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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 soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal...

    Authors: Robert King, Neil Andrew Brown, Martin Urban and Kim E. Hammond-Kosack

    Citation: BMC Genomics 2018 19:269

    Content type: Research article

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  2. Sugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation ar...

    Authors: Paula Fagundes de Gouvêa, Aline Vianna Bernardi, Luis Eduardo Gerolamo, Emerson de Souza Santos, Diego Mauricio Riaño-Pachón, Sergio Akira Uyemura and Taisa Magnani Dinamarco

    Citation: BMC Genomics 2018 19:232

    Content type: Research article

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  3. Trypanosoma brucei brucei, the parasite causing Nagana in domestic animals, is closely related to the parasites causing sleeping sickness, but does not infect humans. In addition to its importance as a pathogen, ...

    Authors: Arunasalam Naguleswaran, Nicholas Doiron and Isabel Roditi

    Citation: BMC Genomics 2018 19:227

    Content type: Research article

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  4. Plant biomass is the most abundant carbon source for many fungal species. In the biobased industry fungi, are used to produce lignocellulolytic enzymes to degrade agricultural waste biomass. Here we evaluated ...

    Authors: Claire Khosravi, Evy Battaglia, Roland S. Kun, Sacha Dalhuijsen, Jaap Visser, María Victoria Aguilar-Pontes, Miaomiao Zhou, Heino M. Heyman, Young-Mo Kim, Scott E. Baker and Ronald P. de Vries

    Citation: BMC Genomics 2018 19:214

    Content type: Research

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  5. Black Aspergilli represent one of the most important fungal resources of primary and secondary metabolites for biotechnological industry. Having several black Aspergilli sequenced genomes should allow targetin...

    Authors: Elodie Choque, Christophe Klopp, Sophie Valiere, José Raynal and Florence Mathieu

    Citation: BMC Genomics 2018 19:200

    Content type: Research article

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  6. Cryptocaryon irritans is an obligate parasitic ciliate protozoan that can infect various commercially important mariculture fish species and cause high lethality and economic loss. Current methods of controlling ...

    Authors: Ruanni Chen, Yong Mao, Jun Wang, Min Liu, Ying Qiao, Libing Zheng, Yongquan Su, Qiaozhen Ke and Weiqiang Zheng

    Citation: BMC Genomics 2018 19:192

    Content type: Research article

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  7. Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. ...

    Authors: Geromy G. Moore, Brian M. Mack, Shannon B. Beltz and Olivier Puel

    Citation: BMC Genomics 2018 19:189

    Content type: Research article

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  8. The volatile metabolites produced by Saccharomyces cerevisiae during alcoholic fermentation, which are mainly esters, higher alcohols and organic acids, play a vital role in the quality and perception of fermente...

    Authors: Matthias Eder, Isabelle Sanchez, Claire Brice, Carole Camarasa, Jean-Luc Legras and Sylvie Dequin

    Citation: BMC Genomics 2018 19:166

    Content type: Research article

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  9. The size of the phenotypic effect of a gene has been thoroughly investigated in terms of fitness and specific morphological traits in the budding yeast Saccharomyces cerevisiae, but little is known about gross mo...

    Authors: Godai Suzuki, Yang Wang, Karen Kubo, Eri Hirata, Shinsuke Ohnuki and Yoshikazu Ohya

    Citation: BMC Genomics 2018 19:149

    Content type: Research article

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  10. Euplotes, a ciliated protozoan, is a useful unicellular model organism. Studies on Euplotes have provided excellent insights into various basic biological principles. We have recently sequenced the macronuclear g...

    Authors: Ruan-lin Wang, Wei Miao, Wei Wang, Jie Xiong and Ai-hua Liang

    Citation: BMC Genomics 2018 19:63

    Content type: Database

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  11. The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta

    Authors: Eddy Patricia Lopez Molano, Odalys García Cabrera, Juliana Jose, Leandro Costa do Nascimento, Marcelo Falsarella Carazzolle, Paulo José Pereira Lima Teixeira, Javier Correa Alvarez, Ricardo Augusto Tiburcio, Paulo Massanari Tokimatu Filho, Gustavo Machado Alvares de Lima, Rafael Victório Carvalho Guido, Thamy Lívia Ribeiro Corrêa, Adriana Franco Paes Leme, Piotr Mieczkowski and Gonçalo Amarante Guimarães Pereira

    Citation: BMC Genomics 2018 19:58

    Content type: Research article

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  12. Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white...

