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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. Regulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes have described accessible chromatin regions, but little work has been done in f...

    Authors: Aileen R. Ferraro, Abigail J. Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz and Zachary A. Lewis

    Citation: BMC Genomics 2021 22:459

    Content type: Research article

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  3. The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was fir...

    Authors: Stefania Bertazzoni, Darcy A. B. Jones, Huyen T. Phan, Kar-Chun Tan and James K. Hane

    Citation: BMC Genomics 2021 22:382

    Content type: Research article

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  4. A healthy microbiome influences host physiology through a mutualistic relationship, which can be important for the host to cope with cellular stress by promoting fitness and survival. The mammalian microbiome ...

    Authors: Orçun Haçariz, Charles Viau, Farial Karimian and Jianguo Xia

    Citation: BMC Genomics 2021 22:364

    Content type: Research article

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  5. The white-rot fungi in the genus Ganoderma interact with both living and dead angiosperm tree hosts. Two Ganoderma species, a North American taxon, G. zonatum and an Asian taxon, G. boninense, have primarily been...

    Authors: Braham Dhillon, Richard C. Hamelin and Jeffrey A. Rollins

    Citation: BMC Genomics 2021 22:326

    Content type: Research article

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  6. Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small v...

    Authors: Karina Brinkrolf, Shantanu P. Shukla, Sven Griep, Oliver Rupp, Philipp Heise, Alexander Goesmann, David G. Heckel, Heiko Vogel and Andreas Vilcinskas

    Citation: BMC Genomics 2021 22:323

    Content type: Research article

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  7. Stem rot caused by Sclerotium rolfsii is a very important soil-borne disease of peanut. S. rolfsii is a necrotrophic plant pathogenic fungus with an extensive host range and worldwide distribution. It can infect ...

    Authors: Liying Yan, Zhihui Wang, Wanduo Song, Pengmin Fan, Yanping Kang, Yong Lei, Liyun Wan, Dongxin Huai, Yuning Chen, Xin Wang, Hari Sudini and Boshou Liao

    Citation: BMC Genomics 2021 22:276

    Content type: Research article

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  8. Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific group IA (AG1-IA) infect a wide range of crops causing diseases such as rice sheath blight (ShB). ShB has become a serious disease...

    Authors: Da-Young Lee, Jongbum Jeon, Ki-Tae Kim, Kyeongchae Cheong, Hyeunjeong Song, Gobong Choi, Jaeho Ko, Stephen O. Opiyo, James C. Correll, Shimin Zuo, Sheshu Madhav, Guo-Liang Wang and Yong-Hwan Lee

    Citation: BMC Genomics 2021 22:242

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2021 22:306

  9. CRISPR/Cas9-mediated transcriptional interference (CRISPRi) enables programmable gene knock-down, yielding loss-of-function phenotypes for nearly any gene. Effective, inducible CRISPRi has been demonstrated in...

    Authors: Nicholas J. McGlincy, Zuriah A. Meacham, Kendra K. Reynaud, Ryan Muller, Rachel Baum and Nicholas T. Ingolia

    Citation: BMC Genomics 2021 22:205

    Content type: Methodology article

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  10. Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. The Prototheca

    Authors: Zofia Bakuła, Paweł Siedlecki, Robert Gromadka, Jan Gawor, Agnieszka Gromadka, Jan J. Pomorski, Hanna Panagiotopoulou and Tomasz Jagielski

    Citation: BMC Genomics 2021 22:168

    Content type: Research article

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  11. Hericium erinaceus, a rare edible and medicine fungus, is widely used in the food and medical field. Polysaccharides from H. erinaceus are the main bioactive compound that exert high bioactive value in the medica...

    Authors: Ming Gong, Henan Zhang, Di Wu, Zhong Zhang, Jinsong Zhang, Dapeng Bao and Yan Yang

    Citation: BMC Genomics 2021 22:160

    Content type: Research article

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  12. Saccharomycodes ludwigii belongs to the poorly characterized Saccharomycodeacea family and is known by its ability to spoil wines, a trait mostly attributable to its high tolerance to sulfur dioxide (SO2). To imp...

    Authors: Maria J. Tavares, Ulrich Güldener, Ana Mendes-Ferreira and Nuno P. Mira

    Citation: BMC Genomics 2021 22:131

    Content type: Research article

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  13. The accumulation of intracellular fat depots is a polygenic trait. Therefore, the extent of lipid storage in the individuals of a species covers a broad range and is determined by many genetic factors. Quantit...

