Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus

Autoři: Thorsten Langner aff001;  Adeline Harant aff001;  Luis B. Gomez-Luciano aff002;  Ram K. Shrestha aff001;  Angus Malmgren aff001;  Sergio M. Latorre aff003;  Hernán A. Burbano aff004;  Joe Win aff001;  Sophien Kamoun aff001
Působiště autorů: The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom aff001;  Biodiversity Research Center, Academia Sinica, Taipei, Taiwan aff002;  Research group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany aff003;  Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom aff004
Vyšlo v časopise: Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus. PLoS Genet 17(2): e1009386. doi:10.1371/journal.pgen.1009386
Kategorie: Research Article
doi: 10.1371/journal.pgen.1009386


Supernumerary mini-chromosomes–a unique type of genomic structural variation–have been implicated in the emergence of virulence traits in plant pathogenic fungi. However, the mechanisms that facilitate the emergence and maintenance of mini-chromosomes across fungi remain poorly understood. In the blast fungus Magnaporthe oryzae (Syn. Pyricularia oryzae), mini-chromosomes have been first described in the early 1990s but, until very recently, have been overlooked in genomic studies. Here we investigated structural variation in four isolates of the blast fungus M. oryzae from different grass hosts and analyzed the sequences of mini-chromosomes in the rice, foxtail millet and goosegrass isolates. The mini-chromosomes of these isolates turned out to be highly diverse with distinct sequence composition. They are enriched in repetitive elements and have lower gene density than core-chromosomes. We identified several virulence-related genes in the mini-chromosome of the rice isolate, including the virulence-related polyketide synthase Ace1 and two variants of the effector gene AVR-Pik. Macrosynteny analyses around these loci revealed structural rearrangements, including inter-chromosomal translocations between core- and mini-chromosomes. Our findings provide evidence that mini-chromosomes emerge from structural rearrangements and segmental duplication of core-chromosomes and might contribute to adaptive evolution of the blast fungus.

Klíčová slova:

Fungal genomics – Genome analysis – Genomics – Plant fungal pathogens – Protein domains – Rice – Sequence alignment – Structural genomics


1. Raffaele S, Win J, Cano LM, Kamoun S. Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics. 2010;11(1):637. doi: 10.1186/1471-2164-11-637 21080964

2. Dong S, Raffaele S, Kamoun S. The two-speed genomes of filamentous pathogens: waltz with plants. Curr Opin Genet Dev. 2015 Dec;35:57–65. doi: 10.1016/j.gde.2015.09.001 26451981

3. Croll D, McDonald BA. The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens. Heitman J, editor. PLoS Pathog. 2012 Apr 26;8(4):e1002608. doi: 10.1371/journal.ppat.1002608 22570606

4. Kämper J, Kahmann R, Bölker M, Ma L-J, Brefort T, Saville BJ, et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature. 2006 Nov;444(7115):97–101. doi: 10.1038/nature05248 17080091

5. Schirawski J, Mannhaupt G, Münch K, Brefort T, Schipper K, Doehlemann G, et al. Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison. Science. 2010 Dec 10;330(6010):1546–8. doi: 10.1126/science.1195330 21148393

6. de Jonge R, Bolton MD, Kombrink A, van den Berg GCM, Yadeta KA, Thomma BPHJ. Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen. Genome Res. 2013 Aug 1;23(8):1271–82. doi: 10.1101/gr.152660.112 23685541

7. Armitage AD, Taylor A, Sobczyk MK, Baxter L, Greenfield BPJ, Bates HJ, et al. Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae. Sci Rep. 2018 Dec;8(1):13530.

