Efficient and specific DNA oligonucleotide rRNA probe-based rRNA removal in Talaromyces marneffei

References

• Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, et al. 2013. Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat Methods. 10(7):623–629. DOI:https://doi.org/10.1038/nmeth.2483.
   PubMed Web of Science ®Google Scholar
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410. DOI:https://doi.org/10.1016/S0022-2836(05)80360-2.
   PubMed Web of Science ®Google Scholar
• Beermann J, Piccoli M-T, Viereck J, Thum T. 2016. Non-coding RNAs in development and disease: background, mechanisms, and therapeutic approaches. Physiol Rev. 96(4):1297–1325. DOI:https://doi.org/10.1152/physrev.00041.2015.
   PubMed Web of Science ®Google Scholar
• Cemel IA, Ha N, Schermann G, Yonekawa S, Brunner M. 2017. The coding and noncoding transcriptome of Neurospora crassa. BMC Genomics. 18(1):978. DOI:https://doi.org/10.1186/s12864-017-4360-8.
   PubMedGoogle Scholar
• Culviner PH, Guegler CK, Laub MT, Cooper VS. 2020. A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies. mBio. 11(2). DOI:https://doi.org/10.1128/mBio.00010-20.
   Google Scholar
• Fatica A, Bozzoni I. 2014. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 15(1):7–21. DOI:https://doi.org/10.1038/nrg3606.
   PubMed Web of Science ®Google Scholar
• Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al. 2014. Pfam: the protein families database. Nucleic Acids Res. 42( Database issue):D222–D230. DOI:https://doi.org/10.1093/nar/gkt1223.
   PubMed Web of Science ®Google Scholar
• Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, et al. 2012. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol. 13(3):R23. DOI:https://doi.org/10.1186/gb-2012-13-3-r23.
   PubMed Web of Science ®Google Scholar
• Huang Y, Sheth RU, Kaufman A, Wang HH. 2020. Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics. Nucleic Acids Res. 48(4):e20. DOI:https://doi.org/10.1093/nar/gkz1169.
   PubMed Web of Science ®Google Scholar
• Kang Y-J, Yang D-C, Kong L, Hou M, Meng Y-Q, Wei L, Gao G. 2017. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res. 45(W1):W12–W16. DOI:https://doi.org/10.1093/nar/gkx428.
   PubMed Web of Science ®Google Scholar
• Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 37(8):907–915. DOI:https://doi.org/10.1038/s41587-019-0201-4.
   PubMed Web of Science ®Google Scholar
• Kim W, Miguel-Rojas C, Wang J, Townsend JP, Trail F, Di Pietro A. 2018. Developmental dynamics of long noncoding rna expression during sexual fruiting body formation in Fusarium graminearum. mBio. 9(4):e01292–01218. DOI:https://doi.org/10.1128/mBio.01292-18.
   PubMed Web of Science ®Google Scholar
• Kraus AJ, Brink BG, Siegel TN. 2019. Efficient and specific oligo-based depletion of rRNA. Sci Rep. 9(1):12281. DOI:https://doi.org/10.1038/s41598-019-48692-2.
   PubMedGoogle Scholar
• Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35(9):3100–3108. DOI:https://doi.org/10.1093/nar/gkm160.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 9(1):559. DOI:https://doi.org/10.1186/1471-2105-9-559.
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9(4):357–359. DOI:https://doi.org/10.1038/nmeth.1923.
   PubMed Web of Science ®Google Scholar
• Lau SKP, Lo GCS, Chow FWN, Fan RYY, Cai JJ, Yuen K-Y, Woo PCY, Taylor JW. 2018. Novel partitivirus enhances virulence of and causes aberrant gene expression in Talaromyces marneffei. mBio. 9(3):e00947–00918. DOI:https://doi.org/10.1128/mBio.00947-18.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15(12):550. DOI:https://doi.org/10.1186/s13059-014-0550-8.
