Journal ArticleDOI
Phylogenetic and phylogenomic overview of the Polyporales
Manfred Binder,Alfredo Justo,Robert Riley,Asaf Salamov,Francesc López-Giráldez,Elisabet Sjökvist,Alex Copeland,Brian Foster,Hui Sun,Ellen Larsson,Karl-Henrik Larsson,Jeffrey P. Townsend,Igor V. Grigoriev,David S. Hibbett +13 more
TLDR
The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.Abstract:
We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000-49 900 00 bp and encode for 12 910-16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.read more
Citations
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Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
Guo Jie Li,Kevin D. Hyde,Kevin D. Hyde,Kevin D. Hyde,Rui-Lin Zhao,Sinang Hongsanan,Sinang Hongsanan,Faten A. Abdel-Aziz,Mohamed A. Abdel-Wahab,Mohamed A. Abdel-Wahab,Pablo Alvarado,Genivaldo Alves-Silva,Joseph F. Ammirati,Hiran A. Ariyawansa,Abhishek Baghela,Ali H. Bahkali,Michael Beug,D. Jayarama Bhat,Dimitar Bojantchev,Thitiya Boonpratuang,Timur S. Bulgakov,Erio Camporesi,Marcela C. Boro,Oldriska Ceska,Dyutiparna Chakraborty,Jia-Jia Chen,K. W. Thilini Chethana,Putarak Chomnunti,Giovanni Consiglio,Bao-Kai Cui,Dong-Qin Dai,Yu Cheng Dai,Dinushani A. Daranagama,Dinushani A. Daranagama,Kanad Das,Monika C. Dayarathne,Monika C. Dayarathne,Eske De Crop,Rafael J. V. De Oliveira,Carlos Alberto Fragoso de Souza,José I. de Souza,Bryn T. M. Dentinger,Bryn T. M. Dentinger,Asha J. Dissanayake,Mingkwan Doilom,Mingkwan Doilom,E. Ricardo Drechsler-Santos,Masoomeh Ghobad-Nejhad,Sean P. Gilmore,Aristóteles Góes-Neto,Michał Gorczak,Charles H. Haitjema,Kalani Kanchana Hapuarachchi,Kalani Kanchana Hapuarachchi,Akira Hashimoto,Akira Hashimoto,Mao Qiang He,Mao Qiang He,John K. Henske,Kazuyuki Hirayama,María Josefina Iribarren,Subashini C. Jayasiri,Ruvishika S. Jayawardena,Sun Jeong Jeon,Gustavo Henrique Jerônimo,Ana L. Jesus,E. B. Gareth Jones,Ji Chuan Kang,Samantha C. Karunarathna,Samantha C. Karunarathna,Paul M. Kirk,Sirinapa Konta,Sirinapa Konta,Eric Kuhnert,Ewald Langer,Haeng Sub Lee,Hyang Burm Lee,Wen-Jing Li,Wen-Jing Li,Xinghong Li,Kare Liimatainen,Diogo Xavier Lima,Chuan Gen Lin,Chuan Gen Lin,Jian-Kui Liu,Xings Zhong Liu,Zuo Yi Liu,J. Jennifer Luangsa-ard,Robert Lücking,H. Thorsten Lumbsch,Saisamorn Lumyong,Eduardo M. Leaño,Agostina V. Marano,Misato Matsumura,Misato Matsumura,Eric H. C. McKenzie,Suchada Mongkolsamrit,Peter E. Mortimer,Thi Thuong Thuong Nguyen,Tuula Niskanen,Chada Norphanphoun,Chada Norphanphoun,Michelle A. O’Malley,Sittiporn Parnmen,Julia Pawłowska,Rekhani H. Perera,Rekhani H. Perera,Rungtiwa Phookamsak,Rungtiwa Phookamsak,Chayanard Phukhamsakda,Chayanard Phukhamsakda,Carmen L. A. Pires-Zottarelli,Olivier Raspé,Mateus Arduvino Reck,Sarah C. O. Rocha,André L. C. M. A. de Santiago,Indunil C. Senanayake,Ledo Setti,Qiu Ju Shang,Sanjay K. Singh,Esteban Benjamin Sir,Kevin V. Solomon,Jie Song,Prasert Srikitikulchai,Marc Stadler,Satinee Suetrong,Hayato Takahashi,Takumasa Takahashi,Kazuaki Tanaka,Li Ping Tang,Kasun M. Thambugala,Donnaya Thanakitpipattana,Michael K. Theodorou,Benjarong Thongbai,Tuksaporn Thummarukcharoen,Qing Tian,Qing Tian,Saowaluck Tibpromma,Saowaluck Tibpromma,Annemieke Verbeken,Alfredo Vizzini,Josef Vlasák,Kerstin Voigt,Dhanushka N. Wanasinghe,Dhanushka N. Wanasinghe,Yong Wang,Gothamie Weerakoon,Hua An Wen,Ting-Chi Wen,Nalin N. Wijayawardene,Sarunyou Wongkanoun,Marta Wrzosek,Yuan Pin Xiao,Yuan Pin Xiao,Jianchu Xu,Ji Ye Yan,Jing Yang,Shu Da Yang,Yu Hu,Jin-Feng Zhang,Jie Zhao,Li-Wei Zhou,Derek Peršoh,Alan J. L. Phillips,Sajeewa S. N. Maharachchikumbura +164 more
TL;DR: This paper is a compilation of notes on 142 fungal taxa, including five new families, 20 new genera, and 100 new species, representing a wide taxonomic and geographic range.
