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Eukaryote microbial genomics

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

Page 1 of 13

  1. The protozoan pathogen Toxoplasma gondii has the unique ability to develop a chronic infection in the brain of its host by transitioning from the fast growing tachyzoite morphology to latent bradyzoite morphology...

    Authors: Andrew L. Garfoot, Gary M. Wilson, Joshua J. Coon and Laura J. Knoll

    Citation: BMC Genomics 2019 20:859

    Content type: Research article

    Published on:

  2. Enzymatic plant biomass degradation by fungi is a highly complex process and one of the leading challenges in developing a biobased economy. Some industrial fungi (e.g. Aspergillus niger) have a long history of u...

    Authors: Claire Khosravi, Joanna E. Kowalczyk, Tania Chroumpi, Evy Battaglia, Maria-Victoria Aguilar Pontes, Mao Peng, Ad Wiebenga, Vivian Ng, Anna Lipzen, Guifen He, Diane Bauer, Igor V. Grigoriev and Ronald P. de Vries

    Citation: BMC Genomics 2019 20:853

    Content type: Research article

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  3. The Metarhizium genus harbors important entomopathogenic fungi. These species have been widely explored as biological control agents, and strategies to improve the fungal virulence are under investigation. Thus, ...

    Authors: Nicolau Sbaraini, Reinaldo Bellini, Augusto Bartz Penteriche, Rafael Lucas Muniz Guedes, Ane Wichine Acosta Garcia, Alexandra Lehmkuhl Gerber, Marilene Henning Vainstein, Ana Tereza Ribeiro de Vasconcelos, Augusto Schrank and Charley Christian Staats

    Citation: BMC Genomics 2019 20:836

    Content type: Research article

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  4. Scylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health.

    Authors: Hongling Wei, Huan Wang, Lei Tang, Changkao Mu, Chunyu Ye, Lizhi Chen and Chunlin Wang

    Citation: BMC Genomics 2019 20:829

    Content type: Research article

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  5. Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and...

    Authors: Alyssa K. Burkhardt, Kevin L. Childs, Jie Wang, Marina L. Ramon and Frank N. Martin

    Citation: BMC Genomics 2019 20:802

    Content type: Research article

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  6. Sarocladium brachiariae is a newly identified endophytic fungus isolated from Brachiaria brizantha. A previous study indicated that S. brachiariae had antifungal activity; however, limited genomic information res...

    Authors: Yang Yang, Xiaobao Liu, Jimiao Cai, Yipeng Chen, Boxun Li, Zhikai Guo and Guixiu Huang

    Citation: BMC Genomics 2019 20:782

    Content type: Research article

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  7. Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mi...

    Authors: Gang Wang, Jingxian Lin, Yang Shi, Xiaoguang Chang, Yuanyuan Wang, Lin Guo, Wenhui Wang, Meijie Dou, Youjin Deng, Ray Ming and Jisen Zhang

    Citation: BMC Genomics 2019 20:765

    Content type: Research article

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  8. One fundamental question in biology is how the evolution of eukaryotic signaling networks has taken place. “Loss of function” (lof) mutants from components of the high osmolarity glycerol (HOG) signaling pathw...

    Authors: Stefan Bohnert, Luis Antelo, Christiane Grünewald, Alexander Yemelin, Karsten Andresen and Stefan Jacob

    Citation: BMC Genomics 2019 20:763

    Content type: Research article

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  9. Clubroot is an important disease of brassica crops world-wide. The causal agent, Plasmodiophora brassicae, has been present in Canada for over a century but was first identified on canola (Brassica napus) in Albe...

    Authors: Afsaneh Sedaghatkish, Bruce D. Gossen, Fengqun Yu, Davoud Torkamaneh and Mary Ruth McDonald

    Citation: BMC Genomics 2019 20:744

    Content type: Research article

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  10. Trypanosomatids of the genus Leishmania are parasites of mammals or reptiles transmitted by bloodsucking dipterans. Many species of these flagellates cause important human diseases with clinical symptoms ranging ...

    Authors: Anzhelika Butenko, Alexei Y. Kostygov, Jovana Sádlová, Yuliya Kleschenko, Tomáš Bečvář, Lucie Podešvová, Diego H. Macedo, David Žihala, Julius Lukeš, Paul A. Bates, Petr Volf, Fred R. Opperdoes and Vyacheslav Yurchenko

    Citation: BMC Genomics 2019 20:726

    Content type: Research article

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  11. Fermentation completion is a major prerequisite in many industrial processes involving the bakery yeast Saccharomyces cerevisiae. Stuck fermentations can be due to the combination of many environmental stresses. ...

