Differentiate Transcriptomes of Aerial and Creepy <i>Agaricus bisporus</i> Hyphae

DAI Jianqing; CHEN Wenzhi; ZENG Zhiheng; CAI Zhixin; CHEN Meiyuan

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DAI J Q, CHEN W Z, ZENG Z H, et al. Differentiate Transcriptomes of Aerial and Creepy Agaricus bisporus Hyphae [J]. Fujian Journal of Agricultural Sciences，2024，39（9）：1−12

Citation:

DAI J Q, CHEN W Z, ZENG Z H, et al. Differentiate Transcriptomes of Aerial and Creepy Agaricus bisporus Hyphae [J]. Fujian Journal of Agricultural Sciences，2024，39（9）：1−12

DAI J Q, CHEN W Z, ZENG Z H, et al. Differentiate Transcriptomes of Aerial and Creepy Agaricus bisporus Hyphae [J]. Fujian Journal of Agricultural Sciences，2024，39（9）：1−12

Citation:

DAI J Q, CHEN W Z, ZENG Z H, et al. Differentiate Transcriptomes of Aerial and Creepy Agaricus bisporus Hyphae [J]. Fujian Journal of Agricultural Sciences，2024，39（9）：1−12

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Differentiate Transcriptomes of Aerial and Creepy Agaricus bisporus Hyphae

Edible Mushroom Institute, Fujian Academy of Agricultural Sciences/National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fuzhou, Fujian　350013, China

Received Date: 2024-08-09
Rev Recd Date: 2024-09-01

Available Online: 2024-10-31

Abstract

Abstract

Objective Key genes associated with Agaricus bisporus of different mycelial morphology were analyzed. [Methods] As 2796, the main cultivated variety of A. bisporus, with aerial or creepy hyphae grown on same plate were collected for RNA transcriptome sequencing and comparison with reference. Results There were 965 differentially expressed genes (DEGs) between the aerial hyphae-A601 and the creepy hyphae-A602. According to the GO enrichment analysis, the hydrophobic DEGs were enriched in the fungal cell wall, such as AGABI2DRAFT_13655, AGABI2DRAFT_136569, and AGABI2DRAFT_193057 that belonged to the ABH3 protein gene family, with expressions significantly higher in A601 than in A602. Thus, they were postulated to be related to the production of aerial hyphae. In addition, the hydrophobic surface binding protein A (HsbA)-related gene, AGABI2DRAFT_194662, showed a FPKM expression of 0 in A601, but 10.24 in A602. Furthermore, 8 enriched DEGs related to lipase isoenzymes exhibited a FPKM expression significantly higher in A601 than in A602. The SNP/InDel analysis indicated that the SNPs in A601 was 110 601 as opposed to 111 188 in A602, the most frequent mutation in SNPs was C:G>T:A, and that 2 374 common InDels were identified. Conclusion The transcriptomes and possibly associated genes and SNP sites in A. bisporus with different mycelial morphology obtained in this study would be of value for the mushroom germplasm evaluation and breeding.
- Agaricus bisporus,
- As 2796,
- creepy hypha,
- aerial hypha,
- transcriptome sequencing,
- differentially expressed genes

