Publications by authors named "Mansi Chovatia"

24 Publications

  • Page 1 of 1

Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi.

Sci Rep 2021 Feb 5;11(1):3217. Epub 2021 Feb 5.

Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Oregon, USA.

The zoosporic obligate endoparasites, Olpidium, hold a pivotal position to the reconstruction of the flagellum loss in fungi, one of the key morphological transitions associated with the colonization of land by the early fungi. We generated genome and transcriptome data from non-axenic zoospores of Olpidium bornovanus and used a metagenome approach to extract phylogenetically informative fungal markers. Our phylogenetic reconstruction strongly supported Olpidium as the closest zoosporic relative of the non-flagellated terrestrial fungi. Super-alignment analyses resolved Olpidium as sister to the non-flagellated terrestrial fungi, whereas a super-tree approach recovered different placements of Olpidium, but without strong support. Further investigations detected little conflicting signal among the sampled markers but revealed a potential polytomy in early fungal evolution associated with the branching order among Olpidium, Zoopagomycota and Mucoromycota. The branches defining the evolutionary relationships of these lineages were characterized by short branch lengths and low phylogenetic content and received equivocal support for alternative phylogenetic hypotheses from individual markers. These nodes were marked by important morphological innovations, including the transition to hyphal growth and the loss of flagellum, which enabled early fungi to explore new niches and resulted in rapid and temporally concurrent Precambrian diversifications of the ancestors of several phyla of fungi.
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http://dx.doi.org/10.1038/s41598-021-82607-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7865070PMC
February 2021

A comparative genomics study of 23 Aspergillus species from section Flavi.

Nat Commun 2020 02 27;11(1):1106. Epub 2020 Feb 27.

Department of Biotechnology and Bioengineering, Technical University of Denmark, Søltoft Plads 223, 2800, Kongens Lyngby, Denmark.

Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.
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http://dx.doi.org/10.1038/s41467-019-14051-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7046712PMC
February 2020

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

Engineered Root Bacteria Release Plant-Available Phosphate from Phytate.

Appl Environ Microbiol 2019 09 29;85(18). Epub 2019 Aug 29.

Department of Energy Joint Genome Institute, Walnut Creek, California, USA

Microorganisms that release plant-available phosphate from natural soil phosphate stores may serve as biological alternatives to costly and environmentally damaging phosphate fertilizers. To explore this possibility, we engineered a collection of root bacteria to release plant-available orthophosphate from phytate, an abundant phosphate source in many soils. We identified 82 phylogenetically diverse phytase genes, refactored their sequences for optimal expression in , and then synthesized and engineered them into the genomes of three root-colonizing bacteria. Liquid culture assays revealed 41 engineered strains with high levels of phytate hydrolysis. Among these, we identified 12 strains across three bacterial hosts that confer a growth advantage on the model plant when phytate is the sole phosphate source. These data demonstrate that DNA synthesis approaches can be used to generate plant-associated strains with novel phosphate-solubilizing capabilities. Phosphate fertilizers are essential for high-yield agriculture yet are costly and environmentally damaging. Microbes that release soluble phosphate from naturally occurring sources in the soil are appealing, as they may reduce the need for such fertilizers. In this study, we used synthetic biology approaches to create a collection of engineered root-associated microbes with the ability to release phosphate from phytate. We demonstrate that these strains improve plant growth under phosphorus-limited conditions. This represents a first step in the development of phosphate-mining bacteria for future use in crop systems.
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http://dx.doi.org/10.1128/AEM.01210-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715853PMC
September 2019

Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae.

New Phytol 2019 10 1;224(2):902-915. Epub 2019 Aug 1.

Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, HAS, Szeged, 6726, Hungary.

Agaricomycetes are fruiting body-forming fungi that produce some of the most efficient enzyme systems to degrade wood. Despite decades-long interest in their biology, the evolution and functional diversity of both wood-decay and fruiting body formation are incompletely known. We performed comparative genomic and transcriptomic analyses of wood-decay and fruiting body development in Auriculariopsis ampla and Schizophyllum commune (Schizophyllaceae), species with secondarily simplified morphologies, an enigmatic wood-decay strategy and weak pathogenicity to woody plants. The plant cell wall-degrading enzyme repertoires of Schizophyllaceae are transitional between those of white rot species and less efficient wood-degraders such as brown rot or mycorrhizal fungi. Rich repertoires of suberinase and tannase genes were found in both species, with tannases restricted to Agaricomycetes that preferentially colonize bark-covered wood, suggesting potential complementation of their weaker wood-decaying abilities and adaptations to wood colonization through the bark. Fruiting body transcriptomes revealed a high rate of divergence in developmental gene expression, but also several genes with conserved expression patterns, including novel transcription factors and small-secreted proteins, some of the latter which might represent fruiting body effectors. Taken together, our analyses highlighted novel aspects of wood-decay and fruiting body development in an important family of mushroom-forming fungi.
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http://dx.doi.org/10.1111/nph.16032DOI Listing
October 2019

Megaphylogeny resolves global patterns of mushroom evolution.

