1. Islam MS, Haque MS, Islam MM, Emdad EM, Halim A, Md Q, Hossen M, Hossain MZ, Ahmed B, Rahim S, Rahman MS, Alam MM, Hou S, Wan X, Saito JA, Alam M: Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina. BMC Genomics 2012, 13:1.
2. Gupta GK, Sharma SK, Rameke R: Biology, epidemiology and management of the pathogenic fungus Macrophomina phaseolina (Tassi) Goid with special reference to charcol rot of Soybean. J Phytopathol 2012, 160:167–180.
3. Kaur S, Dhillon GS, Brar SK, Vallad GE, Chand R, Chauhan VB: Emerging phytopathogen Macrophomina phaseolina : biology, economic importance and current diagnostic trends. Crit Rev Microbiol 2012, 38:136–151.
4. Zveibil A, Mor N, Gnayem N, Freeman S: Survival, Host–Pathogen Interaction, and Management of Macrophomina phaseolina on Strawberry in Israel. Plant Dis 2012, 96:265–272.
5. Mihail JD: Macrophomina phaseolina: Spatio-temporal dynamics of inoculum and of disease in a highly susceptible crop. Phytopathology 1989, 79:848–855.
6. Khan AN, Shair F, Malik K, Hayat Z, Khan MA, Hafeez FY, Hassan MN: Molecular identification and genetic characterization of Macrophomina phaseolina strains causing pathogenicity on sunflower and chickpea. Front Microbiol 2017, 8(JUL):1–11.
7. Su G, Suh R, Schneider W, Russin JS: Host specialization in the charcol rot fungus, Macrophomina phaseolina. Phytopathology 2001, 91:120–126.
8. Koike ST, Arias RS, Hogan CS, Martin FN, Gordon TR: Status of Macrophomina phaseolina on Strawberry in California and Preliminary Characterization of the Pathogen. Int J Fruit Sci 2016, 16:148–159.
9. Mertely J, Seijo T, Peres N: First Report of Macrophomina phaseolina Causing a Crown Rot of Strawberry in Florida. Plant Dis 2005, 89:434–434.
10. Koike ST: Crown Rot of Strawberry Caused by Macrophomina phaseolina in California. Plant Dis 2008, 92:1253–1253.
11. Arias RS, Ray JD, Mengistu A, Scheffler BE: Discriminating microsatellites from Macrophomina phaseolina and their potential association to biological functions. Plant Pathol 2011, 60:709–718.
12. Faino L, Seidl MF, Datema E, Van Den Berg GCM, Janssen A, Wittenberg AHJ, Thomma BPHJ: Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome. MBio 2015, 6:1–11.
13. Faino L, Farmer AD, Papasotiriou DG, Zhou S, Seidl MF, Cottam E, Edel D, Hahn M, Schwartz DC, Dietrich RA, Widdison S, Scalliet G: A gapless genome sequence of the fungus Botrytis cinerea. Mol. Plant Path. 2016, 8(20 17):75–89.
14. Van Dam P, Fokkens L, Ayukawa Y, Van Der Gragt M, Ter Horst A, Brankovics B, Houterman PM, Arie T, Rep M: A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species. Sci Rep 2017, 7:1–15.
15. Bao J, Chen M, Zhong Z, Tang W, Lin L, Zhang X, Jiang H, Zhang D, Miao C, Tang H, Zhang J, Lu G, Ming R, Norvienyeku J, Wang B, Wang Z: PacBio Sequencing Reveals Transposable Elements as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae. Mol Plant 2017, 10:1465–1468.
16. Derbyshire M, Denton-Giles M, Hegedus D, Seifbarghi S, Rollins J, Kan J Van, Seidl MF, Faino L, Mbengue M, Navaud O, Raffaele S, Hammond-Kosack K, Heard S, Oliver R: The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol Evol 2017, 9:593–618.
17. Dallery JF, Lapalu N, Zampounis A, Pigné S, Luyten I, Amselem J, Wittenberg AHJ, Zhou S, de Queiroz M V., Robin GP, Auger A, Hainaut M, Henrissat B, Kim KT, Lee YH, Lespinet O, Schwartz DC, Thon MR, O’Connell RJ: Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genomics 2017, 18:1–22.
18. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM: Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014, 9.
19. Putnam NH, Connell BO, Stites JC, Rice BJ, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.Genome Res 2016, 26:342–350.
20. Teh BT, Lim K, Yong CH, Ng CCY, Rao SR, Rajasegaran V, Lim WK, Ong CK, Chan K, Cheng VKY, Soh PS, Swarup S, Rozen SG, Nagarajan N, Tan P: The draft genome of tropical fruit durian (Durio zibethinus). Nat Genet 2017, 49:1633–1641.
21. RepeatMasker Open-4.0 [http://www.repeatmasker.org]
22. Arkhipova IR: Distribution and phylogeny of penelope-like elements in eukaryotes. Syst Biol 2006, 55:875–885.
23. Castanera R, López-Varas L, Borgognone A, LaButti K, Lapidus A, Schmutz J, Grimwood J, Pérez G, Pisabarro AG, Grigoriev I V., Stajich JE, Ramírez L: Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet 2016, 12:1–27.
24. Wolters PJ, Faino L, van den Bosch TBM, Evenhuis B, Visser RGF, Seidl MF, Vleeshouwers VGAA: Gapless genome assembly of the potato and tomato early blight pathogen Alternaria solani. Mol Plant-Microbe Interact 2018, 31:692–694.
25. Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O’Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC: Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 2016, 13:1050–1054.
26. Kaiser MD, Davis JR, Grinberg BS, Oliver JS, Sage JM, Seward L, Bready B: Automated Structural Variant Verification In Human Genomes Using Single-Molecule Electronic DNA Mapping. bioRxiv 2017:140699.
27. Shi TQ, Liu GN, Ji RY, Shi K, Song P, Ren LJ, Huang H, Ji XJ: CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art. Appl Microbiol Biotechnol 2017, 101:7435–7443.
28. Chin C-S, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O’Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC: Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing. bioRxiv 2016(October):56887.
29. O’Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ: NxTrim: Optimized trimming of Illumina mate pair reads. Bioinformatics 2015, 31:2035–2037.
30. Bolger AM, Lohse M, Usadel B: Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30:2114–2120.
31. Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357.
32. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078–2079.
33. Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 2011, 27:2987–2993.
34. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403–10.
35. Gurevich A, Saveliev V, Vyahhi N, Tesler G: QUAST: Quality assessment tool for genome assemblies. Bioinformatics 2013, 29:1072–1075.
36. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva E V., Zdobnov EM: BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015, 31:3210–3212.
37. Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B, Holt C, Alvarado AS, Yandell M: MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 2008, 18:188–196.
38. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR: STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15–21.
39. 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: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29:644–652.
40. Korf I: Gene finding in novel genomes. BMC Bioinformatics 2004, 5:1–9.
41. Ter-hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M: Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res 2008:1979–1990.
42. Borodovsky M, McIninch J: GeneMark: parallel gene recognition for both strands. Comput Chem 1993, 17:123–133.
43. Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo T-H, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL: A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. Cell Rep 2017, 18:762–776.
44. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LS: UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 2004, 32:115D–119.
45. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A: The Pfam protein families database: Towards a more sustainable future. Nucleic Acids Res 2016, 44:D279–D285.
46. Eddy SR, Wheeler TJ: HMMER-biosequence analysis using profile hidden Markov models. URL http//hmmer janelia org 2007.
47. Petersen TN, Brunak S, von Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8:785.
48. Möller S, Croning MDR, Apweiler R: Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 2001, 17:646–653.
49. Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y: DbCAN2: A meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018, 46:W95–W101.
50. Nattestad M, Schatz MC: Assemblytics: a web analytics tool for the detection of assembly-based variants. bioRxiv 2016(June):44925.
51. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12.
52. Darling AE, Mau B, Perna NT: Progressivemauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5.
53. Emms DM, Kelly S: OrthoFinder: Solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015, 16:1–14.
54. Wang Y, Coleman-Derr D, Chen G, Gu YQ: OrthoVenn: A web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2015, 43:W78–W84.
55. Anders S, Pyl PT, Huber W: HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics 2015, 31:166–169.
56. Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol 2010, 11:R106.
57. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B 1995:289–300.