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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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

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

  7. 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

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  8. 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

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  9. 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

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  10. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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

  15. Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring a relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. ...

    Authors: István Prazsák, Norbert Moldován, Zsolt Balázs, Dóra Tombácz, Klára Megyeri, Attila Szűcs, Zsolt Csabai and Zsolt Boldogkői

    Citation: BMC Genomics 2018 19:873

    Content type: Research article

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  16. Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to c...

    Authors: Kyle Fletcher, Steven J. Klosterman, Lida Derevnina, Frank Martin, Lien D. Bertier, Steven Koike, Sebastian Reyes-Chin-Wo, Beiquan Mou and Richard Michelmore

    Citation: BMC Genomics 2018 19:851

    Content type: Research article

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  17. Plasmodium falciparum exhibits resistance to the artemisinin component of the frontline antimalarial treatment Artemisinin-based Combination Therapy in South East Asia. Millions of lives will be at risk if artemi...

    Authors: Justin Gibbons, Katrina A. Button-Simons, Swamy R. Adapa, Suzanne Li, Maxwell Pietsch, Min Zhang, Xiangyun Liao, John H. Adams, Michael T. Ferdig and Rays H. Y. Jiang

    Citation: BMC Genomics 2018 19:849

    Content type: Research article

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  18. Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishma...

    Authors: Sumudu R. Samarasinghe, Nilakshi Samaranayake, Udeshika L. Kariyawasam, Yamuna D. Siriwardana, Hideo Imamura and Nadira D. Karunaweera

    Citation: BMC Genomics 2018 19:843

    Content type: Research article

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  19. Porcine Circovirus Type 2 (PCV2) is a pathogen that has the ability to cause often devastating disease manifestations in pig populations with major economic implications. How PCV2 establishes subclinical persi...

    Authors: Nicolaas Van Renne, Ruifang Wei, Nathalie Pochet and Hans J. Nauwynck

    Citation: BMC Genomics 2018 19:831

    Content type: Research article

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  20. Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. TcII is among the major DTUs enrolled in human infections in South America sou...

    Authors: João Luís Reis-Cunha, Rodrigo P. Baptista, Gabriela F. Rodrigues-Luiz, Anderson Coqueiro-dos-Santos, Hugo O. Valdivia, Laila Viana de Almeida, Mariana Santos Cardoso, Daniella Alchaar D’Ávila, Fernando Hugo Cunha Dias, Ricardo Toshio Fujiwara, Lúcia M. C. Galvão, Egler Chiari, Gustavo Coutinho Cerqueira and Daniella C. Bartholomeu

    Citation: BMC Genomics 2018 19:816

    Content type: Research article

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  21. The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can...

    Authors: Emilien Peltier, Vikas Sharma, Maria Martí Raga, Miguel Roncoroni, Margaux Bernard, Vladimir Jiranek, Yves Gibon and Philippe Marullo

    Citation: BMC Genomics 2018 19:772

    Content type: Research article

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  22. Hypsizygus marmoreus (Beech mushroom) is a popular ingredient in Asian cuisine. The medicinal effects of its bioactive compounds such as hypsin and hypsiziprenol have been reported, but the genetic basis or biosy...

    Authors: Byoungnam Min, Seunghwan Kim, Youn-Lee Oh, Won-Sik Kong, Hongjae Park, Heejung Cho, Kab-Yeul Jang, Jeong-Gu Kim and In-Geol Choi

    Citation: BMC Genomics 2018 19:789

    Content type: Research article

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  23. A major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types. During Dictyostelid evolution novel specialization occurred within taxon group 4. We here ai...

    Authors: Koryu Kin, Gillian Forbes, Andrew Cassidy and Pauline Schaap

    Citation: BMC Genomics 2018 19:764

    Content type: Research article

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  24. The Ambrosia Fusarium Clade phytopathogenic Fusarium fungi species have a symbiotic relationship with ambrosia beetles in the genus Euwallacea (Coleoptera: Curculionidae). Related beetle species referred to as Eu...

