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Eukaryote microbial genomics

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

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  1. 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...

    Authors: 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

    Citation: BMC Genomics 2017 18:249

    Content type: Research article

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  2. 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...

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

    Citation: BMC Genomics 2017 18:198

    Content type: Research article

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  3. Among twenty amino acids, methionine has a special role as it is coded by the translation initiation codon and methionyl-tRNAi (Met-tRNAi) is required for the assembly of the translation initiation complex. Th...

    Authors: Ke Zou, Qi Ouyang, Hao Li and Jiashun Zheng

    Citation: BMC Genomics 2017 18:189

    Content type: Research Article

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  4. 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...

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

    Citation: BMC Genomics 2017 18:171

    Content type: Research article

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  5. Ochromonas is a genus of mixotrophic chrysophytes that is found ubiquitously in many aquatic environments. Species in this genus can be important consumers of bacteria but vary in thei...

    Authors: Alle A. Y. Lie, Zhenfeng Liu, Ramon Terrado, Avery O. Tatters, Karla B. Heidelberg and David A. Caron

    Citation: BMC Genomics 2017 18:163

    Content type: Research article

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  6. Pisolithus microcarpus (Cooke & Massee) G. Cunn is a gasteromycete that produces closed basidiocarps in symbiosis with eucalypts and acacias. The fungus produces a complex basidiocarp ...

    Authors: Maíra de Freitas Pereira, André Narvaes da Rocha Campos, Thalita Cardoso Anastacio, Emmanuelle Morin, Sérgio Hermínio Brommonschenkel, Francis Martin, Annegret Kohler and Maurício Dutra Costa

    Citation: BMC Genomics 2017 18:157

    Content type: Research article

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  7. Nucleosome plays a role in transcriptional regulation through occluding the binding of proteins to DNA sites. Nucleosome occupancy varies among different cell types. Identification of such variation will help ...

    Authors: Lingjie Liu, Jianming Xie, Xiao Sun, Kun Luo, Zhaohui Steve Qin and Hongde Liu

    Citation: BMC Genomics 2017 18:135

    Content type: Methodology article

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  8. Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vacci...

    Authors: Shen-Bo Chen, Yue Wang, Kokouvi Kassegne, Bin Xu, Hai-Mo Shen and Jun-Hu Chen

    Citation: BMC Genomics 2017 18:131

    Content type: Research article

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  9. Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied.

    Authors: Lirong Jin, Guanglin Li, Dazhao Yu, Wei Huang, Chao Cheng, Shengjie Liao, Qijia Wu and Yi Zhang

    Citation: BMC Genomics 2017 18:130

    Content type: Research article

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  10. Quiescent cells have a low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we defined the genome-wide profiles of three species of histone methylation associated ...

    Authors: Conor P. Young, Cory Hillyer, Karsten Hokamp, Darren J. Fitzpatrick, Nikifor K. Konstantinov, Jacqueline S. Welty, Scott A. Ness, Margaret Werner-Washburne, Alastair B. Fleming and Mary Ann Osley

    Citation: BMC Genomics 2017 18:107

    Content type: Research article

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  11. The food spoilage yeast species Zygosaccharomyces bailii exhibits an extraordinary capacity to tolerate weak acids, in particular acetic acid. In Saccharomyces cerevisiae, the transcription factor Haa1 (ScHaa1) i...

    Authors: Margarida Palma, Paulo Jorge Dias, Filipa de Canaveira Roque, Laura Luzia, Joana Fernandes Guerreiro and Isabel Sá-Correia

    Citation: BMC Genomics 2017 18:75

    Content type: Research Article

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  12. Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species a...

    Authors: E. A. S. Buiate, K. V. Xavier, N. Moore, M. F. Torres, M. L. Farman, C. L. Schardl and L. J. Vaillancourt

    Citation: BMC Genomics 2017 18:67

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2018 19:686

  13. The cyclic peptide toxins of Amanita mushrooms, such as α-amanitin and phalloidin, are encoded by the “MSDIN” gene family and ribosomally biosynthesized. Based on partial genome sequence and PCR analysis, some me...

    Authors: Jane A. Pulman, Kevin L. Childs, R. Michael Sgambelluri and Jonathan D. Walton

    Citation: BMC Genomics 2016 17:1038

    Content type: Research article

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  14. The Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely rel...

