Accuracy of MicroRNA discovery pipelines in non-model organisms using closely related species genomes

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Etebari, Kayvan ^a   Asgari, Sassan ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 11; MICRORNA 11 3P; MICRORNA 12; MICRORNA 12 5P; MICRORNA 14; MICRORNA 184; MICRORNA 1889 5P; MICRORNA 263A; MICRORNA 275 3P; MICRORNA 276 3P; MICRORNA 281 5P; MICRORNA 283; MICRORNA 2940 3P; MICRORNA 2940 5P; MICRORNA 2A 3P; MICRORNA 305 5P; MICRORNA 306; MICRORNA 306 5P; MICRORNA 317; MICRORNA 34 5P; MICRORNA 8; MICRORNA 87; MICRORNA 92A 3P; MICRORNA 92B 3P; MICRORNA 970; MICRORNA 988; MICRORNA 989; MICRORNA 998; UNCLASSIFIED DRUG;

ACCURACY; AEDES AEGYPTI; ANOPHELES GAMBIAE; ARTICLE; BOMBYX MORI; CLIENT SERVER APPLICATION; CONTROLLED STUDY; DOWN REGULATION; DROSOPHILA MELANOGASTER; GENE EXPRESSION PROFILING; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYZER; INSECT GENOME; MOLECULAR LIBRARY; NONHUMAN; UPREGULATION;

AEDES; ANIMALS; CHROMOSOME MAPPING; DATABASES, GENETIC; GENE EXPRESSION REGULATION; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS;

EID: 84896753431     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084747     Document Type: Article

References (42)

