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Proceedings of the National Academy of Sciences of the United States of America, v.117 no.49, 2020년, pp.31267 - 31277
Ke, Huei-Mien (Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan) , Lee, Hsin-Han , Lin, Chan-Yi Ivy (Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan) , Liu, Yu-Ching , Lu, Min R. (Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan) , Hsieh, Jo-Wei Allison , Chang, Chiung-Chih (Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan) , Wu, Pei-Hsuan , Lu, Meiyeh Jade (Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan) , Li, Jeng-Yi , Shang, Gaus (Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 106, Taiwan) , Lu, Rita Jui-Hsien , Nagy, László (Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan) , G. , Chen, Pao-Yang (Master Program for Plant Medicine and Good Agricultural Practice, National Chung Hsing University, Taichung 402, Taiwan) , Kao, Hsiao-Wei , Tsai, Isheng Jason (Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan)
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SignificanceWe present the genomes of five new bonnet mushroom Mycena species, formerly the last fungal bioluminescent lineage lacking reference genomes. These genome-scale datasets allowed us to construct an evolutionary model pinpointing all possible changes in the luciferase cluster across all fu...
1 He M. , Notes, outline and divergence times of Basidiomycota . Fungal Divers. 99 , 105 ？ 367 ( 2019 ).
2 Wei C. , Kirschner R. , A new Mycena species with blue basidiomata and porioid hymenophore from Taiwan . Mycoscience 60 , 10 ？ 13 ( 2019 ).
3 Thoen E. , In vitro evidence of root colonization suggests ecological versatility in the genus Mycena . New Phytol. 227 , 601 ？ 612 ( 2020 ). 32171021
4 Chew A. , Desjardin D. , Tan Y. , Musa M. , Sabaratnam V. , Bioluminescent fungi from Peninsular Malaysia-a taxonomic and phylogenetic overview . Fungal Divers. 70 , 149 ？ 187 ( 2015 ).
5 Cortes-Perez A. , New species and records of bioluminescent Mycena from Mexico . Mycologia 111 , 319 ？ 338 ( 2019 ). 30908110
6 Kaskova Z. M. , Mechanism and color modulation of fungal bioluminescence . Sci. Adv. 3 , e1602847 ( 2017 ). 28508049
7 Kotlobay A. A. , Genetically encodable bioluminescent system from fungi . Proc. Natl. Acad. Sci. U.S.A. 115 , 12728 ？ 12732 ( 2018 ). 30478037
8 Varga T. , Megaphylogeny resolves global patterns of mushroom evolution . Nat. Ecol. Evol. 3 , 668 ？ 678 ( 2019 ). 30886374
9 Sipos G. , Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria . Nat. Ecol. Evol. 1 , 1931 ？ 1941 ( 2017 ). 29085064
10 Floudas D. , Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii . Fungal Genet. Biol. 76 , 78 ？ 92 ( 2015 ). 25683379
11 Park Y. J. , Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation . PLoS One 9 , e93560 ( 2014 ). 24714189
12 Liu D. , Hunt M. , Tsai I. J. , Inferring synteny between genome assemblies: A systematic evaluation . BMC Bioinf. 19 , 26 ( 2018 ).
13 Koren S. , Canu: Scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation . Genome Res. 27 , 722 ？ 736 ( 2017 ). 28298431
14 Ranallo-Benavidez T. R. , Jaron K. S. , Schatz M. C. , GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes . Nat. Commun. 11 , 1432 ( 2020 ). 32188846
15 Shafin K. , Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes . Nat. Biotechnol. 38 , 1044 ？ 1053 ( 2020 ). 32686750
16 Heinzelmann R. , Rigling D. , Sipos G. , Munsterkotter M. , Croll D. , Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae . Heredity 124 , 699 ？ 713 ( 2020 ). 32203246
17 Perez G. , Pangilinan J. , Pisabarro A. G. , Ramirez L. , Telomere organization in the ligninolytic basidiomycete Pleurotus ostreatus . Appl. Environ. Microbiol. 75 , 1427 ？ 1436 ( 2009 ). 19114509
18 Holt C. , Yandell M. , MAKER2: An annotation pipeline and genome-database management tool for second-generation genome projects . BMC Bioinf. 12 , 491 ( 2011 ).