    Authors: Sean Walkowiak, Owen Rowland, Nicolas Rodrigue and Rajagopal Subramaniam

    Citation: BMC Genomics 2016 17:1014

    Content type: Research article

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  15. The switch from photosynthetic or predatory to parasitic life strategies by apicomplexans is accompanied with a reductive evolution of genomes and losses of metabolic capabilities. Cryptosporidium is an extreme e...

    Authors: Shiyou Liu, Dawn M. Roellig, Yaqiong Guo, Na Li, Michael A. Frace, Kevin Tang, Longxian Zhang, Yaoyu Feng and Lihua Xiao

    Citation: BMC Genomics 2016 17:1006

    Content type: Research article

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  16. Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in ...

    Authors: Claudio A. Valero-Jiménez, Luigi Faino, Daphne Spring in’t Veld, Sandra Smit, Bas J. Zwaan and Jan A. L. van Kan

    Citation: BMC Genomics 2016 17:986

    Content type: Research article

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  17. The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but se...

    Authors: Daniel Penselin, Martin Münsterkötter, Susanne Kirsten, Marius Felder, Stefan Taudien, Matthias Platzer, Kevin Ashelford, Konrad H. Paskiewicz, Richard J. Harrison, David J. Hughes, Thomas Wolf, Ekaterina Shelest, Jenny Graap, Jan Hoffmann, Claudia Wenzel, Nadine Wöltje…

    Citation: BMC Genomics 2016 17:953

    Content type: Research article

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  18. Yeast-to-hypha transition is a major morphological change in fungi. Molecular regulators and pathways that are involved in this process have been extensively studied in model species, including Saccharomyces cere...

    Authors: M. Nigg and L. Bernier

    Citation: BMC Genomics 2016 17:920

    Content type: Research article

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  19. The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Pha...

    Authors: Nicolás Bellora, Martín Moliné, Márcia David-Palma, Marco A. Coelho, Chris Todd Hittinger, José P. Sampaio, Paula Gonçalves and Diego Libkind

    Citation: BMC Genomics 2016 17:901

    Content type: Research article

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  20. Babesia microti is an emerging tick-borne apicomplexan parasite with increasing geographic range and incidence in the United States. The rapid expansion of B. microti into its current ...

    Authors: Giovanna Carpi, Katharine S. Walter, Choukri Ben Mamoun, Peter J. Krause, Andrew Kitchen, Timothy J. Lepore, Ankit Dwivedi, Emmanuel Cornillot, Adalgisa Caccone and Maria A. Diuk-Wasser

    Citation: BMC Genomics 2016 17:888

    Content type: Research article

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  21. Pathogenic members of the Fusarium oxysporum species complex are responsible for vascular wilt disease on many important crops including legumes, where they can be one of the most destructive disease causing necr...

    Authors: Louise F. Thatcher, Angela H. Williams, Gagan Garg, Sally-Anne G. Buck and Karam B. Singh

    Citation: BMC Genomics 2016 17:860

    Content type: Research article

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  22. Malaria parasites of the genus Plasmodium possess large hyper-variable families of antigen-encoding genes. These are often variantly-expressed and are major virulence factors for immune evasion and the maintenanc...

    Authors: Adam Stanton, Lynne M. Harris, Gemma Graham and Catherine J. Merrick

    Citation: BMC Genomics 2016 17:859

    Content type: Research Article

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  23. Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been exte...

    Authors: Michele Perazzolli, Noemí Herrero, Lieven Sterck, Luisa Lenzi, Alberto Pellegrini, Gerardo Puopolo, Yves Van de Peer and Ilaria Pertot

    Citation: BMC Genomics 2016 17:838

    Content type: Research article

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  24. African trypanosomes cause lethal diseases in humans and animals and escape host immune attack by switching the expression of Variant Surface Glycoprotein (VSG) genes. The expressed VSGs are located at the ends o...

    Authors: Sebastian Hutchinson, Lucy Glover and David Horn

    Citation: BMC Genomics 2016 17:806

    Content type: Research article

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  25. The ascomycetous family Chaetomiaceae (class Sordariomycetes) includes numerous soilborn, saprophytic, endophytic and pathogenic fungi which can adapt to various growth conditions and living niches by providing a...