8. Bertazzoni S, Williams AH, Jones DA, Syme RA, Tan K-C, Hane JK. Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi. Mol Plant Microbe Interact. 2018 Aug;31(8):779–88. doi: 10.1094/MPMI-06-17-0135-FI 29664319

9. Goodwin SB, Ben M’Barek S, Dhillon B, Wittenberg AHJ, Crane CF, Hane JK, et al. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis. Malik HS, editor. PLoS Genet. 2011 Jun 9;7(6):e1002070. doi: 10.1371/journal.pgen.1002070 21695235

10. Fokkens L, Shahi S, Connolly LR, Stam R, Schmidt SM, Smith KM, et al. The multi-speed genome of Fusarium oxysporum reveals association of histone modifications with sequence divergence and footprints of past horizontal chromosome transfer events [Internet]. Genomics; 2018 Nov [cited 2019 Dec 17]. Available from:

11. Chuma I, Isobe C, Hotta Y, Ibaragi K, Futamata N, Kusaba M, et al. Multiple Translocation of the AVR-Pita Effector Gene among Chromosomes of the Rice Blast Fungus Magnaporthe oryzae and Related Species. Tyler B, editor. PLoS Pathog. 2011 Jul 28;7(7):e1002147. doi: 10.1371/journal.ppat.1002147 21829350

12. Frantzeskakis L, Kusch S, Panstruga R. The need for speed: compartmentalized genome evolution in filamentous phytopathogens: Multiple “speeds” in phytopathogen genomes. Mol Plant Pathol. 2019 Jan;20(1):3–7. doi: 10.1111/mpp.12738 30557450

13. Zolan ME. Chromosome-Length Polymorphism in Fungi. MICROBIOL REV. 1995;59:13. 8531892

14. Covert SF. Supernumerary chromosomes in filamentous fungi. Curr Genet. 1998 Jun 8;33(5):311–9. doi: 10.1007/s002940050342 9618581

15. Jones RN, Viegas W, Houben A. A Century of B Chromosomes in Plants: So What? Ann Bot. 2008 Mar 13;101(6):767–75. doi: 10.1093/aob/mcm167 17704238

16. Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol. 2017 Dec;15(12):756–71. doi: 10.1038/nrmicro.2017.76 28781365

17. Miao V, Covert S, VanEtten H. A fungal gene for antibiotic resistance on a dispensable (“B”) chromosome. Science. 1991 Dec 20;254(5039):1773–6. doi: 10.1126/science.1763326 1763326

18. Balesdent M-H, Fudal I, Ollivier B, Bally P, Grandaubert J, Eber F, et al. The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa. New Phytol. 2013 May;198(3):887–98. doi: 10.1111/nph.12178 23406519

19. Ma L-J, van der Does HC, Borkovich KA, Coleman JJ, Daboussi M-J, Di Pietro A, et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010 Mar;464(7287):367–73. doi: 10.1038/nature08850 20237561

20. Möller M, Habig M, Freitag M, Stukenbrock EH. Extraordinary Genome Instability and Widespread Chromosome Rearrangements During Vegetative Growth. Genetics. 2018 Oct 1;210(2):517. doi: 10.1534/genetics.118.301050 30072376

21. Fouché S, Plissonneau C, McDonald BA, Croll D. Meiosis Leads to Pervasive Copy-Number Variation and Distorted Inheritance of Accessory Chromosomes of the Wheat Pathogen Zymoseptoria tritici. Rose L, editor. Genome Biol Evol. 2018 Jun 1;10(6):1416–29. doi: 10.1093/gbe/evy100 29850789

22. Habig M, Kema GH, Holtgrewe Stukenbrock E. Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus. Rokas A, Weigel D, editors. eLife. 2018 Dec 13;7:e40251.

23. Raffaele S, Kamoun S. Genome evolution in filamentous plant pathogens: why bigger can be better. Nat Rev Microbiol. 2012 Jun;10(6):417–30. doi: 10.1038/nrmicro2790 22565130

24. Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, et al. The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion. Madhani HD, editor. PLoS Genet. 2009 Aug 28;5(8):e1000618. doi: 10.1371/journal.pgen.1000618 19714214

25. Akagi Y, Taga M, Yamamoto M, Tsuge T, Fukumasa-Nakai Y, Otani H, et al. Chromosome constitution of hybrid strains constructed by protoplast fusion between the tomato and strawberry pathotypes of Alternaria alternata. J Gen Plant Pathol. 2009 Apr;75(2):101–9.

26. Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E, Höfte M, et al. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC Genomics. 2016 Dec;17(1):670.

27. He C, Rusu AG, Poplawski AM, Irwin JA, Manners JM. Transfer of a supernumerary chromosome between vegetatively incompatible biotypes of the fungus Colletotrichum gloeosporioides. Genetics. 1998 Dec;150(4):1459–66. 9832523

28. Fisher MC, Henk Daniel A, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, et al. Emerging fungal threats to animal, plant and ecosystem health. Nature. 2012 Apr;484(7393):186–94. doi: 10.1038/nature10947 22498624

29. Savary S, Willocquet L, Pethybridge SJ, Esker P, McRoberts N, Nelson A. The global burden of pathogens and pests on major food crops. Nat Ecol Evol. 2019 Mar;3(3):430–9. doi: 10.1038/s41559-018-0793-y 30718852

30. Hill L, Jones G, Atkinson N, Hector A, Hemery G, Brown N. The £15 billion cost of ash dieback in Britain. Curr Biol. 2019 May;29(9):R315–6. doi: 10.1016/j.cub.2019.03.033 31063720

31. Grünwald NJ, LeBoldus JM, Hamelin RC. Ecology and Evolution of the Sudden Oak Death Pathogen Phytophthora ramorum. Annu Rev Phytopathol. 2019 Aug 25;57(1):301–21. doi: 10.1146/annurev-phyto-082718-100117 31226018

32. Białas A, Zess EK, De la Concepcion JC, Franceschetti M, Pennington HG, Yoshida K, et al. Lessons in Effector and NLR Biology of Plant-Microbe Systems. Mol Plant Microbe Interact. 2018 Jan;31(1):34–45. doi: 10.1094/MPMI-08-17-0196-FI 29144205

33. Lo Presti L, Lanver D, Schweizer G, Tanaka S, Liang L, Tollot M, et al. Fungal Effectors and Plant Susceptibility. Annu Rev Plant Biol. 2015 Apr 29;66(1):513–45. doi: 10.1146/annurev-arplant-043014-114623 25923844

34. Kanzaki H, Yoshida K, Saitoh H, Fujisaki K, Hirabuchi A, Alaux L, et al. Arms race co-evolution of Magnaporthe oryzae AVR-Pik and rice Pik genes driven by their physical interactions: Co-evolution of fungal and rice genes. Plant J. 2012 Dec;72(6):894–907. doi: 10.1111/j.1365-313X.2012.05110.x 22805093

35. Yoshida K, Saunders DGO, Mitsuoka C, Natsume S, Kosugi S, Saitoh H, et al. Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. BMC Genomics. 2016 Dec;17(1):370. doi: 10.1186/s12864-016-2690-6 27194050

36. Jones JDG, Vance RE, Dangl JL. Intracellular innate immune surveillance devices in plants and animals. Science. 2016 Dec 2;354(6316):aaf6395–aaf6395. doi: 10.1126/science.aaf6395 27934708

37. Cesari S. Multiple strategies for pathogen perception by plant immune receptors. New Phytol. 2018 Jul;219(1):17–24. doi: 10.1111/nph.14877 29131341

38. Dean R, Van Kan JAL, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, et al. The Top 10 fungal pathogens in molecular plant pathology: Top 10 fungal pathogens. Mol Plant Pathol. 2012 May;13(4):414–30. doi: 10.1111/j.1364-3703.2011.00783.x 22471698

39. Ou SH. A look at worldwide rice blast disease control. Plant Disease. 1980;64:439–45.

40. Kato H, Yamamoto M, Yamaguchi-Ozaki T, kadouchi H, Iwamoto Y, Nakayashiki H, et al. Pathogenicity, Mating Ability and DNA Restriction Fragment Length Polymorphisms of Pyricularia Populations Isolated from Gramineae, Bambusideae and Zingiberaceae Plants. J Gen Plant Pathol. 2000 Feb 1;66(1):30–47.

41. Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, et al. Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. Taylor JW, editor. mBio. 2018 Feb 27;9(1):e01219–17. doi: 10.1128/mBio.01219-17 29487238

42. Gladieux P, Ravel S, Rieux A, Cros-Arteil S, Adreit H, Milazzo J, et al. Coexistence of Multiple Endemic and Pandemic Lineages of the Rice Blast Pathogen. Guttman D, editor. mBio. 2018 Apr 3;9(2):e01806–17, /mbio/9/2/mBio.01806-17.atom.

43. Zhong Z, Chen M, Lin L, Han Y, Bao J, Tang W, et al. Population genomic analysis of the rice blast fungus reveals specific events associated with expansion of three main clades. ISME J. 2018 Aug;12(8):1867–78. doi: 10.1038/s41396-018-0100-6 29568114

44. Latorre SM, Reyes-Avila CS, Malmgren A, Win J, Kamoun S, Burbano HA. Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus. BMC Biol. 2020 Jul 16;18(1):88. doi: 10.1186/s12915-020-00818-z 32677941

45. Islam MT, Croll D, Gladieux P, Soanes DM, Persoons A, Bhattacharjee P, et al. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biol. 2016 Dec;14(1):84. doi: 10.1186/s12915-016-0309-7 27716181

46. Islam MT, Kim K-H, Choi J. Wheat Blast in Bangladesh: The Current Situation and Future Impacts. Plant Pathol J. 2019 Feb 1;35(1):1–10. doi: 10.5423/PPJ.RW.08.2018.0168 30828274

47. Malaker PK, Barma NCD, Tiwari TP, Collis WJ, Duveiller E, Singh PK, et al. First Report of Wheat Blast Caused by Magnaporthe oryzae Pathotype triticum in Bangladesh. Plant Dis. 2016 Nov;100(11):2330–2330.

48. Chiapello H, Mallet L, Guérin C, Aguileta G, Amselem J, Kroj T, et al. Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants. Genome Biol Evol. 2015 Oct;7(10):2896–912. doi: 10.1093/gbe/evv187 26454013

49. Inoue Y, Vy TTP, Yoshida K, Asano H, Mitsuoka C, Asuke S, et al. Evolution of the wheat blast fungus through functional losses in a host specificity determinant. Science. 2017;357(6346):80–3. doi: 10.1126/science.aam9654 28684523

50. Tosa Y, Osue J, Eto Y, Oh H-S, Nakayashiki H, Mayama S, et al. Evolution of an Avirulence Gene, AVR1-CO39, Concomitant with the Evolution and Differentiation of Magnaporthe oryzae. Mol Plant Microbe Interact. 2005 Nov;18(11):1148–60. doi: 10.1094/MPMI-18-1148 16353550

51. Stukenbrock EH. Evolution, selection and isolation: a genomic view of speciation in fungal plant pathogens. New Phytol. 2013 Sep;199(4):895–907. doi: 10.1111/nph.12374 23782262

52. Talbot NJ, Salch YP, Ma M, Hamer JE. Karyotypic variation within clonal lineages of rice blast fungus Magnaporthe grisea. APPL Env MICROBIOL. 1993;59(2):585–93. doi: 10.1128/AEM.59.2.585-593.1993 16348876

53. Orbach MJ, Chumley FG, Valent B. Electrophoretic karyotypes of Magnaporthe grisea pathogens of diverse grasses. MPMI. 1996;9(4):261–71.