    Authors: Philippe Marullo, Pascal Durrens, Emilien Peltier, Margaux Bernard, Chantal Mansour and Denis Dubourdieu

    Citation: BMC Genomics 2019 20:680

    Content type: Research article

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  12. Iron is an essential micronutrient for the growth and development of virtually all living organisms, playing a pivotal role in the proliferative capability of many bacterial pathogens. The impact that the bioa...

    Authors: Izabela Coimbra Ibraim, Mariana Teixeira Dornelles Parise, Doglas Parise, Michelle Zibetti Tadra Sfeir, Thiago Luiz de Paula Castro, Alice Rebecca Wattam, Preetam Ghosh, Debmalya Barh, Emannuel Maltempi Souza, Aristóteles Góes-Neto, Anne Cybelle Pinto Gomide and Vasco Azevedo

    Citation: BMC Genomics 2019 20:663

    Content type: Research article

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  13. Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first para...

    Authors: Daniele Armaleo, Olaf Müller, François Lutzoni, Ólafur S. Andrésson, Guillaume Blanc, Helge B. Bode, Frank R. Collart, Francesco Dal Grande, Fred Dietrich, Igor V. Grigoriev, Suzanne Joneson, Alan Kuo, Peter E. Larsen, John M. Logsdon Jr, David Lopez, Francis Martin…

    Citation: BMC Genomics 2019 20:605

    Content type: Research article

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  14. Citrus are among the most important crops in the world. However, there are many diseases that affect Citrus caused by different pathogens. Citrus also hosts many symbiotic microorganisms in a relationship that...

    Authors: Carolina Munari Rodrigues, Marco Aurélio Takita, Nicholas Vinicius Silva, Marcelo Ribeiro-Alves and Marcos Antonio Machado

    Citation: BMC Genomics 2019 20:554

    Content type: Research article

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  15. Podosphaera xanthii is the main causal agent of powdery mildew disease in cucurbits and is responsible for important yield losses in these crops worldwide. Powdery mildew fungi are obligate biotrophs. In these pa...

    Authors: Álvaro Polonio, Pedro Seoane, M. Gonzalo Claros and Alejandro Pérez-García

    Citation: BMC Genomics 2019 20:543

    Content type: Research article

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  16. Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. ...

    Authors: Matteo Soverini, Silvia Turroni, Elena Biagi, Patrizia Brigidi, Marco Candela and Simone Rampelli

    Citation: BMC Genomics 2019 20:496

    Content type: Software

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  17. The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicid...

    Authors: Christian P. Kubicek, Andrei S. Steindorff, Komal Chenthamara, Gelsomina Manganiello, Bernard Henrissat, Jian Zhang, Feng Cai, Alexey G. Kopchinskiy, Eva M. Kubicek, Alan Kuo, Riccardo Baroncelli, Sabrina Sarrocco, Eliane Ferreira Noronha, Giovanni Vannacci, Qirong Shen, Igor V. Grigoriev…

    Citation: BMC Genomics 2019 20:485

    Content type: Research article

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  18. Trichophyton rubrum is the main etiological agent of skin and nail infections worldwide. Because of its keratinolytic activity and anthropophilic nature, infection models based on the addition of protein substrat...

    Authors: Tamires Aparecida Bitencourt, Claudia Macedo, Matheus Eloy Franco, Marina Campos Rocha, Igor Sawasaki Moreli, Bruna Aline Micheloto Cantelli, Pablo Rodrigo Sanches, Rene Oliveira Beleboni, Iran Malavazi, Geraldo Aleixo Passos, Mozart Marins and Ana Lúcia Fachin

    Citation: BMC Genomics 2019 20:411

    Content type: Research article

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  19. Cryptosporidiosis is a major cause of gastrointestinal diseases in humans and other vertebrates. Previous analyses of invasion-related proteins revealed that Cryptosporidium parvum, Cryptosporidium hominis, and C...

    Authors: Zhixiao Xu, Yaqiong Guo, Dawn M. Roellig, Yaoyu Feng and Lihua Xiao

    Citation: BMC Genomics 2019 20:406

    Content type: Research article

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  20. Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclero...

