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Hal: an Automated Pipeline for Phylogenetic Analyses of Genomic Data

Barbara Robbertse, Ryan J. Yoder, Alex Boyd, John Reeves, Joseph W. Spatafora
2011 PLOS Currents  
The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous clusters of proteins or genes, and the assembly of alignments of orthologous sequence data into
more » ... dual and concatenated super alignments. Here we report the production of an automated pipeline, Hal that produces multiple alignments and trees from genomic data. These alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. In short, the Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees. The script is available at sourceforge (http://sourceforge.net/projects/bio-hal/). The results from an example analysis of Kingdom Fungi are briefly discussed. Abstract The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous clusters of proteins or genes, and the assembly of alignments of orthologous sequence data into individual and concatenated super alignments. Here we report the production of an automated pipeline, Hal that produces multiple alignments and trees from genomic data. These alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. In short, the Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees. The script is available at sourceforge (http://sourceforge.net/projects/bio-hal/). The results from an example analysis of Kingdom Fungi are briefly discussed. Abstract The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous clusters of proteins or genes, and the assembly of alignments of orthologous sequence data into individual and concatenated super alignments. Here we report the production of an automated pipeline, Hal that produces multiple alignments and trees from genomic data. These alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. In short, the Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees. The script is available at sourceforge (http://sourceforge.net/projects/bio-hal/). The results from an example analysis of Kingdom Fungi are briefly discussed.
doi:10.1371/currents.rrn1213 pmid:21327165 pmcid:PMC3038436 fatcat:tkkiop6clvfa5kz7m4rrtd2nuq

Expressed sequence tags reveal Proctotrupomorpha (minus Chalcidoidea) as sister to Aculeata (Hymenoptera: Insecta)

Barbara J. Sharanowski, Barbara Robbertse, John Walker, S. Randal Voss, Ryan Yoder, Joseph Spatafora, Michael J. Sharkey
2010 Molecular Phylogenetics and Evolution  
As an initial search to identify orthologs, we utilized a predeveloped semi-automated software program designed for identifying orthologs of proteomes (Robbertse et al., 2006) .  ...  All sequences were translated into amino acid sequences and run through the pipeline (Robbertse et al., 2006) which included: a Basic Local Alignment Search Tool (BLASTp) (Altschul et al., 1990) comparing  ... 
doi:10.1016/j.ympev.2010.07.006 pmid:20637293 fatcat:lezvdnecqffl5oym6fjm4am2t4

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation [article]

Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi, Eric P. Nawrocki
2021 bioRxiv   pre-print
The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity,
more » ... e National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron. Results: To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The ribotyper and ribosensor programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The ribodbmaker program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. At least nine freely available blastn rRNA databases created and maintained with Ribovore are used either for checking incoming GenBank submissions or by the blastn browser interface at NCBI or both. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8,350 taxa. Conclusion: Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.
doi:10.1101/2021.02.11.430762 fatcat:b3axwjsmzbd5vh4ydfflbusuh4

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi, Eric P. Nawrocki
2021 BMC Bioinformatics  
Background The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their
more » ... ularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron. Results To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The and programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa. Conclusion Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.
doi:10.1186/s12859-021-04316-z fatcat:v5sdpvc3fzep7bgigra6csezmm