   PubMed Web of Science ®Google Scholar
• Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. MBnet J. 17(1):10–12. DOI:https://doi.org/10.14806/ej.17.1.200.
   Google Scholar
• Morlan JD, Qu K, Sinicropi DV, Dadras SS. 2012. Selective depletion of rRNA enables whole transcriptome profiling of archival fixed tissue. PLoS One. 7(8):e42882. DOI:https://doi.org/10.1371/journal.pone.0042882.
   PubMed Web of Science ®Google Scholar
• Muszewska A, Stepniewska-Dziubinska MM, Steczkiewicz K, Pawlowska J, Dziedzic A, Ginalski K. 2017. Fungal lifestyle reflected in serine protease repertoire. Sci Rep. 7(1):9147. DOI:https://doi.org/10.1038/s41598-017-09644-w.
   PubMedGoogle Scholar
• Pasricha S, MacRae JI, Chua HH, Chambers J, Boyce KJ, McConville MJ, Andrianopoulos A. 2017. Extensive metabolic remodeling differentiates non-pathogenic and pathogenic growth forms of the dimorphic pathogen. Front Cell Infect Microbiol. 7:368. doi:https://doi.org/10.3389/fcimb.2017.00368.
   PubMed Web of Science ®Google Scholar
• Pertea G, Pertea M. 2020. GFF utilities: GffRead and GffCompare. F1000Res. 9:304. doi:https://doi.org/10.12688/f1000research.23297.1.
   Google Scholar
• Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. 2016. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 11(9):1650–1667. DOI:https://doi.org/10.1038/nprot.2016.095.
   PubMed Web of Science ®Google Scholar
• Phelps WA, Carlson AE, Lee MT. 2021. Optimized design of antisense oligomers for targeted rRNA depletion. Nucleic Acids Res. 49(1):e5. DOI:https://doi.org/10.1093/nar/gkaa1072.
   PubMed Web of Science ®Google Scholar
• Reese SE, Archer KJ, Therneau TM, Atkinson EJ, Vachon CM, de Andrade M, Kocher J-PA, Eckel-Passow JE. 2013. A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. Bioinformatics (Oxford, England). 29(22):2877–2883. DOI:https://doi.org/10.1093/bioinformatics/btt480.
   PubMed Web of Science ®Google Scholar
• Stark R, Grzelak M, Hadfield J. 2019. RNA sequencing: the teenage years. Nat Rev Genet. 20(11):631–656. DOI:https://doi.org/10.1038/s41576-019-0150-2.
   PubMed Web of Science ®Google Scholar
• Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, Liu Y, Chen R, Zhao Y. 2013. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 41(17):e166. DOI:https://doi.org/10.1093/nar/gkt646.
   PubMed Web of Science ®Google Scholar
• Tedersoo L, Sánchez-Ramírez S, Kõljalg U, Bahram M, Döring M, Schigel D, May T, Ryberg M, Abarenkov K. 2018. High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Divers. 90(1):135–159. DOI:https://doi.org/10.1007/s13225-018-0401-0.
   Web of Science ®Google Scholar
• Telzrow CL, Zwack PJ, Esher Righi S, Dietrich FS, Chan C, Owzar K, Alspaugh JA, Granek JA, Andrews B. 2021. Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. G3 (Bethesda). 11(11). DOI:https://doi.org/10.1093/g3journal/jkab301.
   Google Scholar
• Thompson MK, Kiourlappou M, Davis I. 2020. Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion. RNA. 26(11):1731–1742. DOI:https://doi.org/10.1261/rna.076562.120.
   PubMed Web of Science ®Google Scholar
• Till P, Pucher ME, Mach RL, Mach-Aigner AR. 2018. A long noncoding RNA promotes cellulase expression in Trichoderma reesei. Biotechnol Biofuels. 11(1):78. DOI:https://doi.org/10.1186/s13068-018-1081-4.