    Authors: Mahsa Mousavi-Derazmahalleh, Steven Chang, Geoff Thomas, Mark Derbyshire, Phillip E. Bayer, David Edwards, Matthew N. Nelson, William Erskine, Francisco J. Lopez-Ruiz, Jon Clements and James K. Hane

    Citation: BMC Genomics 2019 20:385

    Content type: Research article

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  21. Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster ...

    Authors: Swati Sinha, Choy-Eng Nge, Chung Yan Leong, Veronica Ng, Sharon Crasta, Mohammad Alfatah, Falicia Goh, Kia-Ngee Low, Huibin Zhang, Prakash Arumugam, Alexander Lezhava, Swaine L. Chen, Yoganathan Kanagasundaram, Siew Bee Ng, Frank Eisenhaber and Birgit Eisenhaber

    Citation: BMC Genomics 2019 20:374

    Content type: Research article

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  22. Histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 9 tri-methylation (H3K9me3) are widely perceived to be opposing and often mutually exclusive chromatin modifications. However, both are neede...

    Authors: Qiaoqiao Zhu, Mukund Ramakrishnan, Jinhee Park and William J. Belden

    Citation: BMC Genomics 2019 20:350

    Content type: Research article

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  23. Chinese cordyceps, also known as Chinese caterpillar fungus (Ophiocordyceps sinensis, syn. Cordyceps sinensis), is of particular interest for its cryptic life cycle and economic and ecological importance. The lar...

    Authors: Xiao Li, Fen Wang, Qing Liu, Quanping Li, Zhengming Qian, Xiaoling Zhang, Kuan Li, Wenjia Li and Caihong Dong

    Citation: BMC Genomics 2019 20:337

    Content type: Research article

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  24. Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-ind...

    Authors: Elizabeth A. Malinich, Ken Wang, Prasun K. Mukherjee, Michael Kolomiets and Charles M. Kenerley

    Citation: BMC Genomics 2019 20:280

    Content type: Research article

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  25. The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its gen...

    Authors: Vanessa Carvalho Cayres Pamponét, Margarete Magalhães Souza, Gonçalo Santos Silva, Fabienne Micheli, Cláusio Antônio Ferreira de Melo, Sarah Gomes de Oliveira, Eduardo Almeida Costa and Ronan Xavier Corrêa

    Citation: BMC Genomics 2019 20:262

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2019 20:303

  27. We recently described a method for unbiased detection of all known human papillomaviruses (HPV) types with the potential for the determination of their variant and integration from the resulting whole genome s...

    Authors: Tengguo Li, Elizabeth R. Unger and Mangalathu S. Rajeevan

    Citation: BMC Genomics 2019 20:231

    Content type: Methodology article

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  28. Filamentous fungi have evolved to succeed in nature by efficient growth and degradation of substrates, but also due to the production of secondary metabolites including mycotoxins. For Trichoderma reesei, as a bi...

    Authors: Eva Hitzenhammer, Christoph Büschl, Michael Sulyok, Rainer Schuhmacher, Bernhard Kluger, Elisabeth Wischnitzki and Monika Schmoll

    Citation: BMC Genomics 2019 20:211

    Content type: Research article

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  29. Promoter motifs in Entamoeba histolytica were earlier analysed using microarray data with lower dynamic range of gene expression. Additionally, previous transcriptomic studies did not provide information on the n...

    Authors: Sarah Naiyer, Devinder Kaur, Jamaluddin Ahamad, Shashi Shekhar Singh, Yatendra Pratap Singh, Vivek Thakur, Alok Bhattacharya and Sudha Bhattacharya

    Citation: BMC Genomics 2019 20:206

    Content type: Research article

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  30. Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species...

    Authors: Claudio A. Valero-Jiménez, Javier Veloso, Martijn Staats and Jan A. L. van Kan

    Citation: BMC Genomics 2019 20:203

    Content type: Research article

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  31. Genomes of lethal Amanita and Galerina mushrooms have gradually become available in the past ten years; in contrast the other known amanitin-producing genus, Lepiota, is still vacant in this aspect. A fatal mushr...

    Authors: Yunjiao Lüli, Qing Cai, Zuo H. Chen, Hu Sun, Xue-Tai Zhu, Xuan Li, Zhu L. Yang and Hong Luo

    Citation: BMC Genomics 2019 20:198

    Content type: Research article

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  32. Small RNAs (sRNAs) are short non-coding RNA molecules (20–30 nt) that regulate gene expression at transcriptional or post-transcriptional levels in many eukaryotic organisms, through a mechanism known as RNA i...