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References

[1]	BERNAŚ E, JAWORSKA G. Vitamins profile as an indicator of the quality of frozen Agaricus bisporus mushrooms [J]. Journal of Food Composition and Analysis, 2016, 49: 1−8. doi: 10.1016/j.jfca.2016.03.002
[2]	OWAID M N, BARISH A, ALI SHARIATI M. Cultivation of Agaricus bisporus (button mushroom) and its usages in the biosynthesis of nanoparticles [J]. Open Agriculture, 2017, 2(1): 537−543. doi: 10.1515/opag-2017-0056
[3]	MUSZYŃSKA B, KAŁA K, ROJOWSKI J, et al. Composition and biological properties of Agaricus bisporus fruiting bodies- a review [J]. Polish Journal of Food and Nutrition Sciences, 2017, 67(3): 173−181. doi: 10.1515/pjfns-2016-0032
[4]	王翠, 郭仲杰, 尤洁, 等. 双孢蘑菇产、质量性状相关分子标记的初步研究 [J]. 福建农业科技, 2018, 49(7):1−5. WANG C, GUO Z J, YOU J, et al. A preliminary study on molecular markers related to yield and quality traits of Agaricus bisporus [J]. Fujian Agricultural Science and Technology, 2018, 49(7): 1−5. (in Chinese)
[5]	DAS B, DE B, CHETREE R, et al. Medicinal aspect of mushrooms: A view point[J]. Herbal Medicine in India: Indigenous Knowledge, Practice, Innovation and its Value, 2020: 509-532.
[6]	ZHANG M, ZHAO L, TANG F, et al. Chemical structures, biological activities, and biosynthetic analysis of secondary metabolites from Agaricus mushrooms: A review [J]. Journal of Agricultural and Food Chemistry, 2024, 72(22): 12387−12397. doi: 10.1021/acs.jafc.4c01861
[7]	柯斌榕, 兰清秀, 卢政辉, 等. 福建省双孢蘑菇栽培技术的变革与发展 [J]. 食药用菌, 2017, 25(1):12−19. KE B R, LAN Q X, LU Z H, et al. Innovation and development of Agaricus bisporus cultivation techniques in Fujian province [J]. Edible and Medicinal Mushrooms, 2017, 25(1): 12−19. (in Chinese)
[8]	林杰, 林莫翎. 蘑菇异型菌丝与栽培技术的相关性 [J]. 福建农业, 2007(11):20−21. LIN J, LIN M L. Correlation between heteromorphic hyphae of mushrooms and cultivation techniques [J]. Fujian Agriculture, 2007(11): 20−21. (in Chinese)
[9]	詹才新, 凌霞芬. 双孢蘑菇菌落形态和产质量性状间相关性研究 [J]. 食用菌学报, 1997, 4(3):7−12. ZHAN C X, LING X F. Studies on correlation between colonial morphology and characters of productivity and quality of Agaricus bisporus [J]. Acta Edulis Fungi, 1997, 4(3): 7−12. (in Chinese)
[10]	李洪荣. 双孢蘑菇不同菌落形态的同工酶分析 [J]. 福建轻纺, 2011(4):43−45. LI H R. Isozyme analysis of different colony morphology of Agaricus bisporus [J]. The Light & Textile Industries of Fujian, 2011(4): 43−45. (in Chinese)
[11]	CAI Z X, CHEN M Y, LU Y P, et al. Metabolomics and transcriptomics unravel the mechanism of browning resistance in Agaricus bisporus [J]. PLoS One, 2022, 17(3): e0255765. doi: 10.1371/journal.pone.0255765
[12]	LU Y P, GUO Z J, KE B R, et al. Genome-wide association study and transcriptome analysis provide candidate genes for agronomic traits of Agaricus bisporus [J]. Horticulturae, 2024, 10(7): 691. doi: 10.3390/horticulturae10070691
[13]	YANG X M, YANG K X, WANG X H, et al. Transcriptomic analysis reveals the mechanism of bacterial disease resistance of postharvest button mushroom (Agaricus bisporus) [J]. Physiological and Molecular Plant Pathology, 2022, 122: 101903. doi: 10.1016/j.pmpp.2022.101903
[14]	秦煜, 郑向丽, 林钟员. 基于转录组测序的红萍SSR和SNP特征分析 [J]. 福建农业科技, 2023, 54(6):44−48. QIN Y, ZHENG X L, LIN Z Y. Characteristic analysis of SSR and SNP in Azolla imbircata based on transcriptome sequencing [J]. Fujian Agricultural Science and Technology, 2023, 54(6): 44−48. (in Chinese)