19 Simao F. A. , Waterhouse R. M. , Ioannidis P. , Kriventseva E. V. , Zdobnov E. M. , BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs . Bioinformatics 31 , 3210 ？ 3212 ( 2015 ). 26059717
20 Emms D. M. , Kelly S. , OrthoFinder: Phylogenetic orthology inference for comparative genomics . Genome Biol. 20 , 238 ( 2019 ). 31727128
21 Emms D. M. , Kelly S. , OrthoFinder: Solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy . Genome Biol. 16 , 157 ( 2015 ). 26243257
22 Duplessis S. , Obligate biotrophy features unraveled by the genomic analysis of rust fungi . Proc. Natl. Acad. Sci. U.S.A. 108 , 9166 ？ 9171 ( 2011 ). 21536894
23 Zheng A. , The evolution and pathogenic mechanisms of the rice sheath blight pathogen . Nat. Commun. 4 , 1424 ( 2013 ). 23361014
24 Stajich J. E. , Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) . Proc. Natl. Acad. Sci. U.S.A. 107 , 11889 ？ 11894 ( 2010 ). 20547848
25 Chung C. L. , Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees . Mol. Ecol. 26 , 6301 ？ 6316 ( 2017 ). 28926153
26 Ni P. , DeepSignal: Detecting DNA methylation state from nanopore sequencing reads using deep-learning . Bioinformatics 35 , 4586 ？ 4595 ( 2019 ). 30994904
27 Zhang X. , Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis . Cell 126 , 1189 ？ 1201 ( 2006 ). 16949657
28 Wang Y. , Wang X. , Lee T. H. , Mansoor S. , Paterson A. H. , Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in Oryza sativa (rice) . New Phytol. 198 , 274 ？ 283 ( 2013 ). 23356482
29 Montanini B. , Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content . Genome Biol. 15 , 411 ( 2014 ). 25091826
30 Jones P. A. , Functions of DNA methylation: Islands, start sites, gene bodies and beyond . Nat. Rev. Genet. 13 , 484 ？ 492 ( 2012 ). 22641018
31 Elango N. , Hunt B. G. , Goodisman M. A. D. , Yi S. V. , DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera . Proc. Natl. Acad. Sci. U.S.A. 106 , 11206 ？ 11211 ( 2009 ). 19556545
32 Bewick A. J. , Diversity of cytosine methylation across the fungal tree of life . Nat. Ecol. Evol. 3 , 479 ？ 490 ( 2019 ). 30778188
33 Willing E. M. , Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation . Nat. Plants 1 , 14023 ( 2015 ). 27246759
34 Wang H. , CG gene body DNA methylation changes and evolution of duplicated genes in cassava . Proc. Natl. Acad. Sci. U.S.A. 112 , 13729 ？ 13734 ( 2015 ). 26483493
35 Stamatakis A. , RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models . Bioinformatics 22 , 2688 ？ 2690 ( 2006 ). 16928733
36 Mirarab S. , Warnow T. , ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes . Bioinformatics 31 , i44 ？ i52 ( 2015 ). 26072508
37 Yang Z. , PAML 4: Phylogenetic analysis by maximum likelihood . Mol. Biol. Evol. 24 , 1586 ？ 1591 ( 2007 ). 17483113
38 Lupia R. , Lidgard S. , Crane P. , Comparing palynological abundance and diversity: Implications for biotic replacement during the Cretaceous angiosperm radiation . Paleobiology 25 , 305 ？ 340 ( 1999 ).
39 Yue J.-X. , Contrasting evolutionary genome dynamics between domesticated and wild yeasts . Nat. Genet. 49 , 913 ？ 924 ( 2017 ). 28416820
40 Dong S. , Raffaele S. , Kamoun S. , The two-speed genomes of filamentous pathogens: Waltz with plants . Curr. Opin. Genet. Dev. 35 , 57 ？ 65 ( 2015 ). 26451981
41 Haas B. J. , Delcher A. L. , Wortman J. R. , Salzberg S. L. , DAGchainer: A tool for mining segmental genome duplications and synteny . Bioinformatics 20 , 3643 ？ 3646 ( 2004 ). 15247098
42 Rokas A. , Wisecaver J. H. , Lind A. L. , The birth, evolution and death of metabolic gene clusters in fungi . Nat. Rev. Microbiol. 16 , 731 ？ 744 ( 2018 ). 30194403
43 Oliveira A. G. , Circadian control sheds light on fungal bioluminescence . Curr. Biol. 25 , 964 ？ 968 ( 2015 ). 25802150
44 Sharpe M. L. , Dearden P. K. , Gimenez G. , Krause K. L. , Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes . BMC Genom. 16 , 825 ( 2015 ).
45 Fallon T. R. , Firefly genomes illuminate parallel origins of bioluminescence in beetles . eLife 7 , e36495 ( 2018 ). 30324905
46 Desjardin D. E. , Oliveira A. G. , Stevani C. V. , Fungi bioluminescence revisited . Photochem. Photobiol. Sci. 7 , 170 ？ 182 ( 2008 ). 18264584
47 Mihail J. D. , Bioluminescence patterns among North American Armillaria species . Fungal Biol. 119 , 528 ？ 537 ( 2015 ). 25986550
48 Bermudes D. , Petersen R. H. , Nealson K. H. , Low-level bioluminescence detected in Mycena-Haematopus Basidiocarps . Mycologia 84 , 799 ？ 802 ( 1992 ).
