Publications by authors named "Hope Hundley"

12 Publications

  • Page 1 of 1

Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.

Environ Microbiol 2021 Feb 4. Epub 2021 Feb 4.

INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.

Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.
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http://dx.doi.org/10.1111/1462-2920.15423DOI Listing
February 2021

Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi.

New Phytol 2021 04 6;230(2):774-792. Epub 2021 Feb 6.

Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA.

While there has been significant progress characterizing the 'symbiotic toolkit' of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood. We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses of genome dynamics across 46 species were assessed, along with targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins (SSPs), secondary metabolites (SMs) and G-protein coupled receptors (GPCRs). Relative to other ECM fungi, including other host specialists, Suillus had highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions. Targeted analyses supported a role for SMs but not SSPs or GPCRs in Suillus host specificity. Phylogenomic-based ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches between white and red pine hosts. These results suggest that like other defining characteristics of the ECM lifestyle, host specificity is a dynamic process at the genome level. In the case of Suillus, both SMs and pathways involved in the deactivation of reactive oxygen species appear to be strongly associated with enhanced host specificity.
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http://dx.doi.org/10.1111/nph.17160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7969408PMC
April 2021

Draft Genome Sequence of the Ectomycorrhizal Ascomycete .

Microbiol Resour Announc 2019 Dec 12;8(50). Epub 2019 Dec 12.

Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.

is a pioneer ectomycorrhizal fungus with facultative saprophytic capacities. Here, we sequenced the genome of strain Sb_GMNB300, which is estimated at 51.6 Mb in size with 872 assembled contigs accounting for 12,597 predicted coding genes. This genome will be useful for comparative studies of Pezizales ectomycorrhizal symbioses.
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http://dx.doi.org/10.1128/MRA.00857-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908789PMC
December 2019

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Sci Data 2019 11 26;6(1):285. Epub 2019 Nov 26.

DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.
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http://dx.doi.org/10.1038/s41597-019-0287-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879543PMC
November 2019

Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica.

mSphere 2018 12 5;3(6). Epub 2018 Dec 5.

Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA

The yeast undergoes a morphological transition from yeast-to-hyphal growth in response to environmental conditions. A forward genetic screen was used to identify mutants that reliably remain in the yeast phase, which were then assessed by whole-genome sequencing. All the mutants identified, so named because of their colony morphology, exhibit independent loss of DNA at a repetitive locus made up of interspersed ribosomal DNA and short 10- to 40-mer telomere-like repeats. The loss of repetitive DNA is associated with downregulation of genes with stress response elements (5'-CCCCT-3') and upregulation of genes with cell cycle box (5'-ACGCG-3') motifs in their promoter region. The stress response element is bound by the transcription factor Msn2p in We confirmed that the (Yl) ortholog is required for hyphal growth and found that overexpression of Yl enables hyphal growth in strains. The cell cycle box is bound by the Mbp1p/Swi6p complex in to regulate G-to-S phase progression. We found that overexpression of either the Yl or Yl homologs decreased hyphal growth and that deletion of either Yl or Yl promotes hyphal growth in strains. A second forward genetic screen for reversion to hyphal growth was performed with the mutant to identify additional genetic factors regulating hyphal growth in Thirteen of the mutants sequenced from this screen had coding mutations in five kinases, including the histidine kinases Yl and Yl and kinases of the high-osmolarity glycerol response (HOG) mitogen-activated protein (MAP) kinase cascade Yl, Yl, and Yl Together, these results demonstrate that transitions to hyphal growth in response to stress through multiple signaling pathways. Many yeasts undergo a morphological transition from yeast-to-hyphal growth in response to environmental conditions. We used forward and reverse genetic techniques to identify genes regulating this transition in We confirmed that the transcription factor Yl is required for the transition to hyphal growth and found that signaling by the histidine kinases Yl and Yl as well as the MAP kinases of the HOG pathway (Yl, Yl, and Yl) regulates the transition to hyphal growth. These results suggest that transitions to hyphal growth in response to stress through multiple kinase pathways. Intriguingly, we found that a repetitive portion of the genome containing telomere-like and rDNA repeats may be involved in the transition to hyphal growth, suggesting a link between this region and the general stress response.
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http://dx.doi.org/10.1128/mSphere.00541-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282006PMC
December 2018

Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.

