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Article

Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis

by
Junjie Yan
1,2,3,
Zongjun Tong
1,
Xing Han
1,3,
Ying Gan
1,3,
Yuanyuan Liu
2,
Jie Chen
1,3,
Xinlian Duan
1,
Junbin Lin
1,3,
Bingcheng Gan
1,3,* and
Baogui Xie
2,*
1
Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
2
Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
3
Chengdu Agricultural Science and Technology Center, Chengdu 610000, China
*
Authors to whom correspondence should be addressed.
J. Fungi 2023, 9(1), 64; https://doi.org/10.3390/jof9010064
Submission received: 24 November 2022 / Revised: 28 December 2022 / Accepted: 28 December 2022 / Published: 31 December 2022
(This article belongs to the Special Issue Biotechnology of Edible Fungi)
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Abstract

Stipe gradient elongation is an important and remarkable feature in the development of most mushroom fruiting bodies. However, its molecular mechanism has rarely been described. Here, the decreasing trend of stipe elongation and increasing trend of cell length in a gradient from the top to the base of the stipe were determined in a model basidiomycete mushroom: Flammulina filiformis. According to RNA-seq results, 1409 differentially expressed genes (DEGs) were identified among elongation region (ER), transition region (TR), and stable region (SR) samples, including 26 transcription factors (TFs). Based on Short Time-series Expression Miner (STEM) clustering of DEGs, clusters 1 and 3, with obvious expression trends that were consistent with or in contrast to the elongation rate, were screened. The cluster 1 DEGs were mainly involved in the GO cellular component category and KEGG genetic information processing class; however, the cluster 3 DEGs were mainly involved in metabolic processes. Furthermore, qRT-PCR confirmed that key genes of the long-chain fatty acid synthesis pathway were involved in stipe gradient elongation and regulated by NADPH oxidase-derived ROS signaling molecules. These findings provide an essential basis for understanding the molecular mechanism of stipe gradient elongation.
Keywords: needle mushroom; stipe elongation; RNA-seq; ribosome; long-chain fatty acid needle mushroom; stipe elongation; RNA-seq; ribosome; long-chain fatty acid

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MDPI and ACS Style

Yan, J.; Tong, Z.; Han, X.; Gan, Y.; Liu, Y.; Chen, J.; Duan, X.; Lin, J.; Gan, B.; Xie, B. Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis. J. Fungi 2023, 9, 64. https://doi.org/10.3390/jof9010064

AMA Style

Yan J, Tong Z, Han X, Gan Y, Liu Y, Chen J, Duan X, Lin J, Gan B, Xie B. Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis. Journal of Fungi. 2023; 9(1):64. https://doi.org/10.3390/jof9010064

Chicago/Turabian Style

Yan, Junjie, Zongjun Tong, Xing Han, Ying Gan, Yuanyuan Liu, Jie Chen, Xinlian Duan, Junbin Lin, Bingcheng Gan, and Baogui Xie. 2023. "Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis" Journal of Fungi 9, no. 1: 64. https://doi.org/10.3390/jof9010064

APA Style

Yan, J., Tong, Z., Han, X., Gan, Y., Liu, Y., Chen, J., Duan, X., Lin, J., Gan, B., & Xie, B. (2023). Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis. Journal of Fungi, 9(1), 64. https://doi.org/10.3390/jof9010064

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