Transcriptional variation and RNA polymorphism among different Lentinula edodes (Berk.) Pegler strains.
Lentinula edodes
RNA polymorphism
differential gene
mapping
transcriptional variation
Journal
Journal of the science of food and agriculture
ISSN: 1097-0010
Titre abrégé: J Sci Food Agric
Pays: England
ID NLM: 0376334
Informations de publication
Date de publication:
18 Oct 2024
18 Oct 2024
Historique:
revised:
19
09
2024
received:
11
03
2024
accepted:
23
09
2024
medline:
18
10
2024
pubmed:
18
10
2024
entrez:
18
10
2024
Statut:
aheadofprint
Résumé
Lentinula edodes is a commercially important mushroom known for its nutritional and therapeutic values. However, the molecular mechanisms underlying the distinct nutritional and physiological attributes of various L. edodes strains are not well understood. This study focused on three Lentinula strains (DMRO-356, DMRO-623, and DMRO-388s) with different nutritional and productivity profiles. Illumina sequencing was used to perform a whole-transcriptome analysis, conducting 100-base pair paired-end sequencing of total messenger RNA (mRNA) in duplicate, resulting in 28-48 million sequencing reads per strain. After rigorous data filtering, over 99% of high-quality reads were retained, and more than 95% were aligned to the Lentinula genome. Differential gene expression analyses identified 2210 differentially expressed genes between DMRO-356 and DMRO-623, 862 between DMRO-356 and DMRO-388s, and 2212 between DMRO-623 and DMRO-388s. Significant genetic variations were found among the strains, including 7753 single nucleotide polymorphisms (SNPs) in DMRO-356 versus DMRO-623 and 4080 SNPs in DMRO-356 versus DMRO-388s. Additionally, 349 insertions/deletions (InDels) were found in DMRO-356/DMRO-623 and 218 in DMRO-356/DMRO-388 s. Non-synonymous SNPs, which alter amino acid compositions, were analyzed, showing a preference for polar over charged amino acids. These differentially expressed genes were associated with various nutritional and developmental processes, highlighting the importance of genetic variations in shaping amino acid composition and potentially affecting protein function. This study is the first comprehensive exploration of transcriptional differences among Lentinula strains available for its cultivation, providing valuable insights to enhance mushroom quality and productivity. © 2024 Society of Chemical Industry.
Sections du résumé
BACKGROUND
BACKGROUND
Lentinula edodes is a commercially important mushroom known for its nutritional and therapeutic values. However, the molecular mechanisms underlying the distinct nutritional and physiological attributes of various L. edodes strains are not well understood. This study focused on three Lentinula strains (DMRO-356, DMRO-623, and DMRO-388s) with different nutritional and productivity profiles. Illumina sequencing was used to perform a whole-transcriptome analysis, conducting 100-base pair paired-end sequencing of total messenger RNA (mRNA) in duplicate, resulting in 28-48 million sequencing reads per strain. After rigorous data filtering, over 99% of high-quality reads were retained, and more than 95% were aligned to the Lentinula genome.
RESULTS
RESULTS
Differential gene expression analyses identified 2210 differentially expressed genes between DMRO-356 and DMRO-623, 862 between DMRO-356 and DMRO-388s, and 2212 between DMRO-623 and DMRO-388s. Significant genetic variations were found among the strains, including 7753 single nucleotide polymorphisms (SNPs) in DMRO-356 versus DMRO-623 and 4080 SNPs in DMRO-356 versus DMRO-388s. Additionally, 349 insertions/deletions (InDels) were found in DMRO-356/DMRO-623 and 218 in DMRO-356/DMRO-388 s. Non-synonymous SNPs, which alter amino acid compositions, were analyzed, showing a preference for polar over charged amino acids.
CONCLUSION
CONCLUSIONS
These differentially expressed genes were associated with various nutritional and developmental processes, highlighting the importance of genetic variations in shaping amino acid composition and potentially affecting protein function. This study is the first comprehensive exploration of transcriptional differences among Lentinula strains available for its cultivation, providing valuable insights to enhance mushroom quality and productivity. © 2024 Society of Chemical Industry.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024 Society of Chemical Industry.