    Authors: Diana Sánchez-Rangel, Eric-Edmundo Hernández-Domínguez, Claudia-Anahí Pérez-Torres, Randy Ortiz-Castro, Emanuel Villafán, Benjamín Rodríguez-Haas, Alexandro Alonso-Sánchez, Abel López-Buenfil, Nayeli Carrillo-Ortiz, Lervin Hernández-Ramos and Enrique Ibarra-Laclette

    Citation: BMC Genomics 2018 19:721

    Content type: Research article

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  25. Analysis of polymorphic microsatellite markers (STR) is a helpful genotyping technique to differentiate Candida parapsilosis sensu stricto isolates. The aim of this study is to develop and perform an initial vali...

    Authors: Camino Trobajo-Sanmartín, Guillermo Ezpeleta, Célia Pais, Elena Eraso and Guillermo Quindós

    Citation: BMC Genomics 2018 19:718

    Content type: Methodology article

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  26. Erinnyis ello granulovirus (ErelGV) is a betabaculovirus infecting caterpillars of the sphingid moth E. ello ello (cassava hornworm), an important pest of cassava crops (Manihot esculenta). In this study, the gen...

    Authors: A. F. Brito, F. L. Melo, D. M. P. Ardisson-Araújo, W. Sihler, M. L. Souza and B. M. Ribeiro

    Citation: BMC Genomics 2018 19:698

    Content type: Research article

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  27. Pseudocohnilembus persalinus, a unicellular ciliated protozoan, is one of commonest facultative pathogens. We sequenced the macronuclear genome of P. persalinus in 2015, which provided new insights into its patho...

    Authors: Wei Wei, Kai Chen, Wei Miao, Wentao Yang and Jie Xiong

    Citation: BMC Genomics 2018 19:676

    Content type: Database

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  28. Plant fungal pathogens can rapidly evolve and adapt to new environmental conditions in response to sudden changes of host populations in agro-ecosystems. However, the genomic basis of their host adaptation, es...

    Authors: Chongjing Xia, Meinan Wang, Chuntao Yin, Omar E. Cornejo, Scot H. Hulbert and Xianming Chen

    Citation: BMC Genomics 2018 19:664

    Content type: Research article

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  29. Members of the genus Naegleria are free-living eukaryotes with the capability to transform from the amoeboid form into resting cysts or moving flagellates in response to environmental conditions. More than 40 spe...

    Authors: Nicole Liechti, Nadia Schürch, Rémy Bruggmann and Matthias Wittwer

    Citation: BMC Genomics 2018 19:654

    Content type: Research article

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  30. In the past decade, many new paramyxoviruses that do not belong to any of the seven established genera in the family Paramyxoviridae have been discovered. Amongst them are J-virus (JPV), Beilong virus (BeiPV) and...

    Authors: Bert Vanmechelen, Magda Bletsa, Lies Laenen, Ana Rita Lopes, Valentijn Vergote, Leen Beller, Ward Deboutte, Miša Korva, Tatjana Avšič Županc, Joëlle Goüy de Bellocq, Sophie Gryseels, Herwig Leirs, Philippe Lemey, Bram Vrancken and Piet Maes

    Citation: BMC Genomics 2018 19:617

    Content type: Research article

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  31. Direct molecular cloning of full-length cDNAs derived from viral RNA is an approach to identify the individual viral genomes within a virus population. This enables characterization of distinct viral haplotype...

    Authors: Camille Melissa Johnston, Ulrik Fahnøe, Graham J. Belsham and Thomas Bruun Rasmussen

    Citation: BMC Genomics 2018 19:600

    Content type: Methodology article

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  32. Though it is toxic to humans, dichlorvos is a widely used chemical pesticide and plays an important role in the control of plant pests. The application of a combination of the biocontrol agent Trichoderma with di...

