Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim
Abstract Trichosanthes kirilowii Maxim. (TK) is a dioecious plant in the Cucurbitaceae family of which different sexes have separate medicinal uses. We used Illumina high-throughput sequencing technology to sequence miRNAs from male and female flower buds of TK. We performed bioinformatics analysis,...
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| Format: | Article |
| Language: | English |
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BMC
2023-02-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09178-8 |
| _version_ | 1797865454997340160 |
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| author | Xiu-qin Hu Han Song Na Li Chun-xiang Hao Bo Zhang Xin-peng Li Jie Xin Yong-qing Zhang |
| author_facet | Xiu-qin Hu Han Song Na Li Chun-xiang Hao Bo Zhang Xin-peng Li Jie Xin Yong-qing Zhang |
| author_sort | Xiu-qin Hu |
| collection | DOAJ |
| description | Abstract Trichosanthes kirilowii Maxim. (TK) is a dioecious plant in the Cucurbitaceae family of which different sexes have separate medicinal uses. We used Illumina high-throughput sequencing technology to sequence miRNAs from male and female flower buds of TK. We performed bioinformatics analysis, miRNA identification, and target gene prediction on the data obtained from sequencing, and association analysis was performed in combination with the results of a previous transcriptome sequencing study. As a result, there were 80 differentially expressed miRNAs (DESs) between the female and male plants (48 upregulated and 32 downregulated in female plants). Moreover, 27 novel miRNAs in DESs were predicted to have 282 target genes, and 51 known miRNAs were predicted to have 3418 target genes. By establishing a regulatory network between miRNAs and target genes, 12 core genes were screened, including 7 miRNAs and 5 target genes. Among them, tkmiR157a-5p, tkmiR156c, tkmiR156_2, and tkmiR156k_2 jointly target the regulation of tkSPL18 and tkSPL13B. These two target genes are specifically expressed in male and female plants, respectively, and are involved in the biosynthesis process of BR, which is closely related to the sex differentiation process of TK. The identification of these miRNAs will provide a reference for the analysis of the sex differentiation mechanism of TK. |
| first_indexed | 2024-04-09T23:08:58Z |
| format | Article |
| id | doaj.art-19476beb5e6140c0ad1f1cbc1978fc9f |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T23:08:58Z |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-19476beb5e6140c0ad1f1cbc1978fc9f2023-03-22T10:30:50ZengBMCBMC Genomics1471-21642023-02-0124111310.1186/s12864-023-09178-8Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maximXiu-qin Hu0Han Song1Na Li2Chun-xiang Hao3Bo Zhang4Xin-peng Li5Jie Xin6Yong-qing Zhang7Medical College, Linyi UniversityMedical College, Linyi UniversityMedical College, Linyi UniversityMedical College, Linyi UniversityMedical College, Linyi UniversityMedical College, Linyi UniversityMedical College, Linyi UniversitySchool of Pharmacy, Shandong University of Traditional Chinese MedicineAbstract Trichosanthes kirilowii Maxim. (TK) is a dioecious plant in the Cucurbitaceae family of which different sexes have separate medicinal uses. We used Illumina high-throughput sequencing technology to sequence miRNAs from male and female flower buds of TK. We performed bioinformatics analysis, miRNA identification, and target gene prediction on the data obtained from sequencing, and association analysis was performed in combination with the results of a previous transcriptome sequencing study. As a result, there were 80 differentially expressed miRNAs (DESs) between the female and male plants (48 upregulated and 32 downregulated in female plants). Moreover, 27 novel miRNAs in DESs were predicted to have 282 target genes, and 51 known miRNAs were predicted to have 3418 target genes. By establishing a regulatory network between miRNAs and target genes, 12 core genes were screened, including 7 miRNAs and 5 target genes. Among them, tkmiR157a-5p, tkmiR156c, tkmiR156_2, and tkmiR156k_2 jointly target the regulation of tkSPL18 and tkSPL13B. These two target genes are specifically expressed in male and female plants, respectively, and are involved in the biosynthesis process of BR, which is closely related to the sex differentiation process of TK. The identification of these miRNAs will provide a reference for the analysis of the sex differentiation mechanism of TK.https://doi.org/10.1186/s12864-023-09178-8TKSex differentiationTranscriptome and sRNA sequencingmiRNA |
| spellingShingle | Xiu-qin Hu Han Song Na Li Chun-xiang Hao Bo Zhang Xin-peng Li Jie Xin Yong-qing Zhang Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim BMC Genomics TK Sex differentiation Transcriptome and sRNA sequencing miRNA |
| title | Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim |
| title_full | Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim |
| title_fullStr | Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim |
| title_full_unstemmed | Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim |
| title_short | Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim |
| title_sort | identification and analysis of mirnas differentially expressed in male and female trichosanthes kirilowii maxim |
| topic | TK Sex differentiation Transcriptome and sRNA sequencing miRNA |
| url | https://doi.org/10.1186/s12864-023-09178-8 |
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