    Authors: Klavdija Pačnik, Mojca Ogrizović, Matthias Diepold, Tobias Eisenberg, Mia Žganjar, Gašper Žun, Beti Kužnik, Cene Gostinčar, Tomaž Curk, Uroš Petrovič and Klaus Natter

    Citation: BMC Genomics 2021 22:110

    Content type: Research article

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  14. The fungicide fludioxonil over-stimulates the fungal response to osmotic stress, leading to over-accumulation of glycerol and hyphal swelling and bursting. Fludioxonil-resistant fungal strains that are null-mu...

    Authors: Akeem O. Taiwo, Lincoln A. Harper and Mark C. Derbyshire

    Citation: BMC Genomics 2021 22:91

    Content type: Research article

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  15. More accurate and complete reference genomes have improved understanding of gene function, biology, and evolutionary mechanisms. Hybrid genome assembly approaches leverage benefits of both long, relatively err...

    Authors: Zack Saud, Alexandra M. Kortsinoglou, Vassili N. Kouvelis and Tariq M. Butt

    Citation: BMC Genomics 2021 22:87

    Content type: Research article

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  16. The RNA interference (RNAi) pathway is a gene regulation mechanism that utilizes small RNA (sRNA) and Argonaute (Ago) proteins to silence target genes. Our previous work identified a functional RNAi pathway in...

    Authors: Hanbang Zhang, Gretchen M. Ehrenkaufer, Neil Hall and Upinder Singh

    Citation: BMC Genomics 2020 21:879

    Content type: Research article

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  17. The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of...

    Authors: Daryl M. Gohl, John Garbe, Patrick Grady, Jerry Daniel, Ray H. B. Watson, Benjamin Auch, Andrew Nelson, Sophia Yohe and Kenneth B. Beckman

    Citation: BMC Genomics 2020 21:863

    Content type: Methodology article

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  18. Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. gl...

    Authors: Chun-Ji Li, Die Zhao, Ping Cheng, Li Zheng and Guo-Hui Yu

    Citation: BMC Genomics 2020 21:834

    Content type: Research article

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  19. Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based ...

    Authors: Pratima Chapagain, Donald Walker, Tim Leeds, Beth M. Cleveland and Mohamed Salem

    Citation: BMC Genomics 2020 21:820

    Content type: Research article

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  20. Amoebozoa is a eukaryotic supergroup composed of unicellular and multicellular amoebic protozoa (e.g. Acanthamoeba, Dictyostelium, and Entamoeba). They are model organisms for studies in cellular and evolutionary...

    Authors: Tetsuro Kawano-Sugaya, Shinji Izumiyama, Yasuaki Yanagawa, Yumiko Saito-Nakano, Koji Watanabe, Seiki Kobayashi, Kumiko Nakada-Tsukui and Tomoyoshi Nozaki

    Citation: BMC Genomics 2020 21:813

    Content type: Research article

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  21. Ophiocordyceps sinensis (Berk.) is a well-known entomopathogenic and medicinal fungus. It parasitizes and mummifies the underground ghost moth larvae to produce a fruiting body named Chinese cordyceps. Specific f...

    Authors: Miaomiao Li, Qian Meng, Huan Zhang, Ruihao Shu, Yanni Zhao, Peipei Wu, Xuan Li, Guiling Zhou, Qilian Qin and Jihong Zhang

    Citation: BMC Genomics 2020 21:789

    Content type: Research article

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  22. Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3...

    Authors: Jaire A. Ferreira Filho, Maria Augusta C. Horta, Clelton A. dos Santos, Deborah A. Almeida, Natália F. Murad, Juliano S. Mendes, Danilo A. Sforça, Claudio Benício C. Silva, Aline Crucello and Anete P. de Souza

    Citation: BMC Genomics 2020 21:757

    Content type: Research article

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  23. With 9730 protein-coding genes and a nearly complete gene knockout strain collection, Neurospora crassa is a major model organism for filamentous fungi. Despite this abundance of information, the phenotypes of th...

    Authors: Alexander J. Carrillo, Ilva E. Cabrera, Marko J. Spasojevic, Patrick Schacht, Jason E. Stajich and Katherine A. Borkovich

    Citation: BMC Genomics 2020 21:755

    Content type: Research article

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  24. Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been ver...

    Authors: Bai-Ling Chen, Wuttichai Mhuantong, Shih-Hsin Ho, Jo-Shu Chang, Xin-Qing Zhao and Feng-Wu Bai

    Citation: BMC Genomics 2020 21:743

    Content type: Research article

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  25. Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in Cali...

