RTRIP: a comprehensive profile of transposon insertion polymorphisms in rice
A comprehensive profile of transposon insertion polymorphisms (TIPs) is critical to TE family characterization, genetic evolution research as well as molecular marker‐assisted breeding. [...]a variety of sequencing strategies and bioinformatics algorithms have been developed to efficiently identify...
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| Veröffentlicht in: | Plant biotechnology journal 2020-12, Vol.18 (12), p.2379-2381 |
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| container_title | Plant biotechnology journal |
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| creator | Liu, Zhen Wang, Tingzhang Wang, Lin Zhao, Han Yue, Erkui Yan, Yan Irshad, Faiza Zhou, Ling Duan, Ming‐Hua Xu, Jian‐Hong |
| description | A comprehensive profile of transposon insertion polymorphisms (TIPs) is critical to TE family characterization, genetic evolution research as well as molecular marker‐assisted breeding. [...]a variety of sequencing strategies and bioinformatics algorithms have been developed to efficiently identify TE loci based on next‐generation sequencing (NGS) technology, and only few profiles have been constructed in well‐studied model organisms, such as Drosophila melanogaster, Caenorhabditis elegans and Homo sapiens (Kofler et al., 2012; Laricchia et al., 2017; Rishishwar et al., 2015). The average number of TE loci is 6304 for each accession, and shows large difference among accessions, varying from 4898 to 10 155. [...]19 160 TE loci are inserted within or nearby genes (200 bp flanking regions), which may have a potential effect on gene function. [...]Search by varieties’ has been designed to facilitate their application as molecular markers for gene mapping and molecular‐assisted breeding. [...]Search by Genes’ submodule is customized for TE loci associated with genes and will be applied to the study of gene function. |
| doi_str_mv | 10.1111/pbi.13425 |
| format | Article |
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[...]a variety of sequencing strategies and bioinformatics algorithms have been developed to efficiently identify TE loci based on next‐generation sequencing (NGS) technology, and only few profiles have been constructed in well‐studied model organisms, such as Drosophila melanogaster, Caenorhabditis elegans and Homo sapiens (Kofler et al., 2012; Laricchia et al., 2017; Rishishwar et al., 2015). The average number of TE loci is 6304 for each accession, and shows large difference among accessions, varying from 4898 to 10 155. [...]19 160 TE loci are inserted within or nearby genes (200 bp flanking regions), which may have a potential effect on gene function. [...]Search by varieties’ has been designed to facilitate their application as molecular markers for gene mapping and molecular‐assisted breeding. [...]Search by Genes’ submodule is customized for TE loci associated with genes and will be applied to the study of gene function.</description><identifier>ISSN: 1467-7644</identifier><identifier>EISSN: 1467-7652</identifier><identifier>DOI: 10.1111/pbi.13425</identifier><identifier>PMID: 32473053</identifier><language>eng</language><publisher>England: John Wiley & Sons, Inc</publisher><subject>Algorithms ; Anopheles ; Bioinformatics ; Breeding ; Brief Communication ; Brief Communications ; Conflicts of interest ; DNA Transposable Elements - genetics ; Evolution & development ; Gene expression ; Gene mapping ; gene tagging ; Genes ; Genomes ; Genomics ; Insertion ; insertion polymorphisms ; Interfaces ; Loci ; Markers ; molecular marker ; Mutagenesis, Insertional ; next‐generation sequencing ; Oryza - genetics ; Polymorphism ; Polymorphism, Genetic - genetics ; Population ; rice ; Sequence Analysis, DNA ; transposable element ; Transposons</subject><ispartof>Plant biotechnology journal, 2020-12, Vol.18 (12), p.2379-2381</ispartof><rights>2020 The Authors. published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd</rights><rights>COPYRIGHT 2020 John Wiley & Sons, Inc.</rights><rights>2020. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the "License"). 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[...]a variety of sequencing strategies and bioinformatics algorithms have been developed to efficiently identify TE loci based on next‐generation sequencing (NGS) technology, and only few profiles have been constructed in well‐studied model organisms, such as Drosophila melanogaster, Caenorhabditis elegans and Homo sapiens (Kofler et al., 2012; Laricchia et al., 2017; Rishishwar et al., 2015). The average number of TE loci is 6304 for each accession, and shows large difference among accessions, varying from 4898 to 10 155. [...]19 160 TE loci are inserted within or nearby genes (200 bp flanking regions), which may have a potential effect on gene function. [...]Search by varieties’ has been designed to facilitate their application as molecular markers for gene mapping and molecular‐assisted breeding. 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| subjects | Algorithms Anopheles Bioinformatics Breeding Brief Communication Brief Communications Conflicts of interest DNA Transposable Elements - genetics Evolution & development Gene expression Gene mapping gene tagging Genes Genomes Genomics Insertion insertion polymorphisms Interfaces Loci Markers molecular marker Mutagenesis, Insertional next‐generation sequencing Oryza - genetics Polymorphism Polymorphism, Genetic - genetics Population rice Sequence Analysis, DNA transposable element Transposons |
| title | RTRIP: a comprehensive profile of transposon insertion polymorphisms in rice |
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