Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass
Kentucky bluegrass (Poa pratensis L.) is an eminent turfgrass species with a complex genome, but it is sensitive to rust (Puccinia striiformis). The molecular mechanisms of Kentucky bluegrass in response to rust still remain unclear. This study aimed to elucidate differentially expressed lncRNAs (DE...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1158035/full |
| _version_ | 1797830290281857024 |
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| author | Xueying Zhao Xiaoyang Sun Yang Chen Hanfu Wu Yujiao Liu Yiwei Jiang Fuchun Xie Yajun Chen Yajun Chen |
| author_facet | Xueying Zhao Xiaoyang Sun Yang Chen Hanfu Wu Yujiao Liu Yiwei Jiang Fuchun Xie Yajun Chen Yajun Chen |
| author_sort | Xueying Zhao |
| collection | DOAJ |
| description | Kentucky bluegrass (Poa pratensis L.) is an eminent turfgrass species with a complex genome, but it is sensitive to rust (Puccinia striiformis). The molecular mechanisms of Kentucky bluegrass in response to rust still remain unclear. This study aimed to elucidate differentially expressed lncRNAs (DELs) and genes (DEGs) for rust resistance based on the full-length transcriptome. First, we used single-molecule real-time sequencing technology to generate the full-length transcriptome of Kentucky bluegrass. A total of 33,541 unigenes with an average read length of 2,233 bp were obtained, which contained 220 lncRNAs and 1,604 transcription factors. Then, the comparative transcriptome between the mock-inoculated leaves and rust-infected leaves was analyzed using the full-length transcriptome as a reference genome. A total of 105 DELs were identified in response to rust infection. A total of 15,711 DEGs were detected (8,278 upregulated genes, 7,433 downregulated genes) and were enriched in plant hormone signal transduction and plant–pathogen interaction pathways. Additionally, through co-location and expression analysis, it was found that lncRNA56517, lncRNA53468, and lncRNA40596 were highly expressed in infected plants and upregulated the expression of target genes AUX/IAA, RPM1, and RPS2, respectively; meanwhile, lncRNA25980 decreased the expression level of target gene EIN3 after infection. The results suggest that these DEGs and DELs are important candidates for potentially breeding the rust-resistant Kentucky bluegrass. |
| first_indexed | 2024-04-09T13:33:47Z |
| format | Article |
| id | doaj.art-3b43b85f762e4eb5a6198fc31435fa75 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-09T13:33:47Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-3b43b85f762e4eb5a6198fc31435fa752023-05-09T16:18:46ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-05-011410.3389/fpls.2023.11580351158035Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrassXueying Zhao0Xiaoyang Sun1Yang Chen2Hanfu Wu3Yujiao Liu4Yiwei Jiang5Fuchun Xie6Yajun Chen7Yajun Chen8College of Horticulture, Northeast Agricultural University, Harbin, ChinaCollege of Animal Science and Technology, Northeast Agricultural University, Harbin, ChinaCollege of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, ChinaCollege of Animal Science and Technology, Northeast Agricultural University, Harbin, ChinaCollege of Animal Science and Technology, Northeast Agricultural University, Harbin, ChinaDepartment of Agronomy, Purdue University, West Lafayette, IN, United StatesCollege of Animal Science and Technology, Northeast Agricultural University, Harbin, ChinaCollege of Horticulture, Northeast Agricultural University, Harbin, ChinaCollege of Animal Science and Technology, Northeast Agricultural University, Harbin, ChinaKentucky bluegrass (Poa pratensis L.) is an eminent turfgrass species with a complex genome, but it is sensitive to rust (Puccinia striiformis). The molecular mechanisms of Kentucky bluegrass in response to rust still remain unclear. This study aimed to elucidate differentially expressed lncRNAs (DELs) and genes (DEGs) for rust resistance based on the full-length transcriptome. First, we used single-molecule real-time sequencing technology to generate the full-length transcriptome of Kentucky bluegrass. A total of 33,541 unigenes with an average read length of 2,233 bp were obtained, which contained 220 lncRNAs and 1,604 transcription factors. Then, the comparative transcriptome between the mock-inoculated leaves and rust-infected leaves was analyzed using the full-length transcriptome as a reference genome. A total of 105 DELs were identified in response to rust infection. A total of 15,711 DEGs were detected (8,278 upregulated genes, 7,433 downregulated genes) and were enriched in plant hormone signal transduction and plant–pathogen interaction pathways. Additionally, through co-location and expression analysis, it was found that lncRNA56517, lncRNA53468, and lncRNA40596 were highly expressed in infected plants and upregulated the expression of target genes AUX/IAA, RPM1, and RPS2, respectively; meanwhile, lncRNA25980 decreased the expression level of target gene EIN3 after infection. The results suggest that these DEGs and DELs are important candidates for potentially breeding the rust-resistant Kentucky bluegrass.https://www.frontiersin.org/articles/10.3389/fpls.2023.1158035/fullfull-length transcriptomelncRNAsPoa pratensisrustresistance mechanism |
| spellingShingle | Xueying Zhao Xiaoyang Sun Yang Chen Hanfu Wu Yujiao Liu Yiwei Jiang Fuchun Xie Yajun Chen Yajun Chen Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass Frontiers in Plant Science full-length transcriptome lncRNAs Poa pratensis rust resistance mechanism |
| title | Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass |
| title_full | Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass |
| title_fullStr | Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass |
| title_full_unstemmed | Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass |
| title_short | Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass |
| title_sort | mining of long non coding rnas with target genes in response to rust based on full length transcriptome in kentucky bluegrass |
| topic | full-length transcriptome lncRNAs Poa pratensis rust resistance mechanism |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1158035/full |
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