Nat Ecol Evol 2019 04 18;3(4):668-678. Epub 2019 Mar 18.

Synthetic and Systems Biology Unit, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.
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http://dx.doi.org/10.1038/s41559-019-0834-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443077PMC
April 2019

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

Genome Sequence of sp. Strain MCTG156(2b) Isolated from a Phytoplankton Net Trawl on the Scottish West Coast.

Genome Announc 2017 Aug 31;5(35). Epub 2017 Aug 31.

DOE Joint Genome Institute, Walnut Creek, California, USA.

sp. strain MCTG156(2b) was isolated from a phytoplankton net sample collected on the west coast of Scotland and was selected based on its ability to degrade polycyclic aromatic hydrocarbons. Here, we present the genome sequence of this strain, which is 5,113,782 bp, with 5,142 genes and an average G+C content of 60.7%.
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http://dx.doi.org/10.1128/genomeA.00837-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578838PMC
August 2017

Genome Sequence of sp. Strain MCTG156(1a), Isolated from a Scottish Coastal Phytoplankton Net Sample.

Genome Announc 2017 Aug 10;5(32). Epub 2017 Aug 10.

DOE Joint Genome Institute, Walnut Creek, California, USA.

sp. strain MCTG156(1a) was isolated from a phytoplankton net sample collected on the west coast of Scotland and selected based on its ability to degrade polycyclic aromatic hydrocarbons. Here, we present the genome sequence of this strain, which comprises 3,881,122 bp with 3,949 genes and an average G+C content of 62.7%.
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http://dx.doi.org/10.1128/genomeA.00796-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552998PMC
August 2017

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

PLoS One 2017 18;12(5):e0177189. Epub 2017 May 18.

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America.

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177189PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436645PMC
September 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

Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum.

Genome Announc 2016 Sep 8;4(5). Epub 2016 Sep 8.

DOE Joint Genome Institute, Walnut Creek, California, USA.

Marinobacter sp. strain MCTG268 was isolated from the cosmopolitan marine diatom Skeletonema costatum and can degrade oil hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 4,449,396 bp with 4,157 genes and an average G+C content of 57.0%.
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http://dx.doi.org/10.1128/genomeA.00937-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5017223PMC
September 2016

Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

Genome Announc 2016 Aug 4;4(4). Epub 2016 Aug 4.

DOE Joint Genome Institute, Walnut Creek, California, USA.

Arenibacter algicola strain TG409 was isolated from Skeletonema costatum and exhibits the ability to utilize polycyclic aromatic hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 5,550,230 bp with 4,722 genes and an average G+C content of 39.7%.
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http://dx.doi.org/10.1128/genomeA.00765-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4974315PMC
August 2016

Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis.

PLoS One 2016 25;11(3):e0151883. Epub 2016 Mar 25.

Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America.

Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3) that were isolated from blades of Porphyra umbilicalis (P.um.1). These three Operational Taxonomic Units (OTUs) belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators) and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes) or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases) that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase) and stress responses (e.g., efflux pump, amino acid transporter). Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151883PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807772PMC
August 2016

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

Nature 2016 Feb 27;530(7590):331-5. Epub 2016 Jan 27.

Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium.

Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.
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http://dx.doi.org/10.1038/nature16548DOI Listing
February 2016

Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems.

mBio 2015 Jul 21;6(4):e00918. Epub 2015 Jul 21.

Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany

Unlabelled: Microbial fermentation of agro-industrial waste holds great potential for reducing the environmental impact associated with the production of lipids for industrial purposes from plant biomass. However, the chemical complexity of many residues currently prevents efficient conversion into lipids, creating a high demand for strains with the ability to utilize all energy-rich components of agricultural residues. Here, we present results of genome and transcriptome analyses of Trichosporon oleaginosus. This oil-accumulating yeast is able to grow on a wide variety of substrates, including pentoses and N-acetylglucosamine, making it an interesting candidate for biotechnological applications. Transcriptomics shows specific changes in gene expression patterns under lipid-accumulating conditions. Furthermore, gene content and expression analyses indicate that T. oleaginosus is well-adapted for the utilization of chitin-rich biomass. We also focused on the T. oleaginosus mating type, because this species is a member of the Tremellomycetes, a group that has been intensively analyzed as a model for the evolution of sexual development, the best-studied member being Cryptococcus neoformans. The structure of the T. oleaginosus mating-type regions differs significantly from that of other Tremellomycetes and reveals a new evolutionary trajectory paradigm. Comparative analysis shows that recruitment of developmental genes to the ancestral tetrapolar mating-type loci occurred independently in the Trichosporon and Cryptococcus lineages, supporting the hypothesis of a trend toward larger mating-type regions in fungi.