49 Zhang B. , Horvath S. , A general framework for weighted gene co-expression network analysis . Stat. Appl. Genet. Mol. Biol. 4 , ( 2005 ).
50 Langfelder P. , Horvath S. , WGCNA: An R package for weighted correlation network analysis . BMC Bioinf. 9 , 559 ( 2008 ).
51 Krizsan K. , Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi . Proc. Natl. Acad. Sci. U.S.A. 116 , 7409 ？ 7418 ( 2019 ). 30902897
52 Harvey E. N. , Bioluminescence ( Academic Press , New York , 1952 ).
53 Wassink E. C. , “ Luminescence in fungi .” in Bioluminescence in Action , Herring P. J. , Ed. ( Academic Press , London , 1978 ), pp. 171 ？ 197 .
54 De Bie T. , Cristianini N. , Demuth J. P. , Hahn M. W. , CAFE: A computational tool for the study of gene family evolution . Bioinformatics 22 , 1269 ？ 1271 ( 2006 ). 16543274
55 Mondego J. M. , A genome survey of Moniliophthora perniciosa gives new insights into Witches’ Broom Disease of cacao . BMC Genom. 9 , 548 ( 2008 ).
56 Guijarro-Clarke C. , Holland P. W. H. , Paps J. , Widespread patterns of gene loss in the evolution of the animal kingdom . Nat. Ecol. Evol. 4 , 519 ？ 523 ( 2020 ). 32094540
57 Bowles A. M. C. , Bechtold U. , Paps J. , The origin of land plants is rooted in two bursts of genomic novelty . Curr. Biol. 30 , 530 ？ 536.e2 ( 2020 ). 31956023
58 Nagy L. G. , Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts . Nat. Commun. 5 , 4471 ( 2014 ). 25034666
59 Marcet-Houben M. , Gabaldon T. , Evolutionary and functional patterns of shared gene neighbourhood in fungi . Nat. Microbiol. 4 , 2383 ？ 2392 ( 2019 ). 31527797
60 Weinstein P. , Delean S. , Wood T. , Austin A. D. , Bioluminescence in the ghost fungus Omphalotus nidiformis does not attract potential spore dispersing insects . IMA Fungus 7 , 229 ？ 234 ( 2016 ). 27990328
61 Chang C. C. , Chen C. Y. , Lin W. W. , Kao H. W. , Mycena jingyinga, Mycena luguensis, and Mycena venus: Three new species of bioluminescent fungi from Taiwan . Taiwania 65 , 396 ？ 406 ( 2020 ).
62 Vaser R. , Sovi I. , Nagarajan N. , ？iki M. , Fast and accurate de novo genome assembly from long uncorrected reads . Genome Res. 27 , 737 ？ 746 ( 2017 ). 28100585
63 Huang S. , Kang M. , Xu A. , HaploMerger2: Rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly . Bioinformatics 33 , 2577 ？ 2579 ( 2017 ). 28407147
64 Walker B. J. , Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement . PLoS One 9 , e112963 ( 2014 ). 25409509
65 Koren S. , De novo assembly of haplotype-resolved genomes with trio binning . Nat. Biotechnol. 36 , 1174 ？ 1182 ( 2018 ).
66 Benson G. , Tandem repeats finder: A program to analyze DNA sequences . Nucleic Acids Res. 27 , 573 ？ 580 ( 1999 ). 9862982
67 Grigoriev I. V. , MycoCosm portal: Gearing up for 1000 fungal genomes . Nucleic Acids Res. 42 , D699 ？ D704 ( 2014 ). 24297253
68 Dobin A. , STAR: Ultrafast universal RNA-seq aligner . Bioinformatics 29 , 15 ？ 21 ( 2013 ). 23104886
69 Dobin A. , Gingeras T. R. , Mapping RNA-seq reads with STAR . Curr. Protoc. Bioinf. 51 , 11 14 11 ？ 11 14 19 ( 2015 ).
70 Haas B. J. , De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis . Nat. Protoc. 8 , 1494 ？ 1512 ( 2013 ). 23845962
71 Pertea M. , StringTie enables improved reconstruction of a transcriptome from RNA-seq reads . Nat. Biotechnol. 33 , 290 ？ 295 ( 2015 ). 25690850
72 Song L. , Sabunciyan S. , Florea L. , CLASS2: Accurate and efficient splice variant annotation from RNA-seq reads . Nucleic Acids Res. 44 , e98 ( 2016 ). 26975657
73 Trapnell C. , Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks . Nat. Protoc. 7 , 562 ？ 578 ( 2012 ). 22383036
74 Wu T. D. , Watanabe C. K. , GMAP: A genomic mapping and alignment program for mRNA and EST sequences . Bioinformatics 21 , 1859 ？ 1875 ( 2005 ). 15728110
75 Venturini L. , Caim S. , Kaithakottil G. G. , Mapleson D. L. , Swarbreck D. , Leveraging multiple transcriptome assembly methods for improved gene structure annotation . Gigascience 7 , giy093 ( 2018 ).