PLoS Genet 2018 04 9;14(4):e1007322. Epub 2018 Apr 9.

Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering, TU Wien, Vienna, Austria.

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.
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http://dx.doi.org/10.1371/journal.pgen.1007322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5908196PMC
April 2018

Extensive Genetic Diversity is Present within North American Switchgrass Germplasm.

Plant Genome 2018 03;11(1)

Switchgrass ( is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1.9 million high-confidence SNPs were obtained from 1169 individuals from 140 populations (67 upland, 65 lowland, 8 admixed) were used in downstream analyses of genetic diversity and population structure. Seven separate population groups were identified with moderate genetic differentiation [mean fixation index (Fst) estimate of 0.06] between the lowland and the upland populations. Ecotype-specific and population-specific SNPs were identified for use in germplasm evaluations. Relative to rice ( L.), maize ( L.), soybean [ (L.) Merr.], and Gaertn., analyses of nucleotide diversity revealed a high degree of genetic diversity (0.0135) across all individuals, consistent with the outcrossing mode of reproduction and the polyploidy of switchgrass. This study supports the hypothesis that repeated glaciation events, ploidy barriers, and restricted gene flow caused by flowering time differences have resulted in distinct gene pools across ecotypes and geographic regions. These data provide a resource to associate alleles with traits of interest for forage, restoration, and biofuel feedstock efforts in switchgrass.
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http://dx.doi.org/10.3835/plantgenome2017.06.0055DOI Listing
March 2018

Publisher correction: Young inversion with multiple linked QTLs under selection in a hybrid zone.

Nat Ecol Evol 2017 10;1(10):1585

Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.

In Fig. 5 of the version of this Article originally published, the final number on the x axes of each panel was incorrectly written as 1.5; it should have read 7.5. This has now been corrected in all versions of the Article.
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http://dx.doi.org/10.1038/s41559-017-0310-8DOI Listing
October 2017

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

Authors:
John L Bowman Takayuki Kohchi Katsuyuki T Yamato Jerry Jenkins Shengqiang Shu Kimitsune Ishizaki Shohei Yamaoka Ryuichi Nishihama Yasukazu Nakamura Frédéric Berger Catherine Adam Shiori Sugamata Aki Felix Althoff Takashi Araki Mario A Arteaga-Vazquez Sureshkumar Balasubrmanian Kerrie Barry Diane Bauer Christian R Boehm Liam Briginshaw Juan Caballero-Perez Bruno Catarino Feng Chen Shota Chiyoda Mansi Chovatia Kevin M Davies Mihails Delmans Taku Demura Tom Dierschke Liam Dolan Ana E Dorantes-Acosta D Magnus Eklund Stevie N Florent Eduardo Flores-Sandoval Asao Fujiyama Hideya Fukuzawa Bence Galik Daniel Grimanelli Jane Grimwood Ueli Grossniklaus Takahiro Hamada Jim Haseloff Alexander J Hetherington Asuka Higo Yuki Hirakawa Hope N Hundley Yoko Ikeda Keisuke Inoue Shin-Ichiro Inoue Sakiko Ishida Qidong Jia Mitsuru Kakita Takehiko Kanazawa Yosuke Kawai Tomokazu Kawashima Megan Kennedy Keita Kinose Toshinori Kinoshita Yuji Kohara Eri Koide Kenji Komatsu Sarah Kopischke Minoru Kubo Junko Kyozuka Ulf Lagercrantz Shih-Shun Lin Erika Lindquist Anna M Lipzen Chia-Wei Lu Efraín De Luna Robert A Martienssen Naoki Minamino Masaharu Mizutani Miya Mizutani Nobuyoshi Mochizuki Isabel Monte Rebecca Mosher Hideki Nagasaki Hirofumi Nakagami Satoshi Naramoto Kazuhiko Nishitani Misato Ohtani Takashi Okamoto Masaki Okumura Jeremy Phillips Bernardo Pollak Anke Reinders Moritz Rövekamp Ryosuke Sano Shinichiro Sawa Marc W Schmid Makoto Shirakawa Roberto Solano Alexander Spunde Noriyuki Suetsugu Sumio Sugano Akifumi Sugiyama Rui Sun Yutaka Suzuki Mizuki Takenaka Daisuke Takezawa Hirokazu Tomogane Masayuki Tsuzuki Takashi Ueda Masaaki Umeda John M Ward Yuichiro Watanabe Kazufumi Yazaki Ryusuke Yokoyama Yoshihiro Yoshitake Izumi Yotsui Sabine Zachgo Jeremy Schmutz