    Authors: Qiong Wu, Mi Ni, Guisheng Wang, Qianqian Liu, Meixia Yu and Jun Tang

    Citation: BMC Genomics 2018 19:596

    Content type: Research article

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  33. Colletotrichum is a fungal genus in Ascomycota that contain many plant pathogens. Among all Colletotrichum genomes that have been sequenced, C. fructicola contains the largest number of candidate virulence factor...

    Authors: Xiaofei Liang, Shengping Shang, Qiuyue Dong, Bo Wang, Rong Zhang, Mark L. Gleason and Guangyu Sun

    Citation: BMC Genomics 2018 19:557

    Content type: Research article

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  34. Plant-parasitic nematodes cause severe damage to a wide range of crop and forest species worldwide. The migratory endoparasitic nematode, Bursaphelenchus xylophilus, (pinewood nematode) is a quarantine pathogen t...

    Authors: Margarida Espada, Sebastian Eves-van den Akker, Tom Maier, Paramasivan Vijayapalani, Thomas Baum, Manuel Mota and John T. Jones

    Citation: BMC Genomics 2018 19:553

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2018 19:603

  35. Aspergillus fumigatus is the main causative agent of aspergillosis. Infections rarely occur in immunocompetent individuals, indicating efficient clearance of conidia by pulmonary defense mechanisms. Other aspergi...

    Authors: Natalia Escobar, Ivan D. Valdes, Esther M. Keizer, Soledad R. Ordonez, Robin A. Ohm, Han A. B. Wösten and Hans de Cock

    Citation: BMC Genomics 2018 19:534

    Content type: Research article

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  36. The hemibiotrophic pathogens Moniliophthora perniciosa (witches’ broom disease) and Moniliophthora roreri (frosty pod rot disease) are among the most important pathogens of cacao. Moniliophthora perniciosa has a ...

    Authors: Ceslaine Santos Barbosa, Rute R. da Fonseca, Thiago Mafra Batista, Mariana Araújo Barreto, Caio Suzart Argolo, Mariana Rocha de Carvalho, Daniel Oliveira Jordão do Amaral, Edson Mário de Andrade Silva, Enrique Arévalo-Gardini, Karina Solis Hidalgo, Glória Regina Franco, Carlos Priminho Pirovani, Fabienne Micheli and Karina Peres Gramacho

    Citation: BMC Genomics 2018 19:509

    Content type: Research article

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  37. Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Altho...

    Authors: Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser and Kelly V. Ruggles

    Citation: BMC Genomics 2018 19:493

    Content type: Software

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  38. Quahog Parasite Unknown (QPX) is an opportunistic protistan pathogen of the clam Mercenaria mercenaria. Infections with QPX have caused significant economic losses in the Northeastern United States. Previous rese...

    Authors: Sleiman Bassim and Bassem Allam

    Citation: BMC Genomics 2018 19:486

    Content type: Research article

    Published on:

  39. Phytophthora infestans is responsible for late blight, one of the most important potato diseases. Phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 isolated in our laboratory show...

    Authors: Roxane Roquigny, Amy Novinscak, Tanya Arseneault, David L. Joly and Martin Filion

    Citation: BMC Genomics 2018 19:474

    Content type: Research article

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  40. Brown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola, M. laxa and M. fructigena are the most common all over the world. Although they h...

    Authors: Rita M. De Miccolis Angelini, Domenico Abate, Caterina Rotolo, Donato Gerin, Stefania Pollastro and Francesco Faretra

    Citation: BMC Genomics 2018 19:436

    Content type: Research article

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  41. Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obliga...

    Authors: Lamprinos Frantzeskakis, Barbara Kracher, Stefan Kusch, Makoto Yoshikawa-Maekawa, Saskia Bauer, Carsten Pedersen, Pietro D. Spanu, Takaki Maekawa, Paul Schulze-Lefert and Ralph Panstruga

    Citation: BMC Genomics 2018 19:381

    Content type: Research article

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  42. Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. I...