    Authors: Marcel Zámocký, Hakim Tafer, Katarína Chovanová, Ksenija Lopandic, Anna Kamlárová and Christian Obinger

    Citation: BMC Genomics 2016 17:763

    Content type: Research article

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  26. Brucellosis is a bacterial disease caused by Brucella infection. In the late fifties, Brucella suis vaccine strain S2 with reduced virulence was obtained by serial transfer of a virulent B. suis biovar 1 strain i...

    Authors: Dong-dong Di, Hai Jiang, Li-li Tian, Jing-li Kang, Wen Zhang, Xin-ping Yi, Feng Ye, Qi Zhong, Bo Ni, You-yu He, Lin Xia, Yao Yu, Bu-yun Cui, Xiang Mao and Wei-xing Fan

    Citation: BMC Genomics 2016 17:741

    Content type: Research article

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  27. The protozoan parasite Trypanosoma cruzi, causative agent of Chagas disease, depends upon a cell surface-expressed trans-sialidase (ts) to avoid activation of complement-mediated lysis and to enhance intracellula...

    Authors: D. Brent Weatherly, Duo Peng and Rick L. Tarleton

    Citation: BMC Genomics 2016 17:729

    Content type: Research article

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  28. Copy number variants (CNVs) are a class of structural variants (SVs) and are defined as fragments of DNA that are present at variable copy number in comparison with a reference genome. Recent advances in bioin...

    Authors: Jacob L. Steenwyk, John S. Soghigian, John R. Perfect and John G. Gibbons

    Citation: BMC Genomics 2016 17:700

    Content type: Research article

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  29. Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fu...

    Authors: Adriaan Vanheule, Kris Audenaert, Sven Warris, Henri van de Geest, Elio Schijlen, Monica Höfte, Sarah De Saeger, Geert Haesaert, Cees Waalwijk and Theo van der Lee

    Citation: BMC Genomics 2016 17:670

    Content type: Research article

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  30. Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding ...

    Authors: Claire Anderson, Muhammad Adil Khan, Ann-Maree Catanzariti, Cameron A. Jack, Adnane Nemri, Gregory J. Lawrence, Narayana M. Upadhyaya, Adrienne R. Hardham, Jeffrey G. Ellis, Peter N. Dodds and David A. Jones

    Citation: BMC Genomics 2016 17:667

    Content type: Research article

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  31. Exposure of the budding Saccharomyces cerevisiae to an alkaline environment produces a robust transcriptional response involving hundreds of genes. Part of this response is triggered by an almost immediate burst ...

    Authors: Alicia Roque, Silvia Petrezsélyová, Albert Serra-Cardona and Joaquín Ariño

    Citation: BMC Genomics 2016 17:662

    Content type: Research article

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  32. Understanding the regulation mechanism of var gene expression is crucial for explaining antigenic variation in Plasmodium falciparum. Recent work observed that while all var genes produce transcripts, only a few

    Authors: Chengqi Wang, Swamy R. Adapa, Justin Gibbons, Stephen Sutton and Rays H. Y. Jiang

    Citation: BMC Genomics 2016 17:652

    Content type: Research article

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  33. Epstein-Barr virus (EBV) establishes lifelong infections in its human host. The virus is associated with a broad range of malignancies of lymphoid and epithelial origin, including Burkitt’s lymphoma, post-tran...

    Authors: Marjolein J. G. Hooykaas, Elisabeth Kruse, Emmanuel J. H. J. Wiertz and Robert Jan Lebbink

    Citation: BMC Genomics 2016 17:644

    Content type: Research article

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  34. Aspergillus westerdijkiae produces ochratoxin A (OTA) in Aspergillus section Circumdati. It is responsible for the contamination of agricultural crops, fruits, and food commodities, as...

    Authors: Xiaolong Han, Alolika Chakrabortti, Jindong Zhu, Zhao-Xun Liang and Jinming Li

    Citation: BMC Genomics 2016 17:633

    Content type: Research article

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  35. The white-rot fungus Phlebia sp. MG-60 shows valuable properties such as high ethanol yield from several lignocellulosic materials, although white-rot fungi commonly degrade woody components to CO2 and H2O. In or...