[15]	陈美元. 双孢蘑菇As2796全长cDNA文库的构建及鉴定 [J]. 福建农业学报, 2012, 27(11):1201−1204. CHEN M Y. Construction and identification of full-length cDNA library of Agaricus bisporus As2796 [J]. Fujian Journal of Agricultural Sciences, 2012, 27(11): 1201−1204. (in Chinese)
[16]	王泽生. 蘑菇杂交株As2796的种性与栽培技术要点 [J]. 食用菌, 1993, 15(5):9. WANG Z S. Characteristics and cultivation techniques of mushroom hybrid strain As2796 [J]. Edible Fungi, 1993, 15(5): 9. (in Chinese)
[17]	KIM D, PERTEA G, TRAPNELL C, et al. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions [J]. Genome Biology, 2013, 14(4): R36. doi: 10.1186/gb-2013-14-4-r36
[18]	顾鑫, 杨晓贺, 姚亮亮, 等. 大豆灰斑病菌Race15的全基因组测序分析 [J]. 大豆科学, 2021, 40(4):466−475. GU X, YANG X H, YAO L L, et al. Whole-genome sequencing and analysis of Cercospora sojina race 15 [J]. Soybean Science, 2021, 40(4): 466−475. (in Chinese)
[19]	JIANG H, WONG W H. Statistical inferences for isoform expression in RNA-Seq [J]. Bioinformatics, 2009, 25(8): 1026−1032. doi: 10.1093/bioinformatics/btp113
[20]	ANDERS S, HUBER W. Differential expression analysis for sequence count data[J]. Nature Precedings, 2010.
[21]	MCKENNA A, HANNA M, BANKS E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data [J]. Genome Research, 2010, 20(9): 1297−1303. doi: 10.1101/gr.107524.110
[22]	WANG K, LI M, HAKONARSON H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data Nucleic Acids Research[J]. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data Nucleic Acids Research, 2010: 38.
[23]	王秉峰. 匍匐型与气生型双孢蘑菇菌株品比试验 [J]. 中国食用菌, 2010, 29(5):19−20. WANG B F. The comparison test of different strains of prostrate and aerial-type Agaricus bisporas [J]. Edible Fungi of China, 2010, 29(5): 19−20. (in Chinese)
[24]	WANG H C, WANG Z S. The prediction of strain characteristecs of Agaricus bisporus by the application of isozyme electrophoresis [J]. Fujian Mushroom, 1991(1): 38−48. (in Chinese).
[25]	WANG Z S, WANG H C. Isozyme patterns and characteristics of hybrid strains of Agaricus bisporus [J]. Microl. Neotrop. Apl, 1990(3): 19−29.
[26]	金建康, 徐鹤林. 双孢蘑菇气生型与匍匐型的比较研究 [J]. 中国食用菌, 1990, 9(5):3−4. JIN J K, XU H L. Comparative study on aerial type and creeping type of Agaricus bisporus [J]. Edible Fungi of China, 1990, 9(5): 3−4. (in Chinese)
[27]	杜炫星, 牛敏敏, 赵清, 等. 李白盾蚧转录组分析及 SSR 位点开发 [J]. 环境昆虫学报, 2023, 45(5):1318−1332. DU X X, NIU M M, ZHAO Q, et al. Analysis of the transcriptome and development of SSR Loci in Pseudaulacaspis prunicola (Maskell) [J]. Journal of Environmental Entomology, 2023, 45(5): 1318−1332. (in Chinese).
[28]	MORIN E, KOHLER A, BAKER A R, et al. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche [J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(43): 17501−17506.
[29]	LINDER M B, SZILVAY G R, NAKARI-SETÄLÄ T, et al. Hydrophobins: The protein-amphiphiles of filamentous fungi [J]. FEMS Microbiology Reviews, 2005, 29(5): 877−896. doi: 10.1016/j.femsre.2005.01.004
[30]	LUGONES L G, BOSSCHER J S, SCHOLTMEYER K, et al. An abundant hydrophobin (ABH1) forms hydrophobic rodlet layers in Agaricus bisporus fruiting bodies[J]. Microbiology, 1996, 142 ( Pt 5): 1321-1329.
[31]	LUGONES L G, WÖS H A B, WESSELS J G H. A hydrophobin (ABH3) specifically secreted by vegetatively growing hyphae of Agaricus bisporus (common white button mushroom)[J]. Microbiology, 1998, 144 ( Pt 8): 2345-2353.