76 Stanke M. , Tzvetkova A. , Morgenstern B. , AUGUSTUS at EGASP: Using EST, protein and genomic alignments for improved gene prediction in the human genome . Genome Biol. 7 ( suppl. 1 ), S11.1 ？ S11.8 ( 2006 ). 16925833
77 Ter-Hovhannisyan V. , Lomsadze A. , Chernoff Y. O. , Borodovsky M. , Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training . Genome Res. 18 , 1979 ？ 1990 ( 2008 ). 18757608
78 Hoff K. J. , Lange S. , Lomsadze A. , Borodovsky M. , Stanke M. , BRAKER1: Unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS . Bioinformatics 32 , 767 ？ 769 ( 2016 ). 26559507
79 Korf I. , Gene finding in novel genomes . BMC Bioinf. 5 , 59 ( 2004 ).
80 Conesa A. , Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research . Bioinformatics 21 , 3674 ？ 3676 ( 2005 ). 16081474
81 Falda M. , Argot2: A large scale function prediction tool relying on semantic similarity of weighted gene ontology terms . BMC Bioinf. 13 ( suppl. 4 ), S14 ( 2012 ).
82 Yin Y. , dbCAN: A web resource for automated carbohydrate-active enzyme annotation . Nucleic Acids Res. 40 , W445 ？ W451 ( 2012 ). 22645317
83 Finn R. D. , Clements J. , Eddy S. R. , HMMER web server: Interactive sequence similarity searching . Nucleic Acids Res. 39 , W29 ？ W37 ( 2011 ). 21593126
84 Berriman M. , Coghlan A. , Tsai I. J. , Creation of a comprehensive repeat library for a newly sequenced parasitic worm genome . Protoc. Exch. , 10.1038/protex.2018.054 ( 2018 ).
85 Guo W. , BS-Seeker2: A versatile aligning pipeline for bisulfite sequencing data . BMC Genom. 14 , 774 ( 2013 ).
86 Katoh K. , Standley D. M. , MAFFT multiple sequence alignment software version 7: Improvements in performance and usability . Mol. Biol. Evol. 30 , 772 ？ 780 ( 2013 ). 23329690
87 Kozlov A. M. , Darriba D. , Flouri T. , Morel B. , Stamatakis A. , RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference . Bioinformatics 35 , 4453 ？ 4455 ( 2019 ). 31070718
88 dos Reis M. , Yang Z. , Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times . Mol. Biol. Evol. 28 , 2161 ？ 2172 ( 2011 ). 21310946
89 Suyama M. , Torrents D. , Bork P. , PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments . Nucleic Acids Res. 34 , W609 ？ W612 ( 2006 ). 16845082
90 Kumar S. , Stecher G. , Suleski M. , Hedges S. B. , TimeTree: A resource for Timelines, Timetrees, and divergence times . Mol. Biol. Evol. 34 , 1812 ？ 1819 ( 2017 ). 28387841
91 Poinar G. O. Jr , Buckley R. , Evidence of mycoparasitism and hypermycoparasitism in Early Cretaceous amber . Mycol. Res. 111 , 503 ？ 506 ( 2007 ). 17512712
92 Cai C. , Leschen R. A. , Hibbett D. S. , Xia F. , Huang D. , Mycophagous rove beetles highlight diverse mushrooms in the Cretaceous . Nat. Commun. 8 , 14894 ( 2017 ). 28300055
93 Guy L. , Kultima J. R. , Andersson S. G. , genoPlotR: Comparative gene and genome visualization in R . Bioinformatics 26 , 2334 ？ 2335 ( 2010 ). 20624783
94 Bolger A. M. , Lohse M. , Usadel B. , Trimmomatic: A flexible trimmer for Illumina sequence data . Bioinformatics 30 , 2114 ？ 2120 ( 2014 ). 24695404
95 Liao Y. , Smyth G. K. , Shi W. , featureCounts: An efficient general purpose program for assigning sequence reads to genomic features . Bioinformatics 30 , 923 ？ 930 ( 2014 ). 24227677
96 Meinhardt L. W. , Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: Mechanisms of the biotrophic and necrotrophic phases . BMC Genom. 15 , 164 ( 2014 ).
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