    Authors: Peter Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish and Lynn Epstein

    Citation: BMC Genomics 2020 21:730

    Content type: Research article

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  26. Flammulina filiformis (previously known as Asian F. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been iso...

    Authors: Juan Chen, Jia-Mei Li, Yan-Jing Tang, Ke Ma, Bing Li, Xu Zeng, Xiao-Bin Liu, Yang Li, Zhu-Liang Yang, Wei-Nan Xu, Bao-Gui Xie, Hong-Wei Liu and Shun-Xing Guo

    Citation: BMC Genomics 2020 21:719

    Content type: Research article

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  27. Symbiosis is central to ecosystems and has been an important driving force of the diversity of life. Close and long-term interactions are known to develop cooperative molecular mechanisms between the symbiotic...

    Authors: Mieko Kono, Yoshiaki Kon, Yoshihito Ohmura, Yoko Satta and Yohey Terai

    Citation: BMC Genomics 2020 21:671

    Content type: Research article

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  28. Necrotrophic effector proteins secreted by fungal pathogens are important virulence factors that mediate the development of disease in wheat. Pyrenophora tritici-repentis (Ptr), the causal agent of wheat tan spot...

    Authors: Paula Moolhuijzen, Pao Theen See and Caroline S. Moffat

    Citation: BMC Genomics 2020 21:645

    Content type: Research article

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  29. Blue mold is a globally important and economically impactful postharvest disease of apples caused by multiple Penicillium spp. There are currently four postharvest fungicides registered for blue mold control, and...

    Authors: Franz J. Lichtner, Verneta L. Gaskins, Kerik D. Cox and Wayne M. Jurick II

    Citation: BMC Genomics 2020 21:574

    Content type: Research article

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  30. Laurel wilt caused by Raffaelea lauricola is a lethal vascular disease of North American members of the Lauraceae plant family. This fungus and its primary ambrosia beetle vector Xyleborus glabratus originated fr...

    Authors: Yucheng Zhang, Junli Zhang, Dan Vanderpool, Jason A. Smith and Jeffrey A. Rollins

    Citation: BMC Genomics 2020 21:570

    Content type: Research article

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  32. Picophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes. Mychonastes species are among the common eukaryotic picophytoplankton in eutrophic lakes. We used third-generati...

    Authors: Changqing Liu, Xiaoli Shi, Fan Wu, Mingdong Ren, Guang Gao and Qinglong Wu

    Citation: BMC Genomics 2020 21:477

    Content type: Research article

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  33. Beauveria bassiana (B. bassiana) is a famous entomopathogenic fungus that could parasitize on hundreds of insect species, which are being used as an environmentally friendly mycoinsecticide. Nevertheless, the pos...

    Authors: Zhengkun Zhang, Yang Lu, Wenjing Xu, Li Sui, Qian Du, Yangzhou Wang, Yu Zhao and Qiyun Li

    Citation: BMC Genomics 2020 21:451

    Content type: Research article

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  34. Most diversity in the eukaryotic tree of life is represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcripto...

    Authors: Henning Onsbring, Alexander K. Tice, Brandon T. Barton, Matthew W. Brown and Thijs J. G. Ettema

    Citation: BMC Genomics 2020 21:448

    Content type: Methodology article

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  35. Amanitin-producing mushrooms, mainly distributed in the genera Amanita, Galerina and Lepiota, possess MSDIN gene family for the biosynthesis of many cyclopeptides catalysed by prolyl oligopeptidase (POP). Recentl...

    Authors: Zhengmi He, Pan Long, Fang Fang, Sainan Li, Ping Zhang and Zuohong Chen

    Citation: BMC Genomics 2020 21:440

    Content type: Research article

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  37. Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals. However, there is currently little understanding of endophytic fungi at the omics levels about their po...

    Authors: Jin-Tao Cheng, Fei Cao, Xin-Ai Chen, Yong-Quan Li and Xu-Ming Mao

    Citation: BMC Genomics 2020 21:424

    Content type: Research article

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  38. DNA replication in trypanosomatids operates in a uniquely challenging environment, since most of their genomes are constitutively transcribed. Trypanosoma cruzi, the etiological agent of Chagas disease, presents ...