    Authors: Jérémy Berthelier, Nathalie Casse, Nicolas Daccord, Véronique Jamilloux, Bruno Saint-Jean and Grégory Carrier

    Citation: BMC Genomics 2018 19:378

    Content type: Research article

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  43. Gene copy number variants (CNVs), which consist of deletions and amplifications of single or sets of contiguous genes, contribute to the great diversity in the Plasmodium falciparum genome. In vitro studies in th...

    Authors: Joan Simam, Martin Rono, Joyce Ngoi, Mary Nyonda, Sachel Mok, Kevin Marsh, Zbynek Bozdech and Margaret Mackinnon

    Citation: BMC Genomics 2018 19:372

    Content type: Research article

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  44. Soybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response...

    Authors: Hang Dong, Shuangfeng Shi, Chong Zhang, Sihui Zhu, Mei Li, Jie Tan, Yue Yu, Liping Lin, Shirong Jia, Xujing Wang, Yuanhua Wu and Yuhui Liu

    Citation: BMC Genomics 2018 19:366

    Content type: Research article

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  45. The black yeast Hortaea werneckii (Dothideomycetes, Ascomycota) is one of the most extremely halotolerant fungi, capable of growth at NaCl concentrations close to saturation. Although dothideomycetous fungi are t...

    Authors: Cene Gostinčar, Jason E. Stajich, Jerneja Zupančič, Polona Zalar and Nina Gunde-Cimerman

    Citation: BMC Genomics 2018 19:364

    Content type: Research article

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  46. Leaf blight caused by Calonectria spp. is one of the most destructive diseases to affect Eucalyptus nurseries and plantations. These pathogens mainly attack Eucalyptus, a tree with a diversity of secondary metabo...

    Authors: Xiaozhen Ye, Zhenhui Zhong, Hongyi Liu, Lianyu Lin, Mengmeng Guo, Wenshuo Guo, Zonghua Wang, Qinghua Zhang, Lizhen Feng, Guodong Lu, Feiping Zhang and Quanzhu Chen

    Citation: BMC Genomics 2018 19:358

    Content type: Research article

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  47. Aspergillus fumigatus has to cope with a combination of several stress types while colonizing the human body. A functional interplay between these different stress responses can increase the chances of survival f...

    Authors: Vivien Kurucz, Thomas Krüger, Károly Antal, Anna-Maria Dietl, Hubertus Haas, István Pócsi, Olaf Kniemeyer and Tamás Emri

    Citation: BMC Genomics 2018 19:357

    Content type: Research article

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  48. Allopolyploidy is a genomic structure wherein two or more sets of chromosomes derived from divergent parental species coexist within an organism. It is a prevalent genomic configuration in plants, as an import...

    Authors: Tatsuhiro Nomaguchi, Yoshiaki Maeda, Tomoko Yoshino, Toru Asahi, Leila Tirichine, Chris Bowler and Tsuyoshi Tanaka

    Citation: BMC Genomics 2018 19:330

    Content type: Research article

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  49. Accumulating evidence suggests that genome plasticity allows filamentous plant pathogens to adapt to changing environments. Recently, the generalist plant pathogen Phytophthora ramorum has been documented to unde...

    Authors: Marianne Elliott, Jennifer Yuzon, Mathu Malar C, Sucheta Tripathy, Mai Bui, Gary A. Chastagner, Katie Coats, David M. Rizzo, Matteo Garbelotto and Takao Kasuga

    Citation: BMC Genomics 2018 19:320

    Content type: Research article

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  50. Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids a...

    Authors: Jong Im Kim, Hwan Su Yoon, Gangman Yi, Woongghi Shin and John M. Archibald

    Citation: BMC Genomics 2018 19:275

    Content type: Research article

    Published on:

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