Références
Wang H and Ng TB, A novel ribonuclease from the veiled lady mushroom Dictyophora indusiata. Biochem Cell Biol 81:373–377 (2003).
Amin Z, Abbas S, Munir A, Mubeen M, Qadri A, Raza M et al., Role of medicinal mushroom Lentinula edodes in nutrition, Nutraceutics and Ethnopharmacology. J Pharm Res Int 11:18–35 (2022).
Ponnusamy C, Uddandrao VVS, Pudhupalayam SP, Singaravel S, Periyasamy T, Ponnusamy P et al., Lentinula edodes (edible mushroom) as a nutraceutical: a review. Biosci Biotechnol Res Asia 19:1–11 (2022).
Atila F, Cultivation and utilization of shiitake mushroom BT, in Medicinal Plants: Domestication, Biotechnology and Regional Importance, ed. by Ekiert HM, Ramawat KG and Arora J. Springer International Publishing, Cham, pp. 383–413 (2021).
Han Y, Gao S, Muegge K, Zhang W and Zhou B, Advanced applications of RNA sequencing and challenges. Bioinform Biol Insights 9:29–46 (2015).
Hrdlickova R, Toloue M and Tian B, RNA‐Seq methods for transcriptome analysis. Wiley Interdiscip Rev (WIREs) RNA 8:1–18 (2017).
Kukurba KR and Montgomery SB, RNA sequencing and analysis. Cold Spring Harb Protoc 11:951–969 (2015).
Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET et al., A Beginner's guide to analysis of RNA sequencing data. Am J Respir Cell Mol Biol 59:145–157 (2018).
Wang Z, Gerstein M and Snyder M, RNA‐Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63 (2009).
Kassam S, Meyer P, Corfield A, Mikuz G and Sergi C, Single nucleotide polymorphisms (SNPs): history, biotechnological outlook and practical applications. Curr Pharmacogenomics 1:237–245 (2005).
Zheng P, Xia Y, Xiao G, Xiong C, Hu X, Zhang S et al., Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine. Genome Biol 12:R116 (2011).
Chen L, Gong Y, Cai Y, Liu W, Zhou Y, Xiao Y et al., Genome sequence of the edible cultivated mushroom Lentinula edodes (shiitake) reveals insights into lignocellulose degradation. PLoS One 11:1–20 (2016).
Wang N and Huo YX, Using genome and transcriptome analysis to elucidate biosynthetic pathways. Curr Opin Biotechnol 75:102708 (2022).
Annepu SK, Sharma VP, Kumar S and Barh A, Cultivation techniques of shiitake (a medicinal mushroom with culinary delight). ICAR‐Directorate of Mushroom Research, Himachal Pradesh, India, pp. 1–58 (2019).
Sharma VP, Annepu SK, Barh A, Shirur M and Kamal S, Genetic divergence and cluster analysis in shiitake genotypes based on yield‐related traits with commercial breeding significance to shorten the production period. Int J Veg Sci 24:424–431 (2018).
Manikandan K and Manjit S, Proximate composition of different mushroom varieties and effect of UV light exposure on vitamin D content in Agaricus bisporus and Volvariella volvacea. Mushroom Res 25:1–8 (2016).
Ouyang K, Li J, Huang H, Que Q, Li P and Chen X, A simple method for RNA isolation from various tissues of the tree Neolamarckia cadamba. Biotechnol Equip 28:1008–1013 (2014).
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR et al., Differential gene and transcript expression analysis of RNA‐seq experiments with TopHat and cufflinks. Nat Protoc 7:562–578 (2012).
Shankar R, Bhattacharjee A and Jain M, Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses. Sci Rep 6:23719 (2016).
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL and Pachter L, Differential analysis of gene regulation at transcript resolution with RNA‐seq. Nat Biotechnol 31:46–53 (2013).
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R and Salzberg SL, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36 (2013).
Yu H, Zhang L, Shang X, Peng B, Li Y, Xiao S et al., Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes. BMC Genomics 23:120 (2022).
Ghosh S and Chan CKK, Analysis of RNA‐Seq data using TopHat and cufflinks. Methods Mol Biol 1374:339–361 (2016).
Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P et al., Comprehensive evaluation of differential gene expression analysis methods for RNA‐seq data. Genome Biol 14:3158 (2013).
Zhao S, Guo Y, Sheng Q and Shyr Y, Advanced heat map and clustering analysis using heatmap3. Biomed Res Int 2014:1–7 (2014). https://doi.org/10.1155/2014/986048.
Siavoshi A, Taghizadeh M, Dookhe E and Piran M, Gene expression profiles and pathway enrichment analysis to identification of differentially expressed gene and signalling pathways in epithelial ovarian cancer based on high‐throughput RNA‐seq data. Genomics 114:161–170 (2022).
Tomczak A, Mortensen JM, Winnenburg R, Liu C, Alessi DT, Swamy V et al., Interpretation of biological experiments changes with the evolution of the gene ontology and its annotations. Sci Rep 8:5115 (2018).
GO enrichment analysis (2023). Available from: https://geneontology.org/docs/go-enrichment-analysis/
Di Salvatore V, Crispino E, Maleki A, Nicotra G, Russo G and Pappalardo F, Computational identification of differentially‐expressed genes as suggested novel COVID‐19 biomarkers: a bioinformatics analysis of expression profiles. Comput Struct Biotechnol J 21:3339–3354 (2023).
Johnson JL, Adkins D and Chauvin S, A review of the quality indicators of rigor in qualitative research. Am J Pharm Educ 84:7120 (2020).
Zou H, Wu LX, Tan L, Shang FF and Zhou HH, Significance of single‐nucleotide variants in long intergenic non‐protein coding RNAs. Front Cell Dev Biol 8:1–14 (2020). https://www.frontiersin.org/articles/10.3389/fcell.2020.00347.
Shastry BS, SNPs: impact on gene function and phenotype. Methods Mol Biol 578:3–22 (2009).
Jangra S, Chaudhary V, Yadav RC and Yadav NR, High‐throughput phenotyping: a platform to accelerate crop improvement. Phenomics 1:31–53 (2021).
Zhang L, Gong W, Li C, Shen N, Gui Y, Bian Y et al., RNA‐Seq‐based high‐resolution linkage map reveals the genetic architecture of fruiting body development in shiitake mushroom, Lentinula edodes. Comput Struct Biotechnol J 1:19 (2021).
Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE and Savas S, A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Mol Oncol 15:3329–3347 (2021).
Ellegren H and Galtier N, Determinants of genetic diversity. Nat Rev Genet 17:422–433 (2016).
Yates CM and Sternberg MJE, The Effects of Non‐Synonymous Single Nucleotide Polymorphisms (nsSNPs) on Protein–Protein Interactions. J Mol Biol 425:3949–3963 (2013) Available.
Bromberg Y and Rost B, SNAP: predict effect of non‐synonymous polymorphisms on function. Nucleic Acids Res 35:3823–3835 (2007).
Bhattacharya R, Rose PW, Burley SK and Prlić A, Impact of genetic variation on three dimensional structure and function of proteins. PLoS One 12:1–22 (2017).
Zhao J, Zhang S, Jiang Y, Liu Y and Zhu Q, Mutation analysis of pathogenic non‐synonymous single nucleotide polymorphisms (nsSNPs) in WFS1 gene through computational approaches. Sci Rep 13:6774 (2023).
Virolainen SJ, VonHandorf A, Viel KCMF, Weirauch MT and Kottyan LC, Gene‐environment interactions and their impact on human health. Genes Immun 24:1–11 (2023).
Du M‐Z, Liu S, Zeng Z, Alemayehu LA, Wei W and Guo F‐B, Amino acid compositions contribute to the proteins' evolution under the influence of their abundances and genomic GC content. Sci Rep 8:73–82 (2018).
Jose et al., Understanding Genetic Variance and Phenotype Expression. National Academies Press, Washington, DC (2017). Available from: https://www.ncbi.nlm.nih.gov/books/NBK425811/.
Sakamoto Y, Nakade K, Sato S, Yoshida K, Miyazaki K, Natsume S et al., Lentinula edodes genome survey and postharvest transcriptome analysis. Appl Environ Microbiol 83:1–14 (2017).