Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in <i>Tilia tuan</i>
Seed maturation not only determines the qualities and yields of seeds, but also affects seed storage and quality preservation. MicroRNAs (miRNAs) are a ubiquitous regulatory factor of gene expression in eukaryotes, which participate in the complex regulatory network of gene expression during seed ma...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/13/11/1750 |
| _version_ | 1797468251300560896 |
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| author | Xuri Hao Lei Liu Peng Liu Menglei Wang Yuepeng Song |
| author_facet | Xuri Hao Lei Liu Peng Liu Menglei Wang Yuepeng Song |
| author_sort | Xuri Hao |
| collection | DOAJ |
| description | Seed maturation not only determines the qualities and yields of seeds, but also affects seed storage and quality preservation. MicroRNAs (miRNAs) are a ubiquitous regulatory factor of gene expression in eukaryotes, which participate in the complex regulatory network of gene expression during seed maturation. However, miRNAs involved in maturation of <i>Tilia tuan</i> are still unknown. To reveal the role of miRNAs in <i>T. tuan</i>, small RNAs were profiled by high-throughput sequencing during seed maturation at five developmental stages. By predicting the target genes of miRNAs, the expression patterns of miRNAs during seed maturation were analyzed to identify those related to seed maturation. A total of 187 known miRNAs belonging to 42 miRNA families were found at five different seed maturation stages. Based on the analysis of unknown sequences, eight novel miRNAs were identified; 11,775 targets of 195 miRNAs were identified. Large numbers of miRNAs with diverse expression patterns, multiple-targeting and co-targeting of many miRNAs, and a complex regulatory network of miRNA-target genes were identified during seed maturation. These miRNAs and their targets may be involved in fatty acid, ABA, and lignin biosynthesis. Our study provides more information about the miRNA regulatory network and deepens our understanding of the function of miRNAs in <i>T. tuan</i>. miRNAs are revealed to be crucial during seed maturation, which provides a basis for further study of the regulatory role of miRNAs during seed maturation. |
| first_indexed | 2024-03-09T19:04:45Z |
| format | Article |
| id | doaj.art-b005cdf42cb3409c9faf709b47f56f45 |
| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-09T19:04:45Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Forests |
| spelling | doaj.art-b005cdf42cb3409c9faf709b47f56f452023-11-24T04:42:36ZengMDPI AGForests1999-49072022-10-011311175010.3390/f13111750Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in <i>Tilia tuan</i>Xuri Hao0Lei Liu1Peng Liu2Menglei Wang3Yuepeng Song4National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, ChinaNational Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, ChinaNational Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, ChinaNational Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, ChinaNational Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, ChinaSeed maturation not only determines the qualities and yields of seeds, but also affects seed storage and quality preservation. MicroRNAs (miRNAs) are a ubiquitous regulatory factor of gene expression in eukaryotes, which participate in the complex regulatory network of gene expression during seed maturation. However, miRNAs involved in maturation of <i>Tilia tuan</i> are still unknown. To reveal the role of miRNAs in <i>T. tuan</i>, small RNAs were profiled by high-throughput sequencing during seed maturation at five developmental stages. By predicting the target genes of miRNAs, the expression patterns of miRNAs during seed maturation were analyzed to identify those related to seed maturation. A total of 187 known miRNAs belonging to 42 miRNA families were found at five different seed maturation stages. Based on the analysis of unknown sequences, eight novel miRNAs were identified; 11,775 targets of 195 miRNAs were identified. Large numbers of miRNAs with diverse expression patterns, multiple-targeting and co-targeting of many miRNAs, and a complex regulatory network of miRNA-target genes were identified during seed maturation. These miRNAs and their targets may be involved in fatty acid, ABA, and lignin biosynthesis. Our study provides more information about the miRNA regulatory network and deepens our understanding of the function of miRNAs in <i>T. tuan</i>. miRNAs are revealed to be crucial during seed maturation, which provides a basis for further study of the regulatory role of miRNAs during seed maturation.https://www.mdpi.com/1999-4907/13/11/1750miRNA<i>Tilia tuan</i>high-throughput sequencingseed maturation |
| spellingShingle | Xuri Hao Lei Liu Peng Liu Menglei Wang Yuepeng Song Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in <i>Tilia tuan</i> Forests miRNA <i>Tilia tuan</i> high-throughput sequencing seed maturation |
| title | Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in <i>Tilia tuan</i> |
| title_full | Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in <i>Tilia tuan</i> |
| title_fullStr | Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in <i>Tilia tuan</i> |
| title_full_unstemmed | Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in <i>Tilia tuan</i> |
| title_short | Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in <i>Tilia tuan</i> |
| title_sort | genome wide identification of mirnas and its downstream transcriptional regulatory network during seed maturation in i tilia tuan i |
| topic | miRNA <i>Tilia tuan</i> high-throughput sequencing seed maturation |
| url | https://www.mdpi.com/1999-4907/13/11/1750 |
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