Importance: Finite fossil fuel resources pose sustainability challenges to society and industry. Microbial oils are a sustainable feedstock for biofuel and chemical production that does not compete with food production. We describe genome and transcriptome analyses of the oleaginous yeast Trichosporon oleaginosus, which can accumulate up to 70% of its dry weight as lipids. In contrast to conventional yeasts, this organism not only shows an absence of diauxic effect while fermenting hexoses and pentoses but also effectively utilizes xylose and N-acetylglucosamine, which are building blocks of lignocellulose and chitin, respectively. Transcriptome analysis revealed metabolic networks that govern conversion of xylose or N-acetylglucosamine as well as lipid accumulation. These data form the basis for a targeted strain optimization strategy. Furthermore, analysis of the mating type of T. oleaginosus supports the hypothesis of a trend toward larger mating-type regions in fungi, similar to the evolution of sex chromosomes in animals and plants.
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http://dx.doi.org/10.1128/mBio.00918-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513080PMC
July 2015

Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium.

Genome Announc 2015 Jul 16;3(4). Epub 2015 Jul 16.

DOE Joint Genome Institute, Walnut Creek, California, USA.

Halomonas sp. strain MCTG39a was isolated from coastal sea surface water based on its ability to utilize n-hexadecane. During growth in marine medium the strain produces an amphiphilic exopolymeric substance (EPS) amended with glucose, which emulsifies a variety of oil hydrocarbon substrates. Here, we present the genome sequence of this strain, which is 4,979,193 bp with 4,614 genes and an average G+C content of 55.0%.
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http://dx.doi.org/10.1128/genomeA.00793-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4505133PMC
July 2015

Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

Genome Announc 2015 Jun 18;3(3). Epub 2015 Jun 18.

DOE Joint Genome Institute, Walnut Creek, California, USA.

Porticoccus hydrocarbonoclasticus strain MCTG13d is a recently discovered bacterium that is associated with marine eukaryotic phytoplankton and that almost exclusively utilizes polycyclic aromatic hydrocarbons (PAHs) as the sole source of carbon and energy. Here, we present the genome sequence of this strain, which is 2,474,654 bp with 2,385 genes and has an average G+C content of 53.1%.
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http://dx.doi.org/10.1128/genomeA.00672-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472908PMC
June 2015

Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses.

PLoS Pathog 2015 Mar 30;11(3):e1004809. Epub 2015 Mar 30.

Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, California, United States of America; Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

Plant plasma membrane localized pattern recognition receptors (PRRs) detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo)-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24), two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components.
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http://dx.doi.org/10.1371/journal.ppat.1004809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379099PMC
March 2015

Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

Genome Announc 2015 Mar 26;3(2). Epub 2015 Mar 26.

DOE Joint Genome Institute, Walnut Creek, California, USA.

Polycyclovorans algicola strain TG408 is a recently discovered bacterium associated with marine eukaryotic phytoplankton and exhibits the ability to utilize polycyclic aromatic hydrocarbons (PAHs) almost exclusively as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 3,653,213 bp, with 3,477 genes and an average G+C content of 63.8%.
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http://dx.doi.org/10.1128/genomeA.00207-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384147PMC
March 2015

A reference genome for common bean and genome-wide analysis of dual domestications.

Nat Genet 2014 Jul 8;46(7):707-13. Epub 2014 Jun 8.

Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
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http://dx.doi.org/10.1038/ng.3008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048698PMC
July 2014

Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.

PLoS One 2013 4;8(9):e73827. Epub 2013 Sep 4.

Intercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

The Asian longhorned beetle (Anoplophoraglabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A. glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A. glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A. glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases), 36 families of glycoside hydrolases (such as cellulases and xylanases), and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community could serve as a reservoir of novel enzymes to enhance industrial cellulosic biofuels production or targets for novel control methods for this invasive and highly destructive insect.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073827PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762729PMC
April 2014

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883).

Stand Genomic Sci 2009 Nov 22;1(3):254-61. Epub 2009 Nov 22.

Thermanaerovibrio acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 is the type species of the genus Thermanaerovibrio and is of phylogenetic interest because of the very isolated location of the novel phylum Synergistetes. T. acidaminovorans Su883(T) is a Gram-negative, motile, non-spore-forming bacterium isolated from an anaerobic reactor of a sugar refinery in The Netherlands. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from a member of the phylum Synergistetes. The 1,848,474 bp long single replicon genome with its 1765 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.40645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035242PMC
November 2009