    Authors: Alessandro Silvestri, Valentina Fiorilli, Laura Miozzi, Gian Paolo Accotto, Massimo Turina and Luisa Lanfranco

    Citation: BMC Genomics 2019 20:169

    Content type: Research article

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  33. Sclerotinia sclerotiorum is a broad-host range necrotrophic pathogen which is the causative agent of Sclerotinia stem rot (SSR), and a major disease of soybean (Glycine max). A time course transcriptomic analysis...

    Authors: Nathaniel M. Westrick, Ashish Ranjan, Sachin Jain, Craig R. Grau, Damon L. Smith and Mehdi Kabbage

    Citation: BMC Genomics 2019 20:157

    Content type: Research article

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  34. In wine fermentation starter cultures, the blending of non-Saccharomyces yeast with Saccharomyces cerevisiae to improve the complexity of wine has become common practice, but data regarding the impact of co-culti...

    Authors: Kirti Shekhawat, Hugh Patterton, Florian F. Bauer and Mathabatha E. Setati

    Citation: BMC Genomics 2019 20:145

    Content type: Research article

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  35. Genital C. trachomatis infection may cause pelvic inflammatory disease (PID) that can lead to tubal factor infertility (TFI). Understanding the pathogenesis of chlamydial complications including the pathophysiolo...

    Authors: Ifeyinwa Benyeogor, Tankya Simoneaux, Yuehao Wu, Stephanie Lundy, Zenas George, Khamia Ryans, Danielle McKeithen, Roshan Pais, Debra Ellerson, W. Walter Lorenz, Tolulope Omosun, Winston Thompson, Francis O. Eko, Carolyn M. Black, Uriel Blas-Machado, Joseph U. Igietseme…

    Citation: BMC Genomics 2019 20:143

    Content type: Research article

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  36. Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial ti...

    Authors: Seung-il Yoo, Hwa-Yong Lee, Kesavan Markkandan, Suyun Moon, Yong Ju Ahn, Sumin Ji, Junsu Ko, Seong-Jin Kim, Hojin Ryu and Chang Pyo Hong

    Citation: BMC Genomics 2019 20:121

    Content type: Research article

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  37. Genes involved in production of secondary metabolites (SMs) in fungi are exceptionally diverse. Even strains of the same species may exhibit differences in metabolite production, a finding that has important i...

    Authors: Rodrigo A. Olarte, Jon Menke, Ying Zhang, Shawn Sullivan, Jason C. Slot, Yinyin Huang, Jonathan P. Badalamenti, Alisha C. Quandt, Joseph W. Spatafora and Kathryn E. Bushley

    Citation: BMC Genomics 2019 20:120

    Content type: Research article

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  38. The leishmaniasis are parasitic diseases caused by protozoans of the genus Leishmania, highly divergent eukaryotes, characterized by unique biological features. To survive in both the mammalian hosts and insect v...

    Authors: Artur L. Castro Neto, Adriana N. A. L. M. Brito, Antonio M. Rezende, Franklin B. Magalhães and Osvaldo P. de Melo Neto

    Citation: BMC Genomics 2019 20:118

    Content type: Research article

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  39. Pokkah boeng is one of the most serious and devastating diseases of sugarcane and causes significant loss in cane yield and sugar content. Although carbendazim is widely used to prevent fungal diseases, the mo...

    Authors: Shiqiang Xu, Jihua Wang, Haixuan Wang, Yixue Bao, Yisha Li, Muralidharan Govindaraju, Wei Yao, Baoshan Chen and Muqing Zhang

    Citation: BMC Genomics 2019 20:115

    Content type: Research article

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  40. Nicotine-degrading microorganisms (NDMs) have recently received much attention since they can consume nicotine as carbon and nitrogen source for growth. In our previous work, we isolated an efficient nicotine-...

    Authors: Chunjuan He, Yougui Huang, Peng Liu, Jianhuan Wei, Yirui Yang, Li Xu and Min Xiao

    Citation: BMC Genomics 2019 20:86

    Content type: Research article

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  41. The orange pigmentation of the agar cultures of many Fusarium species is due to the production of carotenoids, terpenoid pigments whose synthesis is stimulated by light. The genes of the carotenoid pathway and th...