    Authors: Christiane Bezerra de Araujo, Julia Pinheiro Chagas da Cunha, Davi Toshio Inada, Jeziel Damasceno, Alex Ranieri Jerônimo Lima, Priscila Hiraiwa, Catarina Marques, Evonnildo Gonçalves, Milton Yutaka Nishiyama-Junior, Richard McCulloch and Maria Carolina Elias

    Citation: BMC Genomics 2020 21:414

    Content type: Research article

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  39. Plasmodium parasites undergo several major developmental transitions during their complex lifecycle, which are enabled by precisely ordered gene expression programs. Transcriptomes from the 48-h blood stages of t...

    Authors: Lia Chappell, Philipp Ross, Lindsey Orchard, Timothy J. Russell, Thomas D. Otto, Matthew Berriman, Julian C. Rayner and Manuel Llinás

    Citation: BMC Genomics 2020 21:395

    Content type: Research article

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  40. Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene express...

    Authors: Alexander L. Cope, Brian C. O’Meara and Michael A. Gilchrist

    Citation: BMC Genomics 2020 21:370

    Content type: Research Article

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  41. Increased contamination of European and Asian wheat and barley crops with “emerging” mycotoxins such as enniatins or beauvericin, produced by Fusarium avenaceum and Fusarium tricinctum, suggest that these phyloge...

    Authors: Nadia Ponts, Charlotte Gautier, Jérôme Gouzy, Laetitia Pinson-Gadais, Marie Foulongne-Oriol, Christine Ducos, Florence Richard-Forget, Jean-Michel Savoie, Chen Zhao and Gérard Barroso

    Citation: BMC Genomics 2020 21:358

    Content type: Research article

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  42. The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface...

    Authors: Bo Wang, Xiaofei Liang, Mark L. Gleason, Tom Hsiang, Rong Zhang and Guangyu Sun

    Citation: BMC Genomics 2020 21:321

    Content type: Research article

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  43. Ashbya gossypii naturally overproduces riboflavin and has been utilized for industrial riboflavin production. To improve riboflavin production, various approaches have been developed. In this study, to investigat...

    Authors: Tatsuya Kato, Junya Azegami, Ami Yokomori, Hideo Dohra, Hesham A. El Enshasy and Enoch Y. Park

    Citation: BMC Genomics 2020 21:319

    Content type: Research article

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  44. The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parv...

    Authors: Kyle Tretina, Roger Pelle, Joshua Orvis, Hanzel T. Gotia, Olukemi O. Ifeonu, Priti Kumari, Nicholas C. Palmateer, Shaikh B. A. Iqbal, Lindsay M. Fry, Vishvanath M. Nene, Claudia A. Daubenberger, Richard P. Bishop and Joana C. Silva

    Citation: BMC Genomics 2020 21:279

    Content type: Research article

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  45. The stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), threats world wheat production. Resistance to Pst is often overcome by pathogen virulence changes, but the mechanisms of variation are not clea...

    Authors: Yuxiang Li, Chongjing Xia, Meinan Wang, Chuntao Yin and Xianming Chen

    Citation: BMC Genomics 2020 21:247

    Content type: Research article

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  46. The creation of arrays of yeast strains each encoding a different protein with constant tags is a powerful method for understanding how genes and their proteins control cell function. As genetic tools become m...

    Authors: Lisa K. Berry, Grace Heredge Thomas and Peter H. Thorpe

    Citation: BMC Genomics 2020 21:221

    Content type: Methodology article

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  47. All retroviruses, including human immunodeficiency virus (HIV), must integrate a DNA copy of their genomes into the genome of the infected host cell to replicate. Although integrated retroviral DNA, known as a...

    Authors: Daria W. Wells, Shuang Guo, Wei Shao, Michael J. Bale, John M. Coffin, Stephen H. Hughes and Xiaolin Wu

    Citation: BMC Genomics 2020 21:216

    Content type: Methodology article

    Published on:

    The Correction to this article has been published in BMC Genomics 2020 21:517

  49. Sporobolomyces pararoseus is regarded as an oleaginous red yeast, which synthesizes numerous valuable compounds with wide industrial usages. This species hold biotechnological interests in biodiesel, food and cos...

    Authors: Chun-Ji Li, Die Zhao, Bing-Xue Li, Ning Zhang, Jian-Yu Yan and Hong-Tao Zou

    Citation: BMC Genomics 2020 21:181

    Content type: Research article

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  50. The filamentous fungus Fusarium graminearum causes devastating crop diseases and produces harmful mycotoxins worldwide. Understanding the complex F. graminearum transcriptional regulatory networks (TRNs) is vital...

    Authors: Li Guo, Mengjie Ji and Kai Ye

    Citation: BMC Genomics 2020 21:179

    Content type: Research article

    Published on:

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