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade

J. Cameron Thrash, Alex Boyd, Megan J. Huggett, Jana Grote, Paul Carini, Ryan J. Yoder, Barbara Robbertse, Joseph W. Spatafora, Michael S. Rappé, Stephen J. Giovannoni
2011 Scientific Reports  
Mitochondria share a common ancestor with the Alphaproteobacteria, but determining their precise origins is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. Nonetheless, phylogenetic accuracy improves with more refined tools and expanded taxon sampling. We investigated mitochondrial origins with the benefit of new, deeply branching genome sequences from the ancient and prolific SAR11 clade of Alphaproteobacteria and publicly available
more » ... proteobacterial and mitochondrial genome sequences. Using the automated phylogenomic pipeline Hal, we systematically studied the effect of taxon sampling and missing data to accommodate small mitochondrial genomes. The evidence supports a common origin of mitochondria and SAR11 as a sister group to the Rickettsiales. The simplest explanation of these data is that mitochondria evolved from a planktonic marine alphaproteobacterial lineage that participated in multiple inter-specific cell colonization events, in some cases yielding parasitic relationships, but in at least one case producing a symbiosis that characterizes modern eukaryotic life. V ital to the evolution of all known eukaryotic cells was the endosymbiotic event that resulted in the permanent acquisition of bacteria that through time were transformed into mitochondria. Even eukaryotes that were previously thought to lack mitochondria have now been shown to contain some remnants of that original endosymbiosis, either through the maintenance of hydrogenosomes, mitosomes, or nuclear genes of mitochondrial origin 1,2 . Although argument continues about the circumstances of the founding endosymbiotic event 2,3 , current hypotheses, making use of mitochondrial genome and proteome data, agree that the mitochondrial ancestor was most closely related to Alphaproteobacteria 4-11 . The rooting of the ancestral mitochondria within the Alphaproteobacteria has not yet been resolved, but better phylogenetic methodology and new mitochondrial and bacterial genome sequences offer opportunities to refine understanding of this singular evolutionary event. The sequencing of the first Rickettsia genome provided phylogenomic evidence for the previously established theory that the mitochondrial root was within the Rickettsiales 5,10,12,13 (and references therein). This theory was intellectually satisfying because all known Rickettsia have extremely reduced genomes and obligate intracellular lifestyles, although there was evidence to suggest that the genome reduction in mitochondria and Rickettsia probably happened independently 5,10,11 . While the rooting of mitochondria within the Rickettsiales has been debated based on other phylogenomic studies 4,7,14 , it has gained support more recently with the addition of more genome sequences from taxa in the Rickettsiales, including the globally important SAR11 clade 6,15 . As free-living, predominantly marine bacteria, the phylogenetically diverse 16 organisms of the ubiquitous SAR11 clade are unique in the Rickettsiales order. Like other Rickettsiales, SAR11 have small genomes and, consequently, limited metabolic versatility 5, 7, [17] [18] [19] . However, SAR11 genomes bear distinctly different evolutionary signatures from other Rickettsiales genomes, indicating that selection for a streamlined genome, rather than genetic drift, has been the path of genome reduction in these organisms 9, 17, 19 . For example, the sequence of Candidatus Pelagibacter ubique HTCC1062 has few recent gene duplications, phage, transposons, or pseudogenes, has extremely small intergenic regions, and is optimized for a highly efficient lifestyle 17 , whereas organisms like Rickettsia and those of the Anaplasmataceae contain large numbers of duplications, putatively inactive genes, larger intergenic regions, and/or mobile elements, indicative of the different selective pressures of obligate intracellular life 7,18,20,21 . Despite of the differences in evolutionary history and lifestyle, there is phylogenomic SUBJECT AREAS: ENVIRONMENTAL MICROBIOLOGY EVOLUTION PHYLOGENETICS MICROBIAL GENETICS
doi:10.1038/srep00013 pmid:22355532 pmcid:PMC3216501 fatcat:r4r6tpucfrcd5os3xzkekjs774

The Genera of Fungi: fixing the application of type species of generic names

Pedro W. Crous, Alejandra Giraldo, David L. Hawksworth, Vincent Robert, Paul M. Kirk, Josep Guarro, Barbara Robbertse, Conrad L. Schoch, Ulrike Damm, Thippawan Trakunyingcharoen, Johannes Z. Groenewald
2014 IMA Fungus  
To ensure a stable platform for fungal taxonomy, it is of paramount importance that the genetic application of generic names be based on their DNA sequence data, and wherever possible, not morphology or ecology alone. To facilitate this process, a new database, accessible at www.GeneraofFungi.org (GoF) was established, which will allow deposition of metadata linked to holo-, lecto-, neo-or epitype specimens, cultures and DNA sequence data of the type species of genera. Although there are
more » ... ly more than 18 000 fungal genera described, we aim to initially focus on the subset of names that have been placed on the "Without-prejudice List of Protected Generic Names of Fungi" (see IMA Fungus 4(2): 381-443, 2013). To enable the global mycological community to keep track of typification events and avoid duplication, special MycoBank Typification identfiers (MBT) will be issued upon deposit of metadata in MycoBank. MycoBank is linked to GoF, thus deposited metadata of generic type species will be displayed in GoF (and vice versa), but will also be linked to Index Fungorum (IF) and the curated RefSeq Targeted Loci (RTL) database in GenBank at the National Center for Biotechnology Information (NCBI). This initial paper focuses on eight genera of appendaged coelomycetes, the type species of which are neo-or epitypified here: Bartalinia
doi:10.5598/imafungus.2014.05.01.14 pmid:25083414 pmcid:PMC4107892 fatcat:qdlogbky7rdkbjhvdho7e5usyi

Functional Analysis of All Nonribosomal Peptide Synthetases inCochliobolus heterostrophusReveals a Factor, NPS6, Involved in Virulence and Resistance to Oxidative Stress

