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. Software

    TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

    High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach...

    Daniela Beisser, Nadine Graupner, Lars Grossmann, Henning Timm, Jens Boenigk and Sven Rahmann

    BMC Genomics 2017 18:787

    Published on: 16 October 2017

  2. Methodology article

    Trypanosoma cruzi specific mRNA amplification by in vitro transcription improves parasite transcriptomics in host-parasite RNA mixtures

    Trypanosomatids are a group of protozoan parasites that includes the etiologic agents of important human illnesses as Chagas disease, sleeping sickness and leishmaniasis. These parasites have a significant dis...

    Rafael Luis Kessler, Daniela Parada Pavoni, Marco Aurelio Krieger and Christian Macagnan Probst

    BMC Genomics 2017 18:793

    Published on: 16 October 2017

  3. Research article

    Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry

    Trichoderma harzianum is used in biotechnology applications due to its ability to produce powerful enzymes for the conversion of lignocellulosic substrates into soluble sugars. Active ...

    Jaire Alves Ferreira Filho, Maria Augusta Crivelente Horta, Lilian Luzia Beloti, Clelton Aparecido dos Santos and Anete Pereira de Souza

    BMC Genomics 2017 18:779

    Published on: 12 October 2017

  4. Research article

    A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance

    Tuberculosis (TB) is a major global health problem and drug resistance compromises the efforts to control this disease. Pyrazinamide (PZA) is an important drug used in both first and second line treatment regi...

    Patricia Sheen, David Requena, Eduardo Gushiken, Robert H. Gilman, Ricardo Antiparra, Bryan Lucero, Pilar Lizárraga, Basilio Cieza, Elisa Roncal, Louis Grandjean, Arnab Pain, Ruth McNerney, Taane G. Clark, David Moore and Mirko Zimic

    BMC Genomics 2017 18:769

    Published on: 11 October 2017

  5. Research article

    Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization

    How pathogen genomes evolve to support distinct lifestyles is not well-understood. The oomycete Phytophthora infestans, the potato blight agent, is a largely biotrophic pathogen that feeds from living host cells,...

    Audrey M. V. Ah-Fong, Jolly Shrivastava and Howard S. Judelson

    BMC Genomics 2017 18:764

    Published on: 10 October 2017

  6. Research article

    Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates

    The clinical symptoms of malaria are caused by the asexual replication of Plasmodium parasites in the blood of the vertebrate host. To spread to new hosts, however, the malaria parasite must differentiate into se...

    Lee M. Yeoh, Christopher D. Goodman, Vanessa Mollard, Geoffrey I. McFadden and Stuart A. Ralph

    BMC Genomics 2017 18:734

    Published on: 18 September 2017

  7. Research article

    Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales

    Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A....

    Hariprasath Prakash, Shivaprakash Mandya Rudramurthy, Prasad S. Gandham, Anup Kumar Ghosh, Milner M. Kumar, Chandan Badapanda and Arunaloke Chakrabarti

    BMC Genomics 2017 18:736

    Published on: 18 September 2017

  8. Research article

    Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor

    Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in t...

    Y. Daguerre, E. Levati, J. Ruytinx, E. Tisserant, E. Morin, A. Kohler, B. Montanini, S. Ottonello, A. Brun, C. Veneault-Fourrey and F. Martin

    BMC Genomics 2017 18:737

    Published on: 18 September 2017

  9. Research article

    Lack of 14-3-3 proteins in Saccharomyces cerevisiae results in cell-to-cell heterogeneity in the expression of Pho4-regulated genes SPL2 and PHO84

    Ion homeostasis is an essential property of living organisms. The yeast Saccharomyces cerevisiae is an ideal model organism to investigate ion homeostasis at all levels. In this yeast genes involved in high-affin...

    Janneke H.M. Teunissen, Marjolein E. Crooijmans, Pepijn P.P. Teunisse and G. Paul H. van Heusden

    BMC Genomics 2017 18:701

    Published on: 6 September 2017

  10. Research article

    Characterization of mechanisms underlying degradation of sclerotia of Sclerotinia sclerotiorum by Aspergillus aculeatus Asp-4 using a combined qRT-PCR and proteomic approach

    The biological control agent Aspergillus aculeatus Asp-4 colonizes and degrades sclerotia of Sclerotinia sclerotiorum resulting in reduced germination and disease caused by this important plant pathogen. Molecula...

    Xiaojia Hu, Lu Qin, Daniel P. Roberts, Dilip K. Lakshman, Yangmin Gong, Jude E. Maul, Lihua Xie, Changbing Yu, Yinshui Li, Lei Hu, Xiangsheng Liao and Xing Liao

    BMC Genomics 2017 18:674

    Published on: 31 August 2017

  11. Research article

    Omics data reveal the unusual asexual-fruiting nature and secondary metabolic potentials of the medicinal fungus Cordyceps cicadae

    Ascomycete Cordyceps species have been using as valued traditional Chinese medicines. Particularly, the fruiting bodies of Cordyceps cicadae (syn. Isaria cicadae) have long been utilized for the treatment of chro...

    Yuzhen Lu, Feifei Luo, Kai Cen, Guohua Xiao, Ying Yin, Chunru Li, Zengzhi Li, Shuai Zhan, Huizhan Zhang and Chengshu Wang

    BMC Genomics 2017 18:668

    Published on: 30 August 2017

  12. Research article

    Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

    The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing er...

    Jean-Félix Dallery, Nicolas Lapalu, Antonios Zampounis, Sandrine Pigné, Isabelle Luyten, Joëlle Amselem, Alexander H. J. Wittenberg, Shiguo Zhou, Marisa V. de Queiroz, Guillaume P. Robin, Annie Auger, Matthieu Hainaut, Bernard Henrissat, Ki-Tae Kim, Yong-Hwan Lee, Olivier Lespinet…

    BMC Genomics 2017 18:667

    Published on: 29 August 2017

  13. Research article

    Genome-wide identification of novel intergenic enhancer-like elements: implications in the regulation of transcription in Plasmodium falciparum

    The molecular mechanisms of transcriptional regulation are poorly understood in Plasmodium falciparum. In addition, most of the genes in Plasmodium falciparum are transcriptionally poised and only a handful of ci...

    Suyog Ubhe, Mukul Rawat, Srikant Verma, Krishanpal Anamika and Krishanpal Karmodiya

    BMC Genomics 2017 18:656

    Published on: 23 August 2017

  14. Research article

    Characterization of the cytochrome P450 monooxygenase genes (P450ome) from the carotenogenic yeast Xanthophyllomyces dendrorhous

    The cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases involved in the oxidative metabolism of an enormous diversity of substrates. These enzymes require electrons for their act...

    Pamela Córdova, Ana-María Gonzalez, David R. Nelson, María-Soledad Gutiérrez, Marcelo Baeza, Víctor Cifuentes and Jennifer Alcaíno

    BMC Genomics 2017 18:540

    Published on: 19 July 2017

  15. Research article

    Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

    Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel produ...

    Gustavo Pagotto Borin, Camila Cristina Sanchez, Eliane Silva de Santana, Guilherme Keppe Zanini, Renato Augusto Corrêa dos Santos, Angélica de Oliveira Pontes, Aline Tieppo de Souza, Roberta Maria Menegaldo Tavares Soares Dal’Mas, Diego Mauricio Riaño-Pachón, Gustavo Henrique Goldman and Juliana Velasco de Castro Oliveira

    BMC Genomics 2017 18:501

    Published on: 30 June 2017

  16. 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

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