Eukaryote microbial genomics

Section edited by Gustavo Goldman

This section covers the structure and function of genomes of single-celled parasites, yeasts, fungi and viruses.

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  1. Methodology article

    Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

    The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigene...

    Olivier Arnaiz, Erwin Van Dijk, Mireille Bétermier, Maoussi Lhuillier-Akakpo, Augustin de Vanssay, Sandra Duharcourt, Erika Sallet, Jérôme Gouzy and Linda Sperling

    BMC Genomics 2017 18:483

    Published on: 26 June 2017

  2. Research article

    Regulation of the reserve carbohydrate metabolism by alkaline pH and calcium in Neurospora crassa reveals a possible cross-regulation of both signaling pathways

    Glycogen and trehalose are storage carbohydrates and their levels in microorganisms vary according to environmental conditions. In Neurospora crassa, alkaline pH stress highly influences glycogen levels, and in S...

    Stela Virgilio, Fernanda Barbosa Cupertino, Daniela Luz Ambrosio and Maria Célia Bertolini

    BMC Genomics 2017 18:457

    Published on: 9 June 2017

  3. Research article

    Integrating transcriptomics and metabolomics for the analysis of the aroma profiles of Saccharomyces cerevisiae strains from diverse origins

    During must fermentation thousands of volatile aroma compounds are formed, with higher alcohols, acetate esters and ethyl esters being the main aromatic compounds contributing to floral and fruity aromas. The ...

    Inês Mendes, Isabelle Sanchez, Ricardo Franco-Duarte, Carole Camarasa, Dorit Schuller, Sylvie Dequin and Maria João Sousa

    BMC Genomics 2017 18:455

    Published on: 8 June 2017

  4. Research article

    Identification of candidate transmission-blocking antigen genes in Theileria annulata and related vector-borne apicomplexan parasites

    Vector-borne apicomplexan parasites are a major cause of mortality and morbidity to humans and livestock globally. The most important disease syndromes caused by these parasites are malaria, babesiosis and the...

    Laetitia Lempereur, Stephen D. Larcombe, Zeeshan Durrani, Tulin Karagenc, Huseyin Bilgin Bilgic, Serkan Bakirci, Selin Hacilarlioglu, Jane Kinnaird, Joanne Thompson, William Weir and Brian Shiels

    BMC Genomics 2017 18:438

    Published on: 5 June 2017

  5. Research article

    Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses

    Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several dif...

    Selin Özkan, Irina Mohorianu, Ping Xu, Tamas Dalmay and Robert H. A. Coutts

    BMC Genomics 2017 18:416

    Published on: 30 May 2017

  6. Research article

    The link between adjacent codon pairs and mRNA stability

    Evidence in diverse organisms suggests that codon optimality is a major determinant of mRNA translation and degradation. Codon optimality is thought to act by modulating the efficiency of ribosome elongation. In

    Yuriko Harigaya and Roy Parker

    BMC Genomics 2017 18:364

    Published on: 10 May 2017

  7. Research article

    Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

    Biotrophic fungal plant pathogens cause billions of dollars in losses to North American crops annually. The model for functional investigation of these fungi is Ustilago maydis. Its 20.5 Mb annotated genome seque...

    Michael E. Donaldson, Lauren A. Ostrowski, Kristi M. Goulet and Barry J. Saville

    BMC Genomics 2017 18:340

    Published on: 2 May 2017

  8. Research Article

    Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

    Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and...

    Cecilia H. Deng, Kim M. Plummer, Darcy A. B. Jones, Carl H. Mesarich, Jason Shiller, Adam P. Taranto, Andrew J. Robinson, Patrick Kastner, Nathan E. Hall, Matthew D. Templeton and Joanna K. Bowen

    BMC Genomics 2017 18:339

    Published on: 2 May 2017

  9. Research article

    Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements

    DNA elimination is developmentally programmed in a wide variety of eukaryotes, including unicellular ciliates, and leads to the generation of distinct germline and somatic genomes. The ciliate Paramecium tetraure...