Bee-Na Lee, Scott Kroken, David Y. T. Chou, Barbara Robbertse, O. C. Yoder, B. Gillian Turgeon
2005 Eukaryotic Cell  
Nonribosomal peptides, made by nonribosomal peptide synthetases, have diverse biological activities, including roles as fungal virulence effectors. Inspection of the genome ofCochliobolus heterostrophus, a fungal pathogen of maize and a member of a genus noted for secondary metabolite production, revealed eight multimodular nonribosomal peptide synthase (NPS) genes and three monomodularNPS-like genes, one of which encodes a nonribosomal peptide synthetase/polyketide synthase hybrid enzyme
more » ... ed to be involved in synthesis of a peptide/polyketide molecule. Deletion of eachNPSgene and phenotypic analyses showed that the product of only one of these genes,NPS6, is required for normal virulence on maize. NPS6 is also required for resistance to hydrogen peroxide, suggesting it may protect the fungus from oxidative stress. This and all othernpsmutants had normal growth, mating ability, and appressoria. Real-time PCR analysis showed that expression of allNPSgenes is low (relative to that of actin), that all (except possiblyNPS2) are expressed during vegetative growth, and that expression is induced by nitrogen starvation. OnlyNPS6is unfailingly conserved among euascomycete fungi, including plant and human pathogens and saprobes, suggesting the possibility that NPS6 activity provides oxidative stress protection during both saprobic and parasitic growth.
doi:10.1128/ec.4.3.545-555.2005 pmid:15755917 pmcid:PMC1087798 fatcat:36h7ngb3rrdiva55qkr7ibkehq

Botryosphaeria dothidea: a latent pathogen of global importance to woody plant health

Angelica Marsberg, Martin Kemler, Fahimeh Jami, Jan H. Nagel, Alisa Postma-Smidt, Sanushka Naidoo, Michael J. Wingfield, Pedro W. Crous, Joseph W. Spatafora, Cedar N. Hesse, Barbara Robbertse, Bernard Slippers
2016 Molecular plant pathology  
Botryosphaeria dothidea is the type species of Botryosphaeria (Botryosphaeriaceae, Botryosphaeriales). Fungi residing in this order are amongst the most widespread and important canker and dieback pathogens of trees worldwide, with B. dothidea one of the most common species on a large number of hosts. Its taxonomic circumscription has undergone substantial change in the past decade, making it difficult to interpret the large volume of literature linked to the name B. dothidea. This pathogen
more » ... ile synthesises the current understanding of B. dothidea pertaining to its distribution, host associations and its role as a pathogen in managed and natural woody environments. The prolonged latent infection or endophytic phase is of particular importance as it implies that the fungus can easily pass undetected by quarantine systems in traded living plants, fruits and other plant parts. Infections typically become obvious only under conditions of host stress, when disease symptoms develop. This study also considers the knowledge emerging from the recently sequenced B. dothidea genome elucidating previously unknown aspects of the species, including mating and hostinfection strategies. Despite more than 150 years of research on B. dothidea, there is clearly much to be learned regarding this global tree pathogen. This is increasingly important given the stresses imposed on various woody hosts due to climate change. 3 Host range: Confirmed on more than 24 host genera, including woody plants such as Acacia (=Vachellia), Eucalyptus, Vitis and Pistachio. Disease symptoms: Associated with twig, branch and stem cankers, tip and branch dieback, fruit rot, blue stain and plant death Useful websites:  The Botryosphaeria site for detailed morphological descriptions (http://www.crem.fct.unl.pt/botryosphaeria_site/);  Systematic Mycology and Microbiology Laboratory Fungal Database for all literature and associated hosts (https://nt.ars-grin.gov/fungaldatabases/);  TreeBASE link for the combined ITS and TEF-1α tree [in progress]
doi:10.1111/mpp.12495 pmid:27682468 fatcat:5rz3kvkfcvfqdi6lzmkanisjdi

Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

Jonathan Grandaubert, Rohan GT Lowe, Jessica L Soyer, Conrad L Schoch, Angela P Van de Wouw, Isabelle Fudal, Barbara Robbertse, Nicolas Lapalu, Matthew G Links, Bénédicte Ollivier, Juliette Linglin, Valérie Barbe (+6 others)
2014 BMC Genomics  
Many plant-pathogenic fungi have a tendency towards genome size expansion, mostly driven by increasing content of transposable elements (TEs). Through comparative and evolutionary genomics, five members of the Leptosphaeria maculans-Leptosphaeria biglobosa species complex (class Dothideomycetes, order Pleosporales), having different host ranges and pathogenic abilities towards cruciferous plants, were studied to infer the role of TEs on genome shaping, speciation, and on the rise of better
more » ... ed pathogens. Results: L. maculans 'brassicae', the most damaging species on oilseed rape, is the only member of the species complex to have a TE-invaded genome (32.5%) compared to the other members genomes (<4%). These TEs had an impact at the structural level by creating large TE-rich regions and are suspected to have been instrumental in chromosomal rearrangements possibly leading to speciation. TEs, associated with species-specific genes involved in disease process, also possibly had an incidence on evolution of pathogenicity by promoting translocations of effector genes to highly dynamic regions and thus tuning the regulation of effector gene expression in planta. Conclusions: Invasion of L. maculans 'brassicae' genome by TEs followed by bursts of TE activity allowed this species to evolve and to better adapt to its host, making this genome species a peculiarity within its own species complex as well as in the Pleosporales lineage.
doi:10.1186/1471-2164-15-891 pmid:25306241 pmcid:PMC4210507 fatcat:fin7j7mmwvcxlklnsvcmx6rjae

NCBI Taxonomy: a comprehensive update on curation, resources and tools

Conrad L Schoch, Stacy Ciufo, Mikhail Domrachev, Carol L Hotton, Sivakumar Kannan, Rogneda Khovanskaya, Detlef Leipe, Richard Mcveigh, Kathleen O'Neill, Barbara Robbertse, Shobha Sharma, Vladimir Soussov (+4 others)
2020 Database: The Journal of Biological Databases and Curation  
The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data
more » ... ments can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy
doi:10.1093/database/baaa062 pmid:32761142 fatcat:bnhdt2p6szf4rb2b2cerhg2bbq

Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case

Barbara Robbertse, Pooja K Strope, Priscila Chaverri, Romina Gazis, Stacy Ciufo, Michael Domrachev, Conrad L Schoch
2017 Database: The Journal of Biological Databases and Curation  
Citation details: Robbertse, B., Strope, P. K., Chaverri, P. et al.  ... 
doi:10.1093/database/bax072 pmid:29220466 pmcid:PMC5641268 fatcat:t4oypzpx4nfatl3avfhn44u5ka

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Hiran A. Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde (+15 others)
2020 IMA Fungus  
groups of fungi, such as Hypocreales (Fusarium, Gibberella, Trichoderma), species hypotheses delimited at 98.5% in UNITE include sequences from type material of several to numerous different species (Robbertse  ... 
doi:10.1186/s43008-020-00033-z pmid:32714773 pmcid:PMC7353689 fatcat:shpddgh3zze6fcdakwgl5znpou

MycoBank gearing up for new horizons

Vincent Robert, Duong Vu, Ammar Ben Hadj Amor, Nathalie van de Wiele, Carlo Brouwer, Bernard Jabas, Szaniszlo Szoke, Ahmed Dridi, Maher Triki, Samy Ben Daoud, Oussema Chouchen, Lea Vaas (+24 others)
2013 IMA Fungus  
doi:10.5598/imafungus.2013.04.02.16 pmid:24563843 pmcid:PMC3905949 fatcat:ruiannztrbb4jgdslrlwhphosa

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Viola A. Manning, Iovanna Pandelova, Braham Dhillon, Larry J. Wilhelm, Stephen B. Goodwin, Aaron M. Berlin, Melania Figueroa, Michael Freitag, James K. Hane, Bernard Henrissat, Wade H. Holman, Chinnappa D. Kodira (+14 others)
2013 G3: Genes, Genomes, Genetics  
MATERIALS AND METHODS Phylogenetic analysis Phylogenetic analyses were performed using the phylogenetic pipeline, Hal (Robbertse et al. 2006 (Robbertse et al. , 2011 .  ... 
doi:10.1534/g3.112.004044 pmid:23316438 pmcid:PMC3538342 fatcat:rqcol6e5rzcpbabxa4o27q4lke

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Diego Martinez, Randy M Berka, Bernard Henrissat, Markku Saloheimo, Mikko Arvas, Scott E Baker, Jarod Chapman, Olga Chertkov, Pedro M Coutinho, Dan Cullen, Etienne G J Danchin, Igor V Grigoriev (+33 others)
2008 Nature Biotechnology  
Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its
more » ... e encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.
doi:10.1038/nbt1403 pmid:18454138 fatcat:7ny7tyjj4jbdddfjwtuqgfs6ui
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