Abstract
FunGAP is a Python-wrapped fungal genome annotation pipeline running under the Linux/Unix operating system. The annotation procedure used in FunGAP requires two inputs, genome assembly and RNA-seq reads. FunGAP aims to predict the most feasible gene from all plausible gene models obtained from various gene prediction programs using multiple strategies such as ab initio, EST-, and/or homology-based methods. This guide covers how to run the FunGAP from the command line and use various options for practical gene prediction. Users can choose options for quality control of the input sequences, selecting model database, filtration of predicted gene models, and post-process such as checking genome completeness and transposable elements. Using FunGAP, the user will acquire a high-quality fungal gene prediction for post-genome sequencing analysis.
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References
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M (2016) BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32(5):767–769. https://doi.org/10.1093/bioinformatics/btv661
Reid I, O'Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PM, Soh J, Butler G, Sensen CW, Tsang A (2014) SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models. BMC Bioinformatics 15:229. https://doi.org/10.1186/1471-2105-15-229
Zickmann F, Renard BY (2015) IPred—integrating ab initio and evidence based gene predictions to improve prediction accuracy. BMC Genomics 16:134. https://doi.org/10.1186/s12864-015-1315-9
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9(1):R7. https://doi.org/10.1186/gb-2008-9-1-r7
Holt C, Yandell M (2011) MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12:491. https://doi.org/10.1186/1471-2105-12-491
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34:W435–W439. https://doi.org/10.1093/nar/gkl200
Borodovsky M, Lomsadze A (2011) Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES. Current Protoc Bioinformatics. Chapter 4:Unit 4.6.1-10. https://doi.org/10.1002/0471250953.bi0406s35
Min B, Grigoriev IV, Choi IG (2017) FunGAP: fungal genome annotation pipeline using evidence-based gene model evaluation. Bioinformatics 33(18):2936–2937. https://doi.org/10.1093/bioinformatics/btx353
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. https://doi.org/10.1186/1471-2105-10-421
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31(19):3210–3212. https://doi.org/10.1093/bioinformatics/btv351
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30(9):1236–1240. https://doi.org/10.1093/bioinformatics/btu031
Smit A, Hubley R (2008) RepeatModeler Open-1.0. http://www.repeatmasker.org. Accessed 26 Sep 2018
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652. https://doi.org/10.1038/nbt.1883
Krueger F (2015) Trim galore. A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore. Accessed 26 Sep 2018
Tarailo-Graovac M, Chen N (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. Chapter 4:Unit 4.10. https://doi.org/10.1002/0471250953.bi0410s25
Peter M, Kohler A, Ohm RA, Kuo A, Krutzmann J, Morin E, Arend M, Barry KW, Binder M, Choi C, Clum A, Copeland A, Grisel N, Haridas S, Kipfer T, LaButti K, Lindquist E, Lipzen A, Maire R, Meier B, Mihaltcheva S, Molinier V, Murat C, Poggeler S, Quandt CA, Sperisen C, Tritt A, Tisserant E, Crous PW, Henrissat B, Nehls U, Egli S, Spatafora JW, Grigoriev IV, Martin FM (2016) Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nat Commun 7:12662. https://doi.org/10.1038/ncomms12662
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014) Pfam: the protein families database. Nucleic Acids Res 42:D222–D230. https://doi.org/10.1093/nar/gkt1223
Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42:D699–D704. https://doi.org/10.1093/nar/gkt1183
Baker SE, Schackwitz W, Lipzen A, Martin J, Haridas S, LaButti K, Grigoriev IV, Simmons BA, McCluskey K (2015) Draft genome sequence of Neurospora crassa strain FGSC 73. Genome Announc 3(2). https://doi.org/10.1128/genomeA.00074-15
Acknowledgments
This work is supported by the Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01044003 and No. PJ01337602) Rural Development Administration, Republic of Korea, and Dr. Byoungnam Min was supported by the Korea University grant.
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Min, B., Choi, IG. (2019). Practical Guide for Fungal Gene Prediction from Genome Assembly and RNA-Seq Reads by FunGAP. In: Kollmar, M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9173-0_4
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DOI: https://doi.org/10.1007/978-1-4939-9173-0_4
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