which transpose via excision and the subsequent reinsertion at random genomic loci. The increase of their copy number occurs only when the transposition event is coupled with the replication. IS630/Tc1/mariner DNA transposon superfamily is one of the largest and widely distributed among the Class II elements. In this work, we provide a detailed analysis of IS630/Tc1/mariner DNA transposons from the Pacific oyster, Crassostrea gigas. IS630/Tc1/mariner transposons represented in the genome of the Pacific oyster belong to four families, Tc1 (DD34E), mariner (DD34D), pogo (DDxD), and rosa (DD41D). More than a half of IS630/Tc1/mariner elements from C. gigas belong to Tc1 family. Furthermore, Mariner-31_CGi element was shown to represent a new and previously unknown family with DD37E signature. We also discovered the full-size transcripts of eight elements from Tc1, mariner, and pogo families, three of which can, presumably, retain their transposition activity.
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Hou F, Ma B, Xin Y, Kuang L, He N. Horizontal transfers of LTR retrotransposons in seven species of Rosales. Genome 2018; 61:587-594. [PMID: 29958091 DOI: 10.1139/gen-2017-0208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Horizontal transposable element transfer (HTT) events have occurred among a large number of species and play important roles in the composition and evolution of eukaryotic genomes. HTTs are also regarded as effective forces in promoting genomic variation and biological innovation. In the present study, HTT events were identified and analyzed in seven sequenced species of Rosales using bioinformatics methods by comparing sequence conservation and Ka/Ks value of reverse transcriptase (RT) with 20 conserved genes, estimating the dating of HTTs, and analyzing the phylogenetic relationships. Seven HTT events involving long terminal repeat (LTR) retrotransposons, two HTTs between Morus notabilis and Ziziphus jujuba, and five between Malus domestica and Pyrus bretschneideri were identified. Further analysis revealed that these LTR retrotransposons had functional structures, and the copy insertion times were lower than the dating of HTTs, particularly in Mn.Zj.1 and Md.Pb.3. Altogether, the results demonstrate that LTR retrotransposons still have potential transposition activity in host genomes. These results indicate that HTT events are another strategy for exchanging genetic material among species and are important for the evolution of genomes.
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Affiliation(s)
- Fei Hou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.,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.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China
| | - Youchao Xin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China
| | - Lulu Kuang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.,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.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China
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Puzakova LV, Puzakov MV. The Tc1/mariner DNA transposons in the genome of mollusk Littorina saxatilis. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417120110] [Citation(s) in RCA: 2] [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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15
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Filho JAF, de Brito LS, Leão AP, Alves AA, Formighieri EF, Júnior MTS. In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms. Bioinform Biol Insights 2017; 11:1177932217702388. [PMID: 28469420 PMCID: PMC5402704 DOI: 10.1177/1177932217702388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/02/2017] [Indexed: 11/16/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm). The estimated total coverage of TEs was 50.96% (523 572 kb) and 42.31% (593 463 kb), 39.41% (605 015 kb), and 33.67% (187 361 kb), respectively. A total of 155 726 microsatellite loci were identified in the genomes of oil and date palms. This is the first detailed description of repeats in the genomes of oil and date palms. A relatively high diversity and abundance of TEs were found in the genomes, opening a range of further opportunities for applied research in these genera. The development of molecular markers (mainly simple sequence repeat), which may be immediately applied in breeding programs of those species to support the selection of superior genotypes and to enhance knowledge of the genetic structure of the breeding and natural populations, is the most notable opportunity.
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Affiliation(s)
- Jaire Alves Ferreira Filho
- Graduate Program in Plant Biotechnology, Federal University of Lavras (UFLA), Lavras, Brazil.,Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil.,Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | | | | | - Manoel Teixeira Souza Júnior
- Graduate Program in Plant Biotechnology, Federal University of Lavras (UFLA), Lavras, Brazil.,Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil
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Zhang HH, Li GY, Xiong XM, Han MJ, Zhang XG, Dai FY. TRT, a Vertebrate and Protozoan Tc1-Like Transposon: Current Activity and Horizontal Transfer. Genome Biol Evol 2016; 8:2994-3005. [PMID: 27667131 PMCID: PMC5630946 DOI: 10.1093/gbe/evw213] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We report a Danio rerio transposon named DrTRT, for D. rerio Transposon Related to Tc1. The complete sequence of the DrTRT transposon is 1,563 base pairs (bp) in length, and its transposase putatively encodes a 338-amino acid protein that harbors a DD37E motif in its catalytic domain. We present evidence based on searches of publicly available genomes that TRT elements commonly occur in vertebrates and protozoa. Phylogenetic and functional domain comparisons confirm that TRT constitutes a new subfamily within the Tc1 family. Hallmark features of having no premature termination codons within the transposase, the presence of all expected functional domains, and its occurrence in the bony fish transcriptome suggest that TRT might have current or recent activity in these species. Further analysis showed that the activity of TRT elements in these species might have arisen about between 4 and 19 Ma. Interestingly, our results also implied that the widespread distribution of TRT among fishes, frog, and snakes is the result of multiple independent HT events, probably from bony fishes to snakes or frog. Finally, the mechanisms underlying horizontal transfer of TRT elements are discussed.
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Affiliation(s)
- Hua-Hao Zhang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Guo-Yin Li
- Department of pathology, Hanzhoung Hospital, Hanzhoung city, Shaanxi, China
| | - Xiao-Min Xiong
- Clinical Medical College, Jiujiang University, Jiujiang, China
| | - Min-Jin Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Fang-Yin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
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18
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Origins and evolvability of the PAX family. Semin Cell Dev Biol 2015; 44:64-74. [DOI: 10.1016/j.semcdb.2015.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 08/07/2015] [Accepted: 08/22/2015] [Indexed: 01/18/2023]
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