54. Luo C-X, Yin L-F, Ohtaka K, Kusaba M. The 1.6Mb chromosome carrying the avirulence gene AvrPik in Magnaporthe oryzae isolate 84R-62B is a chimera containing chromosome 1 sequences. Mycol Res. 2007 Feb;111(2):232–9. doi: 10.1016/j.mycres.2006.10.008 17188484

55. Kusaba M, Mochida T, Naridomi T, Fujita Y, Chuma I, Tosa Y. Loss of a 1.6 Mb chromosome in Pyricularia oryzae harboring two alleles of AvrPik leads to acquisition of virulence to rice cultivars containing resistance alleles at the Pik locus. Curr Genet. 2014 Nov;60(4):315–25. doi: 10.1007/s00294-014-0437-y 25056242

56. Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, et al. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. Lin X, editor. PLOS Genet. 2019 Sep 12;15(9):e1008272. doi: 10.1371/journal.pgen.1008272 31513573

57. Win J, Chanclud E, Reyes-Avila S, Langner T, Islam MT, Kamoun S. Nanopore sequencing of genomic DNA from Magnaporthe oryzae isolates from different hosts. Zenodo [Internet]. 2019 Feb 14 [cited 2019 Dec 17]; Available from:

58. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature. 2005 Apr;434(7036):980–6. doi: 10.1038/nature03449 15846337

59. Soanes Darren, Antonio Nhani João L. Nunes Maciel Jr, Nicholas J Talbot. Genome assemblies of Magnaporthe oryzae [Internet]. 2017. Available from:

60. Soanes Darren, Ryder Lauren S., M. Tofazzal Islam, Nicholas J. Talbot. Genome assemblies of Magnaporthe oryzae isolated from Bangladesh in 2016 and 2017 [Internet]. 2017. Available from:

61. Thierry M, Milazzo J, Adreit H, Ravel S, Borron S, Sella V, et al. Ecological Differentiation and Incipient Speciation in the Fungal Pathogen Causing Rice Blast. bioRxiv. 2020 Jan 1;2020.06.02.129296.

62. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094–100. doi: 10.1093/bioinformatics/bty191 29750242

63. Collemare J, Pianfetti M, Houlle A-E, Morin D, Camborde L, Gagey M-J, et al. Magnaporthe grisea avirulence gene ACE1 belongs to an infection-specific gene cluster involved in secondary metabolism. New Phytol. 2008 Jul;179(1):196–208. doi: 10.1111/j.1469-8137.2008.02459.x 18433432

64. de Guillen K, Ortiz-Vallejo D, Gracy J, Fournier E, Kroj T, Padilla A. Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi. Xu J-R, editor. PLOS Pathog. 2015 Oct 27;11(10):e1005228. doi: 10.1371/journal.ppat.1005228 26506000

65. Gómez Luciano LB, Tsai IJ, Chuma I, Tosa Y, Chen Y-H, Li J-Y, et al. Blast Fungal Genomes Show Frequent Chromosomal Changes, Gene Gains and Losses, and Effector Gene Turnover. Mol Biol Evol. 2019 Mar 5;36(6):1148–61. doi: 10.1093/molbev/msz045 30835262

66. Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. Reordering contigs of draft genomes using the Mauve aligner. Bioinforma Oxf Engl. 2009 Aug 15;25(16):2071–3.

67. Cruz CD, Valent B. Wheat blast disease: danger on the move. Trop Plant Pathol. 2017 Jun;42(3):210–22.

68. Yadav V, Yang F, Reza MdH, Liu S, Valent B, Sanyal K, et al. Cellular Dynamics and Genomic Identity of Centromeres in Cereal Blast Fungus. Idnurm A, editor. mBio. 2019 Jul 30;10(4):e01581–19, /mbio/10/4/mBio.01581-19.atom. doi: 10.1128/mBio.01581-19 31363034

69. Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GCM, Wittenberg AHJ, et al. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res. 2016 Aug;26(8):1091–100. doi: 10.1101/gr.204974.116 27325116