[32]	OHTAKI S, MAEDA H, TAKAHASHI T, et al. Novel hydrophobic surface binding protein, HsbA, produced by Aspergillus oryzae [J]. Applied and Environmental Microbiology, 2006, 72(4): 2407−2413. doi: 10.1128/AEM.72.4.2407-2413.2006
[33]	张烨. 球孢白僵菌疏水表面结合蛋白HsbA的克隆及功能研究[D]. 北京: 中国农业科学院, 2013 ZHANG Y. cDNA clone and functional research on hydrophobic surface binding protein HsbA in Beauveria bassiana [D]. Beijing: Chinese Academy of Agricultural Sciences, 2013. (in Chinese)
[34]	PARK J, LEE S, CHOI J, et al. Fungal cytochrome P450 database [J]. BMC Genomics, 2008, 9: 402. doi: 10.1186/1471-2164-9-402
[35]	HLAVICA P. Evaluation of structural features in fungal cytochromes P450 predicted to rule catalytic diversification [J]. Biochimica et Biophysica Acta, 2013, 1834(1): 205−220. doi: 10.1016/j.bbapap.2012.09.012
[36]	SMIDA A D, VALDERRAMA X P, AGOSTINI M C, et al. Cadmium stimulates transcription of the cytochrome p450 side chain cleavage gene in genetically modified stable porcine granulosa cells [J]. Biology of Reproduction, 2004, 70(1): 25−31. doi: 10.1095/biolreprod.103.019000
[37]	ZHANG M, LIU X C, YUAN L Y, et al. Transcriptional profiling in cadmium-treated rice seedling roots using suppressive subtractive hybridization [J]. Plant Physiology and Biochemistry, 2012, 50: 79−86. doi: 10.1016/j.plaphy.2011.07.015
[38]	WANG L L, LI H B, WEI H L, et al. Identification of cadmium-induced Agaricus blazei genes through suppression subtractive hybridization [J]. Food and Chemical Toxicology, 2014, 63: 84−90. doi: 10.1016/j.fct.2013.10.036
[39]	宋媛, 胡秋辉, 苏安祥, 等. 转录组学解析茉莉酸甲酯对双孢蘑菇个体大小的影响机制 [J]. 食品科学, 2021, 42(4):130−137. SONG Y, HU Q H, SU A X, et al. Transcriptomic analysis of the mechanism underlying the effect of methyl jasmonate on the size of Agaricus bisporus [J]. Food Science, 2021, 42(4): 130−137. (in Chinese)
[40]	刘俊敏. 镉胁迫对双孢蘑菇抗氧化系统的影响及耐受性相关基因的筛选与鉴定[D]. 厦门: 厦门大学, 2018. LIU J M. Cadmium stress on the effect of antioxidant system in Agaricus bisporus and the identification of differentially expressed genes [D]. Xiamen: Xiamen University, 2018. (in Chinese)
[41]	XU K H, ZHAO Y, ZHAO Y, et al. Soybean F-box-like protein GmFBL144 interacts with small heat shock protein and negatively regulates plant drought stress tolerance [J]. Frontiers in Plant Science, 2022, 13: 823529. doi: 10.3389/fpls.2022.823529
[42]	MÜLLER-STARCK G. Isozymes[M]//Molecular Tools for Screening Biodiversity. Dordrecht: Springer Netherlands, 1998: 75-81.
[43]	时如霞, 曾琴, 赵丹. 基于楠木转录组的SSR、SNP、Indel分子标记技术特征分析 [J]. 山地农业生物学报, 2023, 42(4):83−87. SHI R X, ZENG Q, ZHAO D. SSR, SNP and InDel characterization of Phoebe zhennan based on the transcriptome sequence [J]. Journal of Mountain Agriculture and Biology, 2023, 42(4): 83−87. (in Chinese)
[44]	贾定洪, 王波, 何晓兰, 等. 基于基因组重测序发掘金针菇 InDel, SV 及丰度 SNP 标记 [J]. 菌物学报, 2024, 43(7):230228. JIA D H, WANG B, HE X L, et al. Exploitation of InDel, SV and abundance SNP markers in Flammulina filiformis based on genome resequencing [J]. Mycosystema, 2024, 43(7): 23022. (in Chinese).
[45]	施肖堃, 蔡志欣, 郭仲杰, 等. 18个双孢蘑菇核心种质的重测序初步分析 [J]. 福建农业学报, 2019, 34(10):1167−1172. SHI X K, CAI Z X, GUO Z J, et al. A preliminary report on resequencing 18 representative strains of Agaricus bisporus [J]. Fujian Journal of Agricultural Sciences, 2019, 34(10): 1167−1172. (in Chinese).