Comparative Transcriptome Analysis Revealed Genes Involved in the Fruiting Body Development of

Overview

Journal PeerJ

Specialties Biology
Environmental Health
General Medicine

Date 2020 Jan 29

PMID 31988806

Citations 11

Authors

Xinxin Tong

Han Zhang

Fang Wang

Zhengyao Xue

Jing Cao

Cheng Peng

Jinlin Guo

Affiliations

Soon will be listed here.

Abstract

is a highly valued fungus that has been used as traditional Asian medicine. This fungus is one of the most important sources of income for the nomadic populations of the Tibetan Plateau. With global warming and excessive collection, the wild resources declined dramatically. The cultivation of hasn't been fully operational due to the unclear genetic basis of the fruiting body development. Here, our study conducted pairwise comparisons between transcriptomes acquired from different growth stages of including asexual mycelium (CM), developing fruiting body (DF) and mature fruiting body (FB). All RNA-Seq reads were aligned to the genome of CO18 prior to comparative analyses. Cluster analysis showed that the expression profiles of FB and DF were highly similar compared to CM. Alternative splicing analysis (AS) revealed that the stage-specific splicing genes may have important functions in the development of fruiting body. Functional enrichment analyses showed that differentially expressed genes (DEGs) were enriched in protein synthesis and baseline metabolism during fruiting body development, indicating that more protein and energy might be required for fruiting body development. In addition, some fruiting body development-associated genes impacted by ecological factors were up-regulated in FB samples, such as the nucleoside diphosphate kinase gene (), β subunit of the fatty acid synthase gene () and the superoxide dismutase gene (). Moreover, the expression levels of several cytoskeletons genes were significantly altered during all these growth stages, suggesting that these genes play crucial roles in both vegetative growth and the fruiting body development. Quantitative PCR (qPCR) was used to validate the gene expression profile and the results supported the accuracy of the RNA-Seq and DEGs analysis. Our study offers a novel perspective to understand the underlying growth stage-specific molecular differences and the biology of fruiting body development.

Citing Articles

Unveiling mycoviral diversity in through transcriptome analyses.

Kang Q, Zhang J, Chen F, Dong C, Qin Q, Li X Front Microbiol. 2024; 15:1493365.

PMID: 39654673 PMC: 11625762. DOI: 10.3389/fmicb.2024.1493365.

Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in .

Ke S, Ding L, Niu X, Shan H, Song L, Xi Y PeerJ. 2023; 11:e16288.

PMID: 37904843 PMC: 10613438. DOI: 10.7717/peerj.16288.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of .

Nagy L, Vonk P, Kunzler M, Foldi C, Viragh M, Ohm R Stud Mycol. 2023; 104:1-85.

PMID: 37351542 PMC: 10282164. DOI: 10.3114/sim.2022.104.01.

Stable reference gene selection for Ophiocordyceps sinensis gene expression studies under different developmental stages and light-induced conditions.

Tong C, Wei J, Mao X, Pan G, Li C, Zhou Z PLoS One. 2023; 18(4):e0284486.

PMID: 37079619 PMC: 10118168. DOI: 10.1371/journal.pone.0284486.

Medium optimization for high mycelial soluble protein content of using response surface methodology.

Tang C, Wang J, Liu X, Chen J, Liang J, Wang T Front Microbiol. 2022; 13:1055055.

PMID: 36569047 PMC: 9780674. DOI: 10.3389/fmicb.2022.1055055.

References

Busch S, Hoffmann B, Valerius O, Starke K, Duvel K, Braus G . Regulation of the Aspergillus nidulans hisB gene by histidine starvation. Curr Genet. 2001; 38(6):314-22. DOI: 10.1007/s002940000171. View

Busch S, Eckert S, Krappmann S, Braus G . The COP9 signalosome is an essential regulator of development in the filamentous fungus Aspergillus nidulans. Mol Microbiol. 2003; 49(3):717-30. DOI: 10.1046/j.1365-2958.2003.03612.x. View

Eckert S, Hoffmann B, Wanke C, Braus G . Sexual development of Aspergillus nidulans in tryptophan auxotrophic strains. Arch Microbiol. 1999; 172(3):157-66. DOI: 10.1007/s002030050755. View