Journal ArticleDOI
The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
Subashini C. Jayasiri,Kevin D. Hyde,Kevin D. Hyde,Kevin D. Hyde,Hiran A. Ariyawansa,Hiran A. Ariyawansa,Jayarama D. Bhat,Bart Buyck,Lei Cai,Yu-Cheng Dai,Kamel A. Abd-Elsalam,Damien Ertz,Iman Hidayat,Rajesh Jeewon,E. B. Gareth Jones,Ali H. Bahkali,Samantha C. Karunarathna,Samantha C. Karunarathna,Jian-Kui Liu,Jian-Kui Liu,J. Jennifer Luangsa-ard,H. Thorsten Lumbsch,Sajeewa S. N. Maharachchikumbura,Sajeewa S. N. Maharachchikumbura,Eric H. C. McKenzie,Jean-Marc Moncalvo,Masoomeh Ghobad-Nejhad,Henrik R. Nilsson,Ka-Lai Pang,Olinto Liparini Pereira,Alan J. L. Phillips,Olivier Raspé,Adam W. Rollins,Andrea Irene Romero,Javier Etayo,Faruk Selçuk,Steven L. Stephenson,Satinee Suetrong,Joanne E. Taylor,Clement K. M. Tsui,Alfredo Vizzini,Mohamed A. Abdel-Wahab,Ting-Chi Wen,Saranyaphat Boonmee,Dong-Qin Dai,Dong-Qin Dai,Dinushani A. Daranagama,Dinushani A. Daranagama,Asha J. Dissanayake,Anusha H. Ekanayaka,Sally C. Fryar,Sinang Hongsanan,Ruvishika S. Jayawardena,Wen-Jing Li,Wen-Jing Li,Rekhani H. Perera,Rungtiwa Phookamsak,Nimali I. de Silva,Kasun M. Thambugala,Kasun M. Thambugala,Qing Tian,Qing Tian,Nalin N. Wijayawardene,Nalin N. Wijayawardene,Rui-Lin Zhao,Qi Zhao,Ji-Chuan Kang,Itthayakorn Promputtha +67 more
TL;DR: The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups.
Journal ArticleDOI
Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes
Johanna Rytioja,Kristiina Hildén,Jennifer Yuzon,Annele Hatakka,Ronald P. de Vries,Miia R. Mäkelä +5 more
TL;DR: This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats and compares these data to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiaomycetes with respect to plant poly Saccharide degradation.
Journal ArticleDOI
Notes, outline and divergence times of Basidiomycota
Mao Qiang He,Mao Qiang He,Rui-Lin Zhao,Kevin D. Hyde,Dominik Begerow,Martin Kemler,Andrey Yurkov,Eric H. C. McKenzie,Olivier Raspé,Makoto Kakishima,Santiago Sánchez-Ramírez,Else C. Vellinga,Roy E. Halling,Viktor Papp,Ivan V. Zmitrovich,Bart Buyck,Damien Ertz,Nalin N. Wijayawardene,Bao-Kai Cui,Nathan Schoutteten,Xin Zhan Liu,Tai Hui Li,Yi Jian Yao,Xin Yu Zhu,An Qi Liu,Guo Jie Li,Ming Zhe Zhang,Zhi Lin Ling,Bin Cao,Vladimír Antonín,Teun Boekhout,Bianca Denise Barbosa da Silva,Eske De Crop,Cony Decock,Bálint Dima,Arun Kumar Dutta,Jack W. Fell,József Geml,Masoomeh Ghobad-Nejhad,Admir José Giachini,Tatiana Baptista Gibertoni,Sergio P. Gorjón,Danny Haelewaters,Danny Haelewaters,Shuang Hui He,Brendan P. Hodkinson,Egon Horak,Tamotsu Hoshino,Alfredo Justo,Young Woon Lim,Nelson Menolli,Armin Mešić,Jean-Marc Moncalvo,Jean-Marc Moncalvo,Gregory M. Mueller,László Nagy,R. Henrik Nilsson,Machiel E. Noordeloos,Jorinde Nuytinck,Takamichi Orihara,Cheewangkoon Ratchadawan,Mario Rajchenberg,Alexandre G. S. Silva-Filho,Marcelo Aloisio Sulzbacher,Zdenko Tkalčec,Ricardo Valenzuela,Annemieke Verbeken,Alfredo Vizzini,Felipe Wartchow,Tie Zheng Wei,Michael Weiß,Chang Lin Zhao,Paul M. Kirk +72 more
TL;DR: Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
References
More filters
Journal ArticleDOI
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space
Fredrik Ronquist,Maxim Teslenko,Paul van der Mark,Daniel L. Ayres,Aaron E. Darling,Sebastian Höhna,Bret Larget,Liang Liu,Marc A. Suchard,John P. Huelsenbeck +9 more
TL;DR: The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly, and provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates.
Journal ArticleDOI
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Journal ArticleDOI
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
TL;DR: A computerized method is presented that reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.
Journal ArticleDOI
A Rapid Bootstrap Algorithm for the RAxML Web Servers
TL;DR: This work developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms and can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses.
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