Cell 2017 Oct;171(2):287-304.e15

Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.
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http://dx.doi.org/10.1016/j.cell.2017.09.030DOI Listing
October 2017

Young inversion with multiple linked QTLs under selection in a hybrid zone.

Nat Ecol Evol 2017 Apr 3;1(5):119. Epub 2017 Apr 3.

Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA.

Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.
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http://dx.doi.org/10.1038/s41559-017-0119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607633PMC
April 2017

Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels.

Appl Microbiol Biotechnol 2017 Mar 12;101(6):2603-2618. Epub 2017 Jan 12.

Biomass Science and Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, 94551, USA.

Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called "mycodiesel," while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their CBP potential. Analysis of their genomes indicates that these endophytes have a rich reservoir of biomass-deconstructing carbohydrate-active enzymes (CAZys), which includes enzymes active on both polysaccharides and lignin, as well as terpene synthases (TPSs), enzymes that may produce fuel-like molecules, suggesting that they do indeed have CBP potential. GC-MS analyses of their VOCs when grown on four representative lignocellulosic feedstocks revealed that these endophytes produce a wide spectrum of hydrocarbons, the majority of which are monoterpenes and sesquiterpenes, including some known biofuel candidates. Analysis of their cellulase activity when grown under the same conditions revealed that these endophytes actively produce endoglucanases, exoglucanases, and β-glucosidases. The richness of CAZymes as well as terpene synthases identified in these four endophytic fungi suggests that they are great candidates to pursue for development into platform CBP organisms.
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http://dx.doi.org/10.1007/s00253-017-8091-1DOI Listing
March 2017

The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation.

Environ Microbiol 2017 03 6;19(3):1338-1354. Epub 2017 Feb 6.

Ecologie Microbienne, Université de Lyon, F-69622, Lyon, France.

To clarify the early molecular interaction between ectomycorrhizal partners, we performed a RNA-Seq study of transcriptome reprogramming of the basidiomycete Hebeloma cylindrosporum before symbiotic structure differentiation with Pinus pinaster. Mycorrhiza transcriptome was studied for comparison. By reference to asymbiotic mycelium, 47 and 46 genes were specifically upregulated over fivefold (p ≤ 0.05) upon rhizosphere colonization and root adhesion respectively. Other 45 were upregulated throughout the symbiotic interaction, from rhizosphere colonization to differentiated mycorrhizas, whereas 274 were specifically upregulated in mycorrhizas. Although exoproteome represents 5.6% of H. cylindrosporum proteome, 38.5% of the genes upregulated upon pre-infectious root colonization encoded extracellular proteins. The proportion decreased to 23.5% in mycorrhizas. At all studied time points, mycorrhiza-induced small secreted proteins (MiSSPs), representing potential effectors, were over-represented among upregulated genes. This was also the case for carbohydrate-active enzymes (CAZymes). Several CAZymes were upregulated at all studied stages of the interaction. Consistent with a role in fungal morphogenesis and symbiotic interface differentiation, CAZymes over-expressed before and upon root attachment targeted fungal and both fungal and plant polysaccharides respectively. Different hydrophobins were upregulated upon early root adhesion, in mycorrhizas or throughout interaction. The functional classification of genes upregulated only in mycorrhizas pointed to intense metabolic activity and nutritional exchanges.
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http://dx.doi.org/10.1111/1462-2920.13670DOI Listing
March 2017