Henn MR

References (4)

Title : Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis - Desjardins_2011_PLoS.Genet_7_e1002345
Author(s) : Desjardins CA , Champion MD , Holder JW , Muszewska A , Goldberg J , Bailao AM , Brigido MM , Ferreira ME , Garcia AM , Grynberg M , Gujja S , Heiman DI , Henn MR , Kodira CD , Leon-Narvaez H , Longo LV , Ma LJ , Malavazi I , Matsuo AL , Morais FV , Pereira M , Rodriguez-Brito S , Sakthikumar S , Salem-Izacc SM , Sykes SM , Teixeira MM , Vallejo MC , Walter ME , Yandava C , Young S , Zeng Q , Zucker J , Felipe MS , Goldman GH , Haas BJ , McEwen JG , Nino-Vega G , Puccia R , San-Blas G , Soares CMF , Birren BW , Cuomo CA
Ref : PLoS Genet , 7 :e1002345 , 2011
Abstract : Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.
ESTHER : Desjardins_2011_PLoS.Genet_7_e1002345
PubMedSearch : Desjardins_2011_PLoS.Genet_7_e1002345
PubMedID: 22046142
Gene_locus related to this paper: parbd-c1gc95 , parbp-c0s0d7 , parbp-c0s257 , parbd-c1g8z9 , parba-c1grf0 , parbp-c0s816 , parbp-c0s5g4 , parbd-c1g5f5 , parbd-c1fzf9 , parba-kex1 , parbd-kex1 , parbp-kex1 , parba-cbpya , parbp-cbpya

Title : Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control - Neafsey_2010_Genome.Res_20_938
Author(s) : Neafsey DE , Barker BM , Sharpton TJ , Stajich JE , Park DJ , Whiston E , Hung CY , McMahan C , White J , Sykes S , Heiman D , Young S , Zeng Q , Abouelleil A , Aftuck L , Bessette D , Brown A , FitzGerald M , Lui A , Macdonald JP , Priest M , Orbach MJ , Galgiani JN , Kirkland TN , Cole GT , Birren BW , Henn MR , Taylor JW , Rounsley SD
Ref : Genome Res , 20 :938 , 2010
Abstract : We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. Our data confirm earlier microsatellite-based findings that these species are genetically differentiated, but our population genomics approach reveals that hybridization and genetic introgression have recently occurred between the two species. The directionality of introgression is primarily from C. posadasii to C. immitis, and we find more than 800 genes exhibiting strong evidence of introgression in one or more sequenced isolates. We performed PCR-based sequencing of one region exhibiting introgression in 40 C. immitis isolates to confirm and better define the extent of gene flow between the species. We find more coding sequence than expected by chance in the introgressed regions, suggesting that natural selection may play a role in the observed genetic exchange. We find notable heterogeneity in repetitive sequence composition among the sequenced genomes and present the first detailed genome-wide profile of a repeat-induced point mutation (RIP) process distinctly different from what has been observed in Neurospora. We identify promiscuous HLA-I and HLA-II epitopes in both proteomes and discuss the possible implications of introgression and population genomic data for public health and vaccine candidate prioritization. This study highlights the importance of population genomic data for detecting subtle but potentially important phenomena such as introgression.
ESTHER : Neafsey_2010_Genome.Res_20_938
PubMedSearch : Neafsey_2010_Genome.Res_20_938
PubMedID: 20516208
Gene_locus related to this paper: cocp7-c5p2u8 , cocp7-c5p5s7 , cocp7-c5pe69 , cocp7-c5pf68 , cocp7-c5pgk6 , cocim-j3ka92 , cocp7-c5phc6 , cocps-e9d3i4 , cocit-a0a0j8rde7 , cocps-e9csw0 , cocps-e9dgm8