    Frédéric Guérin, Olivier Arnaiz, Nicole Boggetto, Cyril Denby Wilkes, Eric Meyer, Linda Sperling and Sandra Duharcourt

    BMC Genomics 2017 18:327

    Published on: 26 April 2017

  10. Research article

    Genomic characterization of two novel pathogenic avipoxviruses isolated from pacific shearwaters (Ardenna spp.)

    Over the past 20 years, many marine seabird populations have been gradually declining and the factors driving this ongoing deterioration are not always well understood. Avipoxvirus infections have been found i...

    Subir Sarker, Shubhagata Das, Jennifer L. Lavers, Ian Hutton, Karla Helbig, Jacob Imbery, Chris Upton and Shane R. Raidal

    BMC Genomics 2017 18:298

    Published on: 13 April 2017

  11. Research Article

    sRNAs as possible regulators of retrotransposon activity in Cryptococcus gattii VGII

    The absence of Argonaute genes in the fungal pathogen Cryptococcus gattii R265 and other VGII strains indicates that yeasts of this genotype cannot have a functional RNAi pathway, an evolutionarily conserved gene...

    Patrícia Aline Gröhs Ferrareze, Rodrigo Silva Araujo Streit, Francine Melise dos Santos, Augusto Schrank, Livia Kmetzsch, Marilene Henning Vainstein and Charley Christian Staats

    BMC Genomics 2017 18:294

    Published on: 12 April 2017

  12. Research article

    Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale

    The economically important Ergot fungus Claviceps purpurea is an interesting biotrophic model system because of its strict organ specificity (grass ovaries) and the lack of any detectable plant defense reactions....

    Birgitt Oeser, Sabine Kind, Selma Schurack, Thomas Schmutzer, Paul Tudzynski and Janine Hinsch

    BMC Genomics 2017 18:273

    Published on: 4 April 2017

  13. Research article

    Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs

    Cephalosporins and penicillins are the most frequently used β-lactam antibiotics for the treatment of human infections worldwide. The main industrial producers of these antibiotics are Acremonium chrysogenum and

    Dominik Terfehr, Tim A. Dahlmann and Ulrich Kück

    BMC Genomics 2017 18:272

    Published on: 31 March 2017

  14. Research article

    Highly diverse population of Picornaviridae and other members of the Picornavirales, in Cameroonian fruit bats

    The order Picornavirales represents a diverse group of positive-stranded RNA viruses with small non-enveloped icosahedral virions. Recently, bats have been identified as an important reservoir of several highly p...

    Claude Kwe Yinda, Roland Zell, Ward Deboutte, Mark Zeller, Nádia Conceição-Neto, Elisabeth Heylen, Piet Maes, Nick J. Knowles, Stephen Mbigha Ghogomu, Marc Van Ranst and Jelle Matthijnssens

    BMC Genomics 2017 18:249

    Published on: 23 March 2017

  15. Research article

    Landscape of genomic diversity and host adaptation in Fusarium graminearum

    Fusarium graminearum is one of the main causal agents of the Fusarium Head Blight, a worldwide disease affecting cereal cultures, whose presence can lead to contaminated grains with ch...

    Benoit Laurent, Magalie Moinard, Cathy Spataro, Nadia Ponts, Christian Barreau and Marie Foulongne-Oriol

    BMC Genomics 2017 18:203

    Published on: 23 February 2017

  16. Research article

    RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development

    The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathoge...

    Audrey M. V. Ah-Fong, Kyoung Su Kim and Howard S. Judelson

    BMC Genomics 2017 18:198

    Published on: 23 February 2017

  17. Research article

    Comparative analysis of the mitochondrial genomes of Colletotrichum gloeosporioides sensu lato: insights into the evolution of a fungal species complex interacting with diverse plants

    The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show...

    Xiaofei Liang, Xianglin Tian, Wenkui Liu, Tingyu Wei, Wei Wang, Qiuyue Dong, Bo Wang, Yanan Meng, Rong Zhang, Mark L. Gleason and Guangyu Sun

    BMC Genomics 2017 18:171

    Published on: 15 February 2017

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