   PubMedGoogle Scholar
• Volders P-J, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J. 2019. LNCipedia 5: towards a reference set of human long non-coding RNAs. Nucleic Acids Res. 47(D1):D135–D139. DOI:https://doi.org/10.1093/nar/gky1031.
   PubMed Web of Science ®Google Scholar
• Wang Y, Shao Y, Zhu Y, Wang K, Ma B, Zhou Q, Chen A, Chen H. 2019a. XRN1-associated long non-coding RNAs may contribute to fungal virulence and sexual development in entomopathogenic fungus Cordyceps militaris. Pest Manag Sci. 75(12):3302–3311. DOI:https://doi.org/10.1002/ps.5453.
   PubMed Web of Science ®Google Scholar
• Wang Z, Jiang Y, Wu H, Xie X, Huang B. 2019b. Genome-wide identification and functional prediction of long non-coding RNAs involved in the heat stress response in Metarhizium robertsii. Front Microbiol. 10:2336. doi:https://doi.org/10.3389/fmicb.2019.02336.
   PubMed Web of Science ®Google Scholar
• Woo PCY, Lau SKP, Liu B, Cai JJ, Chong KTK, Tse H, Kao RYT, Chan C-M, Chow W-N, Yuen K-Y. 2011. Draft genome sequence of Penicillium marneffei strain PM1. Eukaryotic Cell. 10(12):1740–1741. DOI:https://doi.org/10.1128/EC.05255-11.
   PubMedGoogle Scholar
• Wu THE, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu X, et al. 2021. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. The Innovation. 2(3):100141. DOI:https://doi.org/10.1016/j.xinn.2021.100141.
   PubMedGoogle Scholar
• Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, et al. 2017. FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res. 45(8):e57. DOI:https://doi.org/10.1093/nar/gkw1306.
   PubMed Web of Science ®Google Scholar
• Yang E, Chow W-N, Wang G, Woo PCY, Lau SKP, Yuen K-Y, Lin X, Cai JJ, Richardson PM. 2014. Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei. PLoS Genet. 10(10):e1004662. DOI:https://doi.org/10.1371/journal.pgen.1004662.
   PubMed Web of Science ®Google Scholar
• Yang L, Duff MO, Graveley BR, Carmichael GG, Chen L-L. 2011. Genomewide characterization of non-polyadenylated RNAs. Genome Biol. 12(2):R16. DOI:https://doi.org/10.1186/gb-2011-12-2-r16.
   PubMed Web of Science ®Google Scholar
• Ye G, Zhang L, Zhou X. 2021. Long noncoding RNAs are potentially involved in the degeneration of virulence in an aphid-obligate pathogen, Conidiobolus obscurus (Entomophthoromycotina). Virulence. 12(1):1705–1716. DOI:https://doi.org/10.1080/21505594.2021.1938806.
   PubMed Web of Science ®Google Scholar
• Yu Y, Zhang Y, Chen X, Chen Y. 2019. Plant noncoding RNAs: hidden players in development and stress responses. Annu Rev Cell Dev Biol. 35(1):407–431. DOI:https://doi.org/10.1146/annurev-cellbio-100818-125218.
   PubMedGoogle Scholar
• Zeng Z, Huang B, Wang X, Fan J, Zhang B, Yang L, Feng Y, Wu X, Luo H, Zhang J, et al. 2020. A reverse transcriptase-mediated ribosomal RNA depletion (RTR2D) strategy for the cost-effective construction of RNA sequencing libraries. J Adv Res. 24:239–250. DOI:https://doi.org/10.1016/j.jare.2019.12.005.
   PubMed Web of Science ®Google Scholar
• Zhao S, Zhang Y, Gamini R, Zhang B, Von Schack D. 2018. Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion. Sci Rep. 8(1):4781. DOI:https://doi.org/10.1038/s41598-018-23226-4.
   PubMedGoogle Scholar