Identification of short open reading frames in plant genomes
The roles of short/small open reading frames (sORFs) have been increasingly recognized in recent years due to the rapidly growing number of sORFs identified in various organisms due to the development and application of the Ribo-Seq technique, which sequences the ribosome-protected footprints (RPFs)...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-02-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1094715/full |
| _version_ | 1797924578159230976 |
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| author | Yong Feng Mengyun Jiang Mengyun Jiang Weichang Yu Weichang Yu Jiannan Zhou |
| author_facet | Yong Feng Mengyun Jiang Mengyun Jiang Weichang Yu Weichang Yu Jiannan Zhou |
| author_sort | Yong Feng |
| collection | DOAJ |
| description | The roles of short/small open reading frames (sORFs) have been increasingly recognized in recent years due to the rapidly growing number of sORFs identified in various organisms due to the development and application of the Ribo-Seq technique, which sequences the ribosome-protected footprints (RPFs) of the translating mRNAs. However, special attention should be paid to RPFs used to identify sORFs in plants due to their small size (~30 nt) and the high complexity and repetitiveness of the plant genome, particularly for polyploidy species. In this work, we compare different approaches to the identification of plant sORFs, discuss the advantages and disadvantages of each method, and provide a guide for choosing different methods in plant sORF studies. |
| first_indexed | 2024-04-10T15:03:13Z |
| format | Article |
| id | doaj.art-8ed25151e77b4d889092dc06838807ad |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T15:03:13Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-8ed25151e77b4d889092dc06838807ad2023-02-15T09:02:18ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-02-011410.3389/fpls.2023.10947151094715Identification of short open reading frames in plant genomesYong Feng0Mengyun Jiang1Mengyun Jiang2Weichang Yu3Weichang Yu4Jiannan Zhou5Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, ChinaGuangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, ChinaLiaoning Peanut Research Institute, Liaoning Academy of Agricultural Sciences, Fuxing, ChinaKey Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, ChinaThe roles of short/small open reading frames (sORFs) have been increasingly recognized in recent years due to the rapidly growing number of sORFs identified in various organisms due to the development and application of the Ribo-Seq technique, which sequences the ribosome-protected footprints (RPFs) of the translating mRNAs. However, special attention should be paid to RPFs used to identify sORFs in plants due to their small size (~30 nt) and the high complexity and repetitiveness of the plant genome, particularly for polyploidy species. In this work, we compare different approaches to the identification of plant sORFs, discuss the advantages and disadvantages of each method, and provide a guide for choosing different methods in plant sORF studies.https://www.frontiersin.org/articles/10.3389/fpls.2023.1094715/fullsmall open reading framesORFsribo-seqplantgenome |
| spellingShingle | Yong Feng Mengyun Jiang Mengyun Jiang Weichang Yu Weichang Yu Jiannan Zhou Identification of short open reading frames in plant genomes Frontiers in Plant Science small open reading frame sORFs ribo-seq plant genome |
| title | Identification of short open reading frames in plant genomes |
| title_full | Identification of short open reading frames in plant genomes |
| title_fullStr | Identification of short open reading frames in plant genomes |
| title_full_unstemmed | Identification of short open reading frames in plant genomes |
| title_short | Identification of short open reading frames in plant genomes |
| title_sort | identification of short open reading frames in plant genomes |
| topic | small open reading frame sORFs ribo-seq plant genome |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1094715/full |
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