    Authors: Jianqiao Wang, Tomohiro Suzuki, Hideo Dohra, Shoko Takigami, Hiroko Kako, Ayumi Soga, Ichiro Kamei, Toshio Mori, Hirokazu Kawagishi and Hirofumi Hirai

    Citation: BMC Genomics 2016 17:616

    Content type: Research article

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  36. Lasiodiplodia theobromae is a fungus of the Botryosphaeriaceae that causes grapevine vascular disease, especially in regions with hot climates. Fungi in this group often remain latent ...

    Authors: Marcos Paolinelli-Alfonso, José Manuel Villalobos-Escobedo, Philippe Rolshausen, Alfredo Herrera-Estrella, Clara Galindo-Sánchez, José Fabricio López-Hernández and Rufina Hernandez-Martinez

    Citation: BMC Genomics 2016 17:615

    Content type: Research article

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  37. Green mold caused by Penicillium digitatum is the most damaging postharvest diseases of citrus fruit. Previously, we have observed that citral dose-dependently inhibited the mycelial growth of P. digitatum, with ...

    Authors: Qiuli OuYang, Nengguo Tao and Guoxing Jing

    Citation: BMC Genomics 2016 17:599

    Content type: Research article

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  38. Most fungi, including entomopathogenic fungi, have two different conidiation patterns, normal and microcycle conidiation, under different culture conditions, eg, in media containing different nutrients. Howeve...

    Authors: Zhenglong Wang, Kai Jin and Yuxian Xia

    Citation: BMC Genomics 2016 17:586

    Content type: Research article

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  39. Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before...

    Authors: Graham R. D. McGrann, Ambrose Andongabo, Elisabet Sjökvist, Urmi Trivedi, Francois Dussart, Maciej Kaczmarek, Ashleigh Mackenzie, James M. Fountaine, Jeanette M. G. Taylor, Linda J. Paterson, Kalina Gorniak, Fiona Burnett, Kostya Kanyuka, Kim E. Hammond-Kosack, Jason J. Rudd, Mark Blaxter…

    Citation: BMC Genomics 2016 17:584

    Content type: Research article

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  40. Echinocandins are nonribosomal lipopeptides produced by ascommycete fungi. Due to their strong inhibitory effect on fungal cell wall biosynthesis and lack of human toxicity, they have been developed to an impo...

    Authors: Wolfgang Hüttel, Loubna Youssar, Björn A. Grüning, Stefan Günther and Katharina G. Hugentobler

    Citation: BMC Genomics 2016 17:570

    Content type: Research article

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  41. Pichia pastoris has emerged as an important alternative host for producing recombinant biopharmaceuticals, owing to its high cultivation density, low host cell protein burden, and the ...

    Authors: Kerry R. Love, Kartik A. Shah, Charles A. Whittaker, Jie Wu, M. Catherine Bartlett, Duanduan Ma, Rachel L. Leeson, Margaret Priest, Jonathan Borowsky, Sarah K. Young and J. Christopher Love

    Citation: BMC Genomics 2016 17:550

    Content type: Research article

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    The Erratum to this article has been published in BMC Genomics 2016 17:762

  42. The cell wall is essential for the yeast to hypha (Y-H) transition that enables Candida albicans to invade human tissues and evade the immune system. The main constituent, β(1,3)-glucan, is remodeled by glucanosy...

    Authors: Genny Degani, Enrico Ragni, Pedro Botias, Davide Ravasio, Julia Calderon, Elena Pianezzola, Jose Manuel Rodriguez-Peña, Maria Antonietta Vanoni, Javier Arroyo, William A. Fonzi and Laura Popolo

    Citation: BMC Genomics 2016 17:482

    Content type: Research article

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  43. Infectious disease involving multiple genetically distinct populations of pathogens is frequently concurrent, but difficult to detect or describe with current routine methodology. Cryptosporidium sp. is a widespr...

    Authors: Karin Troell, Björn Hallström, Anna-Maria Divne, Cecilia Alsmark, Romanico Arrighi, Mikael Huss, Jessica Beser and Stefan Bertilsson

    Citation: BMC Genomics 2016 17:471

    Content type: Research article

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