1. Ibanez-Ventoso C, Vora M, Driscoll M (2008) Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology. PLoS One 3: e2818.
2. Bartel DP (2009) MicroRNAs: Target recognition and regulatory functions. Cell 136: 215-233.
3. Fullaondo A, Lee SY (2012) Identification of putative miRNA involved in Drosophila melanogaster immune response. Dev Comp Immunol 36: 267-273.
4. Freitak D, Knorr E, Vogel H, Vilcinskas A (2012) Gender-and stressor-specific microRNA expression in Tribolium castaneum. Biol Lett 8: 860-863.
5. Asgari S (2013) MicroRNA functions in insects. Insect Biochemistry and Molecular Biology 43: 388-397.
6. Yu X, Zhou Q, Li S-C, Luo Q, Cai Y, et al. (2008) The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages. PLoS One 3: e2997.
7. Gomez-Orte E, Belles X (2009) MicroRNA-dependent metamorphosis in hemimetabolan insects. Proc Natl Acad Sci USA 106: 21678-21682.
8. Yu X, Zhou Q, Cai Y, Luo Q, Lin H, et al. (2009) A discovery of novel microRNAs in the silkworm (Bombyx mori) genome. Genomics 94: 438-444.
9. Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: MicroRNAs can up-regulate translation. Science 318: 1931-1934.
10. Hobert O (2007) miRNAs play a tune. Cell 131: 22-24. (Pubitemid 47498545)
11. Gu LQ, Wanunu M, Wang MX, McReynolds L, Wang Y (2012) Detection of miRNAs with a nanopore single-molecule counter. Expert Rev Mol Diagn 12: 573-584.
12. Van Roosbroeck K, Pollet J, Calin GA (2013) miRNAs and long noncoding RNAs as biomarkers in human diseases. Expert Rev Mol Diagn 13: 183-204.
13. Chen X, Ba Y, Ma L, Cai X, Yin Y, et al. (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18: 997-1006.
14. Wilbert ML, Yeo GW (2011) Genome-wide approaches in the study of microRNA biology. Wiley Interdiscip Rev Syst Biol Med 3: 491-512.
15. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864. (Pubitemid 33032105)
16. Belles X, Cristino AS, Tanaka ED, Rubio M, Piulachs MD (2012) Insect MicroRNAs: from molecular mechanisms to biological roles. In: Lawrence IG, editor. Insect Molecular Biology and Biochemistry. San Diego: Academic Press. 30-56.
17. Wang W-C, Lin F-M, Chang W-C, Lin K-Y, Huang H-D, et al. (2009) miRExpress: Analyzing high-throughput sequencing data for profiling micro-RNA expression. BMC Bioinformatics 10: 328.
18. Huang P-J, Liu Y-C, Lee C-C, Lin W-C, Gan RR-C, et al. (2010) DSAP: deepsequencing small RNA analysis pipeline. Nucleic Acids Res 38: W385-W391.
19. Wu W, Ren Q, Li C, Wang Y, Sang M, et al. (2013) Characterization and comparative profiling of microRNAs in a sexual dimorphism insect, Eupolyphaga sinensis Walker. PLoS One 8: e0059016.
20. Mehrabadi M, Hussain M, Asgari S (2013) MicroRNAome of Spodoptera frugiperda cells (Sf9) and its alteration following baculovirus infection. J Gen Virol 94: 1385-1397.
21. Etebari K, Hussain M, Asgari S (2013) Identification of microRNAs from Plutella xylostella larvae associated with parasitization by Diadegma semiclausum. Insect Biochem Mol Biol 43: 309-318.
22. Yu D-B, Jiang B-C, Gong J, Dong F-L, Lu Y-L, et al. (2013) Identification of novel and differentially expressed microRNAs in the ovaries of laying and nonlaying ducks. J Integr Agric 12: 136-146.
23. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157.
24. Williamson V, Kim A, Xie B, McMichael GO, Gao Y, et al. (2013) Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation. Brief Bioinform 14: 36-45.
25. Hackenberg M, Sturm M, Langenberger D, Manuel Falcon-Perez J, Aransay AM (2009) miRanalyzer: a microRNA detection and analysis tool for nextgeneration sequencing experiments. Nucleic Acids Res 37: W68-W76.
26. Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q, et al. (2012) Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Res 40: 4298-4305.
27. Behura SK, Haugen M, Flannery E, Sarro J, Tessier CR, et al. (2011) Comparative genomic analysis of Drosophila melanogaster and vector mosquito developmental genes. Plos One 6: e21504.
28. Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, et al. (2006) The expansion of the metazoan microRNA repertoire. BMC Genomics 7: 25.
29. Tanzer A, Stadler PF (2006) Evolution of MicroRNAs. In: Ying SY, editor. Methods in Molecular Biology: Humana Press Inc, 999 Riverview Dr, Ste 208, Totowa, Nj 07512-1165 USA. 335-350.
30. Li SC, Chan WC, Hu LY, Lai CH, Hsu CN, et al. (2010) Identification of homologous microRNAs in 56 animal genomes. Genomics 96: 1-9.
31. Li S, Mead EA, Liang S, Tu Z (2009) Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs. BMC Genomics 10: 581.
32. Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR (2010) Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. BMC Genomics 11: 119.
33. Gu J, Hu W, Wu J, Zheng P, Chen M, et al. (2013) miRNA genes of an invasive vector mosquito, Aedes albopictus. PLoS One 8: e67638.
34. Zhang G, Fedyunin I, Kirchner S, Xiao C, Valleriani A, et al. (2012) FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads. Nucleic Acids Res 40: e83.
35. Lunter G, Goodson M (2011) Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21: 936-939.
36. Hussain M, Frentiu FD, Moreira LA, O'Neill SL, Asgari S (2011) Wolbachia uses host microRNAs to manipulate host gene expression and facilitate colonization of the dengue vector Aedes aegypti. Proc Natl Acad Sci USA 108: 9250-9255.
37. Zhang G, Hussain M, O'Neill SL, Asgari S (2013) Wolbachia uses a host microRNA to regulate transcripts of a methyltransferase, contributing to dengue virus inhibition in Aedes aegypti. Proc Natl Acad Sci USA 110: 10276-10281.
38. Frentiu FD, Robinson J, Young PR, McGraw EA, O'Neill SL (2010) Wolbachiamediated resistance to Dengue virus infection and death at the cellular level. PLoS One 5: e13398.
39. Hornett EA, Wheat CW (2012) Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. BMC Genomics 13: 361.
40. Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, et al. (2009) Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol 26: 2731-2744.
41. Hackenberg M, Rodriguez-Ezpeleta N, Aransay AM (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res 39: W132-W138.
42. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.