    Authors: Macarena Ruger-Herreros, Obdulia Parra-Rivero, Javier Pardo-Medina, Francisco J. Romero-Campero, M. Carmen Limón and Javier Avalos

    Citation: BMC Genomics 2019 20:67

    Content type: Research article

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  42. Many small peptides regulate eukaryotic cell biology. In fungi, some of these peptides are produced after KEX2 protease activity on proteins displaying repetitions of identical or nearly identical motifs. Foll...

    Authors: Morgane Le Marquer, Hélène San Clemente, Christophe Roux, Bruno Savelli and Nicolas Frei dit Frey

    Citation: BMC Genomics 2019 20:64

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:94

  43. Chromatin-immunoprecipitation followed by sequencing (ChIP-seq) is the method of choice for mapping genome-wide binding of chromatin-associated factors. However, broadly applicable methods for between-sample c...

    Authors: Luis A. Vale-Silva, Tovah E. Markowitz and Andreas Hochwagen

    Citation: BMC Genomics 2019 20:54

    Content type: Methodology article

    Published on:

  44. Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilizat...

    Authors: Liana Apolis, Joanna Olivas, Prakash Srinivasan, Ambuj K. Kushwaha and Sanjay A. Desai

    Citation: BMC Genomics 2019 20:47

    Content type: Research article

    Published on:

  45. Cryptosporidium parvum is an important zoonotic parasitic disease worldwide, but the molecular mechanisms of the host–parasite interaction are not fully understood. Noncoding microRNAs (miRNAs) are considered key...

    Authors: Chenrong Wang, Limin Liu, Huili Zhu, Lu Zhang, Rongjun Wang, Zhenjie Zhang, Jianying Huang, Sumei Zhang, Fuchun Jian, Changshen Ning and Longxian Zhang

    Citation: BMC Genomics 2019 20:37

    Content type: Research article

    Published on:

  46. The prevalence of azole resistance in clinical and environmental Aspergillus fumigatus isolates is rising over the past decades, but the molecular basis of the development of antifungal drug resistance is not wel...

    Authors: Margriet W. J. Hokken, Jan Zoll, Jordy P. M. Coolen, Bas J. Zwaan, Paul E. Verweij and Willem J. G. Melchers

    Citation: BMC Genomics 2019 20:28

    Content type: Research article

    Published on:

  47. Trichophyton rubrum (T. rubrum) is an important model organism of dermatophytes, which are the most common fungal pathogens worldwide. Despite the severity and prevalence of the infection caused by these pathogen...

    Authors: Lingling Wang, Xingye Xu, Jian Yang, Lihong Chen, Bo Liu, Tao Liu and Qi Jin

    Citation: BMC Genomics 2018 19:933

    Content type: Research article

    Published on:

  48. A number of Pyricularia species are known to infect different grass species. In the case of Pyricularia oryzae (syn. Magnaporthe oryzae), distinct populations are known to be adapted to a wide variety of grass ho...

    Authors: Huakun Zheng, Zhenhui Zhong, Mingyue Shi, Limei Zhang, Lianyu Lin, Yonghe Hong, Tian Fang, Yangyan Zhu, Jiayuan Guo, Limin Zhang, Jie Fang, Hui Lin, Justice Norvienyeku, Xiaofeng Chen, Guodong Lu, Hongli Hu…

    Citation: BMC Genomics 2018 19:927

    Content type: Research article

    Published on:

  49. Malaria parasites are genetically polymorphic and phenotypically plastic. In studying transcriptome variation among parasites from different infections, it is challenging to overcome potentially confounding te...

    Authors: Sarah J. Tarr, Ofelia Díaz-Ingelmo, Lindsay B. Stewart, Suzanne E. Hocking, Lee Murray, Craig W. Duffy, Thomas D. Otto, Lia Chappell, Julian C. Rayner, Gordon A. Awandare and David J. Conway

    Citation: BMC Genomics 2018 19:894

    Content type: Research article

    Published on:

  50. The eukaryotic unicellular protist Plasmodiophora brassicae is an endocellular parasite of cruciferous plants. In host cortical cells, this protist develops a unicellular structure that is termed the plasmodium. ...

    Authors: Kai Bi, Tao Chen, Zhangchao He, Zhixiao Gao, Ying Zhao, Yanping Fu, Jiasen Cheng, Jiatao Xie and Daohong Jiang

    Citation: BMC Genomics 2018 19:881

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:346

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