70. Depotter JRL, Shi-Kunne X, Missonnier H, Liu T, Faino L, van den Berg GCM, et al. Dynamic virulence-related regions of the fungal plant pathogen Verticillium dahliae display remarkably enhanced sequence conservation [Internet]. Microbiology; 2018 Mar [cited 2019 Dec 17]. Available from:

71. Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco CS, Croll D. Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen. Mol Biol Evol [Internet]. 2019 Sep 23 [cited 2019 Dec 18];(msz216). Available from:

72. Langner T, Białas A, Kamoun S. The Blast Fungus Decoded: Genomes in Flux. mBio. 2018 Apr 17;9(2):e00571–18. doi: 10.1128/mBio.00571-18 29666287

73. Mehrabi R, Bahkali AH, Abd-Elsalam KA, Moslem M, Ben M’Barek S, Gohari AM, et al. Horizontal gene and chromosome transfer in plant pathogenic fungi affecting host range. FEMS Microbiol Rev. 2011 May;35(3):542–54. doi: 10.1111/j.1574-6976.2010.00263.x 21223323

74. Schwessinger B. High quality DNA from Fungi for long read sequencing e.g. PacBio v10 ( [Internet]. [cited 2019 Dec 17]. Available from:

75. Langner T, Harant A, Kamoun S. Isolation of supernumerary mini-chromosomes from fungi for enrichment sequencing. [Internet]. 2019 Dec 17 [cited 2019 Dec 18]; Available from:

76. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation. Genome Res. 2017 May;27(5):722–36. doi: 10.1101/gr.215087.116 28298431

77. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;9. doi: 10.1186/gb-2004-5-2-r12 14759262

78. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011 Feb 15;27(4):578–9. doi: 10.1093/bioinformatics/btq683 21149342

79. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. Wang J, editor. PLoS ONE. 2014 Nov 19;9(11):e112963. doi: 10.1371/journal.pone.0112963 25409509

80. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015 Oct 1;31(19):3210–2. doi: 10.1093/bioinformatics/btv351 26059717

81. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114–20. doi: 10.1093/bioinformatics/btu170 24695404

82. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078–9. doi: 10.1093/bioinformatics/btp352 19505943

83. Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics. 2014 Oct;30(19):2811–2. doi: 10.1093/bioinformatics/btu393 24930139

84. Gel B, Serra E. karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Hancock J, editor. Bioinformatics. 2017 Oct 1;33(19):3088–90. doi: 10.1093/bioinformatics/btx346 28575171

85. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–10. doi: 10.1016/S0022-2836(05)80360-2 2231712

86. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng Des Sel. 1997 Jan 1;10(1):1–6.

87. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007 Apr;2(4):953–71. doi: 10.1038/nprot.2007.131 17446895

88. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen. J Mol Biol. 2001 Jan;305(3):567–80. doi: 10.1006/jmbi.2000.4315 11152613

89. El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019 Jan 8;47(D1):D427–32. doi: 10.1093/nar/gky995 30357350

90. Enright AJ. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002 Apr 1;30(7):1575–84. doi: 10.1093/nar/30.7.1575 11917018

Článek vyšel v časopise

PLOS Genetics

2021 Číslo 2
Nejčtenější tento týden
Nejčtenější v tomto čísle

Zvyšte si kvalifikaci online z pohodlí domova

Konsenzuální postupy v léčbě močových infekcí
nový kurz

Hereditární TTR amyloidóza – vzácné, nebo jen neodhalené onemocnění? 2. díl

Současné možnosti v léčbě psoriázy

Svět praktické medicíny 4/2022 (znalostní test z časopisu)

COVID-19 up to date
Autoři: doc. MUDr. Vladimír Koblížek, Ph.D., MUDr. Mikuláš Skála, prof. MUDr. František Kopřiva, Ph.D., prof. MUDr. Roman Prymula, CSc., Ph.D.

Všechny kurzy
Kurzy Podcasty Doporučená témata Časopisy
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.


Nemáte účet?  Registrujte se