Title : Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives - Sharpton_2009_Genome.Res_19_1722
Author(s) : Sharpton TJ , Stajich JE , Rounsley SD , Gardner MJ , Wortman JR , Jordar VS , Maiti R , Kodira CD , Neafsey DE , Zeng Q , Hung CY , McMahan C , Muszewska A , Grynberg M , Mandel MA , Kellner EM , Barker BM , Galgiani JN , Orbach MJ , Kirkland TN , Cole GT , Henn MR , Birren BW , Taylor JW
Ref : Genome Res , 19 :1722 , 2009
Abstract : While most Ascomycetes tend to associate principally with plants, the dimorphic fungi Coccidioides immitis and Coccidioides posadasii are primary pathogens of immunocompetent mammals, including humans. Infection results from environmental exposure to Coccidiodies, which is believed to grow as a soil saprophyte in arid deserts. To investigate hypotheses about the life history and evolution of Coccidioides, the genomes of several Onygenales, including C. immitis and C. posadasii; a close, nonpathogenic relative, Uncinocarpus reesii; and a more diverged pathogenic fungus, Histoplasma capsulatum, were sequenced and compared with those of 13 more distantly related Ascomycetes. This analysis identified increases and decreases in gene family size associated with a host/substrate shift from plants to animals in the Onygenales. In addition, comparison among Onygenales genomes revealed evolutionary changes in Coccidioides that may underlie its infectious phenotype, the identification of which may facilitate improved treatment and prevention of coccidioidomycosis. Overall, the results suggest that Coccidioides species are not soil saprophytes, but that they have evolved to remain associated with their dead animal hosts in soil, and that Coccidioides metabolism genes, membrane-related proteins, and putatively antigenic compounds have evolved in response to interaction with an animal host.
ESTHER : Sharpton_2009_Genome.Res_19_1722
PubMedSearch : Sharpton_2009_Genome.Res_19_1722
PubMedID: 19717792
Gene_locus related to this paper: ajecg-c0nbn5 , ajecg-c0nbz4 , ajecg-c0ndw0 , ajecg-c0nqc6 , ajecg-c0nst6 , ajecg-c0ntx5 , ajecg-c0nu33 , ajecg-c0nzh6 , ajecg-c0p0h0 , ajech-c6h1y9 , ajecn-a6qs62 , ajecn-a6quy7 , ajecn-a6r2c0 , ajecn-a6r491 , ajecn-a6r635 , ajecn-a6rab7 , ajecn-a6ram0 , ajecn-a6rf08 , ajecn-a6rf70 , ajecn-atg15 , ajecn-dapb , ajeds-c5jqx1 , cocim-atg15 , cocim-bst1 , cocim-j3k8a1 , cocp7-c5p0f2 , cocp7-c5p0i6 , cocp7-c5p1s3 , cocp7-c5p1u2 , cocp7-c5p2u8 , cocp7-c5p4s8 , cocp7-c5p4z1 , cocp7-c5p5s7 , cocp7-c5p129 , cocp7-c5p172 , cocp7-c5p250 , cocps-e9ctz7 , cocp7-c5pae0 , cocp7-c5pby4 , cocp7-c5pdn8 , cocp7-c5pdv9 , cocp7-c5pe69 , cocp7-c5pf68 , cocp7-c5pgk6 , cocp7-c5pid0 , cocp7-dapb , cocps-e9cz73 , cocps-e9dbi4 , cocps-e9dbu0 , cocps-e9dfh7 , uncre-c4jf72 , uncre-c4jf79 , uncre-c4ji27 , uncre-c4jj62 , uncre-c4jjs9 , uncre-c4jk71 , uncre-c4jlm9 , uncre-c4jlp5 , uncre-c4jlr7 , uncre-c4jnk2 , uncre-c4jnn3 , uncre-c4juj6 , uncre-c4jve9 , uncre-c4jvh5 , uncre-c4jw09 , uncre-c4jyw9 , uncre-c4jzs5 , uncre-dapb , ajech-c6h9r4 , uncre-c4jds5 , cocp7-c5pii3 , ajecn-a6r5v8 , cocim-j3ka92 , cocp7-c5phc6 , ajecn-a6qtc4 , ajecn-a6r145 , cocps-e9d3i4 , cocp7-c5p7x1 , cocps-e9csw0 , ajecg-c0nww6 , ajecn-kex1 , uncre-kex1 , uncre-cbpya , cocps-kex1 , ajecn-cbpya

Title : Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions - Martin-Cuadrado_2008_ISME.J_2_865
Author(s) : Martin-Cuadrado AB , Rodriguez-Valera F , Moreira D , Alba JC , Ivars-Martinez E , Henn MR , Talla E , Lopez-Garcia P
Ref : Isme J , 2 :865 , 2008
Abstract : Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite their obvious ecological importance, little is known about them. Metagenomic analyses of large genome fragments allow access to both gene content and genome structure from single individuals of these cultivation-reluctant organisms. We present the comparative analysis of 22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South Atlantic, Antarctic Polar Front, Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we analysed clones that had identical or nearly identical 16S rRNA genes and that were retrieved from distant geographical locations, that is, that defined pan-oceanic operational taxonomic units (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes involved in carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could confirm the idea that these are mixotrophic. A two-component system resembling that found in ammonia-oxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic respiratory chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high, and recombination and gene shuffling extensive within and between OTUs in Group I Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant genome-shaping forces. These observations, along with variations in GC content, led us to hypothesize that the two groups of organisms have fundamentally different lifestyles.
ESTHER : Martin-Cuadrado_2008_ISME.J_2_865
PubMedSearch : Martin-Cuadrado_2008_ISME.J_2_865
PubMedID: 18463691
Gene_locus related to this paper: 9arch-b3v596 , 9eury-b3v6i2