Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing
<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as <it>A...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-01-01
|
| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/11/5 |
| _version_ | 1811297051849261056 |
|---|---|
| author | Chen Shou-Yi Ma Biao Zhang Wan-Ke Hu Xing-Yu Liu Yun-Feng Song Qing-Xin Zhang Jin-Song |
| author_facet | Chen Shou-Yi Ma Biao Zhang Wan-Ke Hu Xing-Yu Liu Yun-Feng Song Qing-Xin Zhang Jin-Song |
| author_sort | Chen Shou-Yi |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as <it>Arabidopsis </it>and rice; however, the number of identified miRNAs in soybean (<it>Glycine max</it>) is limited, and global identification of the related miRNA targets has not been reported in previous research.</p> <p>Results</p> <p>In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis SUPPRESSOR OF GENE SLIENCING 3 (<it>AtSGS3</it>) was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis.</p> <p>Conclusions</p> <p>We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.</p> |
| first_indexed | 2024-04-13T05:58:19Z |
| format | Article |
| id | doaj.art-179e888458324d32aa2a729e4e0835a7 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-13T05:58:19Z |
| publishDate | 2011-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-179e888458324d32aa2a729e4e0835a72022-12-22T02:59:32ZengBMCBMC Plant Biology1471-22292011-01-01111510.1186/1471-2229-11-5Identification of miRNAs and their target genes in developing soybean seeds by deep sequencingChen Shou-YiMa BiaoZhang Wan-KeHu Xing-YuLiu Yun-FengSong Qing-XinZhang Jin-Song<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as <it>Arabidopsis </it>and rice; however, the number of identified miRNAs in soybean (<it>Glycine max</it>) is limited, and global identification of the related miRNA targets has not been reported in previous research.</p> <p>Results</p> <p>In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis SUPPRESSOR OF GENE SLIENCING 3 (<it>AtSGS3</it>) was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis.</p> <p>Conclusions</p> <p>We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.</p>http://www.biomedcentral.com/1471-2229/11/5 |
| spellingShingle | Chen Shou-Yi Ma Biao Zhang Wan-Ke Hu Xing-Yu Liu Yun-Feng Song Qing-Xin Zhang Jin-Song Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing BMC Plant Biology |
| title | Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing |
| title_full | Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing |
| title_fullStr | Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing |
| title_full_unstemmed | Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing |
| title_short | Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing |
| title_sort | identification of mirnas and their target genes in developing soybean seeds by deep sequencing |
| url | http://www.biomedcentral.com/1471-2229/11/5 |
| work_keys_str_mv | AT chenshouyi identificationofmirnasandtheirtargetgenesindevelopingsoybeanseedsbydeepsequencing AT mabiao identificationofmirnasandtheirtargetgenesindevelopingsoybeanseedsbydeepsequencing AT zhangwanke identificationofmirnasandtheirtargetgenesindevelopingsoybeanseedsbydeepsequencing AT huxingyu identificationofmirnasandtheirtargetgenesindevelopingsoybeanseedsbydeepsequencing AT liuyunfeng identificationofmirnasandtheirtargetgenesindevelopingsoybeanseedsbydeepsequencing AT songqingxin identificationofmirnasandtheirtargetgenesindevelopingsoybeanseedsbydeepsequencing AT zhangjinsong identificationofmirnasandtheirtargetgenesindevelopingsoybeanseedsbydeepsequencing |