Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes
Lyophyllum decastes is a mushroom that is highly regarded for its culinary and medicinal properties. Its delectable taste and texture make it a popular choice for consumption. To gain a deeper understanding of the molecular mechanisms involved in the development of the fruiting body of L. decastes,...
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PeerJ Inc.
2023-10-01
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| author | Shanwen Ke LingQiang Ding Xin Niu Huajia Shan Liru Song Yali Xi Jiuhai Feng Shenglong Wei Qianqian Liang |
| author_facet | Shanwen Ke LingQiang Ding Xin Niu Huajia Shan Liru Song Yali Xi Jiuhai Feng Shenglong Wei Qianqian Liang |
| author_sort | Shanwen Ke |
| collection | DOAJ |
| description | Lyophyllum decastes is a mushroom that is highly regarded for its culinary and medicinal properties. Its delectable taste and texture make it a popular choice for consumption. To gain a deeper understanding of the molecular mechanisms involved in the development of the fruiting body of L. decastes, we used RNA sequencing to conduct a comparative transcriptome analysis. The analysis encompassed various developmental stages, including the vegetative mycelium, primordial initiation, young fruiting body, medium-size fruiting body, and mature fruiting body stages. A range of 40.1 to 60.6 million clean reads were obtained, and de novo assembly generated 15,451 unigenes with an average length of 1,462.68 bp. Functional annotation of transcriptomes matched 76.84% of the unigenes to known proteins available in at least one database. The gene expression analysis revealed a significant number of differentially expressed genes (DEGs) between each stage. These genes were annotated and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Highly differentially expressed unigenes were also identified, including those that encode extracellular enzymes, transcription factors, and signaling pathways. The accuracy of the RNA-Seq and DEG analyses was validated using quantitative PCR. Enzyme activity analysis experiments demonstrated that the extracellular enzymes exhibited significant differences across different developmental stages. This study provides valuable insights into the molecular mechanisms that underlie the development of the fruiting body in L. decastes. |
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| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:01:36Z |
| publishDate | 2023-10-01 |
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| spelling | doaj.art-b9518e77f9464c70a76367aa1f796a9d2023-12-03T12:08:47ZengPeerJ Inc.PeerJ2167-83592023-10-0111e1628810.7717/peerj.16288Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastesShanwen Ke0LingQiang Ding1Xin Niu2Huajia Shan3Liru Song4Yali Xi5Jiuhai Feng6Shenglong Wei7Qianqian Liang8Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaGansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaGansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaGansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaGansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaGansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaGansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaGansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaGansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, ChinaLyophyllum decastes is a mushroom that is highly regarded for its culinary and medicinal properties. Its delectable taste and texture make it a popular choice for consumption. To gain a deeper understanding of the molecular mechanisms involved in the development of the fruiting body of L. decastes, we used RNA sequencing to conduct a comparative transcriptome analysis. The analysis encompassed various developmental stages, including the vegetative mycelium, primordial initiation, young fruiting body, medium-size fruiting body, and mature fruiting body stages. A range of 40.1 to 60.6 million clean reads were obtained, and de novo assembly generated 15,451 unigenes with an average length of 1,462.68 bp. Functional annotation of transcriptomes matched 76.84% of the unigenes to known proteins available in at least one database. The gene expression analysis revealed a significant number of differentially expressed genes (DEGs) between each stage. These genes were annotated and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Highly differentially expressed unigenes were also identified, including those that encode extracellular enzymes, transcription factors, and signaling pathways. The accuracy of the RNA-Seq and DEG analyses was validated using quantitative PCR. Enzyme activity analysis experiments demonstrated that the extracellular enzymes exhibited significant differences across different developmental stages. This study provides valuable insights into the molecular mechanisms that underlie the development of the fruiting body in L. decastes.https://peerj.com/articles/16288.pdfLyophyllum decastesFruiting bodyComparative transcriptomeExtracellular enzymeDifferential expressed genes |
| spellingShingle | Shanwen Ke LingQiang Ding Xin Niu Huajia Shan Liru Song Yali Xi Jiuhai Feng Shenglong Wei Qianqian Liang Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes PeerJ Lyophyllum decastes Fruiting body Comparative transcriptome Extracellular enzyme Differential expressed genes |
| title | Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes |
| title_full | Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes |
| title_fullStr | Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes |
| title_full_unstemmed | Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes |
| title_short | Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes |
| title_sort | comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in lyophyllum decastes |
| topic | Lyophyllum decastes Fruiting body Comparative transcriptome Extracellular enzyme Differential expressed genes |
| url | https://peerj.com/articles/16288.pdf |
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