Pandey A, Roca M, Read N, Glass N . Role of a mitogen-activated protein kinase pathway during conidial germination and hyphal fusion in Neurospora crassa. Eukaryot Cell. 2004; 3(2):348-58. PMC: 387641. DOI: 10.1128/EC.3.2.348-358.2004. View

Ogura Y, Yoshida Y, YABE N, Hasunuma K . A point mutation in nucleoside diphosphate kinase results in a deficient light response for perithecial polarity in Neurospora crassa. J Biol Chem. 2001; 276(24):21228-34. DOI: 10.1074/jbc.M011381200. View

Martin F, Kohler A, Murat C, Balestrini R, Coutinho P, Jaillon O . Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature. 2010; 464(7291):1033-8. DOI: 10.1038/nature08867. View

Shestakova E, Singer R, Condeelis J . The physiological significance of beta -actin mRNA localization in determining cell polarity and directional motility. Proc Natl Acad Sci U S A. 2001; 98(13):7045-50. PMC: 34620. DOI: 10.1073/pnas.121146098. View

Xu J, Huang Y, Chen X, Zheng S, Chen P, Mo M . The Mechanisms of Pharmacological Activities of Ophiocordyceps sinensis Fungi. Phytother Res. 2016; 30(10):1572-1583. DOI: 10.1002/ptr.5673. View

Bouhouche K, Zickler D, Debuchy R, Arnaise S . Altering a gene involved in nuclear distribution increases the repeat-induced point mutation process in the fungus Podospora anserina. Genetics. 2004; 167(1):151-9. PMC: 1470861. DOI: 10.1534/genetics.167.1.151. View

10.

Wen J, Zhang Z, Gong L, Xun H, Li J, Qi B . Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Species. Genes (Basel). 2019; 10(6). PMC: 6627472. DOI: 10.3390/genes10060465. View

11.

Pertea M, Kim D, Pertea G, Leek J, Salzberg S . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11(9):1650-67. PMC: 5032908. DOI: 10.1038/nprot.2016.095. View

12.

Zhong X, Gu L, Li S, Kan X, Zhang G, Liu X . Transcriptome analysis of Ophiocordyceps sinensis before and after infection of Thitarodes larvae. Fungal Biol. 2016; 120(6-7):819-26. DOI: 10.1016/j.funbio.2016.02.003. View

13.

Purschwitz J, Muller S, Kastner C, Fischer R . Seeing the rainbow: light sensing in fungi. Curr Opin Microbiol. 2006; 9(6):566-71. DOI: 10.1016/j.mib.2006.10.011. View

14.

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

15.

Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M . Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res. 2010; 38(15):5075-87. PMC: 2926611. DOI: 10.1093/nar/gkq256. View

16.

Oda K, Hasunuma K . Genetic analysis of signal transduction through light-induced protein phosphorylation in Neurospora crassa perithecia. Mol Gen Genet. 1998; 256(6):593-601. DOI: 10.1007/s004380050607. View

17.

Yin Y, Yu G, Chen Y, Jiang S, Wang M, Jin Y . Genome-wide transcriptome and proteome analysis on different developmental stages of Cordyceps militaris. PLoS One. 2012; 7(12):e51853. PMC: 3522581. DOI: 10.1371/journal.pone.0051853. View

18.

Xiang L, Li Y, Zhu Y, Luo H, Li C, Xu X . Transcriptome analysis of the Ophiocordyceps sinensis fruiting body reveals putative genes involved in fruiting body development and cordycepin biosynthesis. Genomics. 2014; 103(1):154-9. DOI: 10.1016/j.ygeno.2014.01.002. View

19.

Langmead B . Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics. 2010; Chapter 11:Unit 11.7. PMC: 3010897. DOI: 10.1002/0471250953.bi1107s32. View

20.

Qin Q, Zhou G, Zhang H, Meng Q, Zhang J, Wang H . Obstacles and approaches in artificial cultivation of Chinese cordyceps. Mycology. 2018; 9(1):7-9. PMC: 6059063. DOI: 10.1080/21501203.2018.1442132. View