    Authors: Deepak K. Gupta, Martin Rühl, Bagdevi Mishra, Vanessa Kleofas, Martin Hofrichter, Robert Herzog, Marek J. Pecyna, Rahul Sharma, Harald Kellner, Florian Hennicke and Marco Thines

    Citation: BMC Genomics 2018 19:48

    Content type: Research article

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  13. The early phases of Diaporthe helianthi pathogenesis on sunflower are characterized by the production of phytotoxins that may play a role in host colonisation. In previous studies, phytotoxins of a polyketidic na...

    Authors: Michelina Ruocco, Riccardo Baroncelli, Santa Olga Cacciola, Catello Pane, Maurilia Maria Monti, Giuseppe Firrao, Mariarosaria Vergara, Gaetano Magnano di San Lio, Giovanni Vannacci and Felice Scala

    Citation: BMC Genomics 2018 19:27

    Content type: Research article

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  14. Pleurotus tuoliensis (Bailinggu) is a commercially cultivated mushroom species with an increasing popularity in China and other Asian countries. Commercial profits are now low, mainly due to a low yield, long cul...

    Authors: Wei Gao, Jibin Qu, Jinxia Zhang, Anton Sonnenberg, Qiang Chen, Yan Zhang and Chenyang Huang

    Citation: BMC Genomics 2018 19:18

    Content type: Research article

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  15. Brassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is on...

    Authors: Johan Fogelqvist, Georgios Tzelepis, Sarosh Bejai, Jonas Ilbäck, Arne Schwelm and Christina Dixelius

    Citation: BMC Genomics 2018 19:14

    Content type: Research article

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  16. Long non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these RNA species but their regulation and funct...

    Authors: Ibrahim Avi Cemel, Nati Ha, Geza Schermann, Shusuke Yonekawa and Michael Brunner

    Citation: BMC Genomics 2017 18:978

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2018 19:325

  17. The lytic cycle of the protozoan parasite Toxoplasma gondii, which involves a brief sojourn in the extracellular space, is characterized by defined transcriptional profiles. For an obligate intracellular parasite...

    Authors: Musa A. Hassan, Juan J. Vasquez, Chew Guo-Liang, Markus Meissner and T. Nicolai Siegel

    Citation: BMC Genomics 2017 18:961

    Content type: Research article

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  18. Avian poxviruses are important pathogens of both wild and domestic birds. To date, seven isolates from subclades A and B and one from proposed subclade E, have had their genomes completely sequenced. The genom...

    Authors: Olivia Carulei, Nicola Douglass and Anna-Lise Williamson

    Citation: BMC Genomics 2017 18:947

    Content type: Research Article

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  19. Aspergillus fumigatus is a human fungal pathogen that causes aspergillosis in immunocompromised hosts. A. fumigatus is believed to be exposed to diverse environmental stresses in the h...

    Authors: Hiroki Takahashi, Yoko Kusuya, Daisuke Hagiwara, Azusa Takahashi-Nakaguchi, Kanae Sakai and Tohru Gonoi

    Citation: BMC Genomics 2017 18:942

    Content type: Research article

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  20. The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of ...

    Authors: Birgit S. Gruben, Miia R. Mäkelä, Joanna E. Kowalczyk, Miaomiao Zhou, Isabelle Benoit-Gelber and Ronald P. De Vries

    Citation: BMC Genomics 2017 18:900

    Content type: Research article

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  21. Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are g...

    Authors: Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun and Ryohei Terauchi

    Citation: BMC Genomics 2017 18:897

    Content type: Research article

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  22. Trichophyton mentagrophytes is an important zoonotic dermatophytic (ringworm) pathogen; causing severe skin infection in humans and other animals worldwide. Fortunately, commonly used ...

    Authors: Xinke Zhang, Pengxiu Dai, Yongping Gao, Xiaowen Gong, Hao Cui, Yipeng Jin and Yihua Zhang

    Citation: BMC Genomics 2017 18:888

    Content type: Research article

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  23. Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of ...

    Authors: Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt LaButti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V. Grigoriev, Antonio G. Pisabarro and Lucía Ramírez

    Citation: BMC Genomics 2017 18:883

    Content type: Research article

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  24. Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. New amplicon sequencing and data analysis pro...

    Authors: Anita Lerch, Cristian Koepfli, Natalie E. Hofmann, Camilla Messerli, Stephen Wilcox, Johanna H. Kattenberg, Inoni Betuela, Liam O’Connor, Ivo Mueller and Ingrid Felger

    Citation: BMC Genomics 2017 18:864

    Content type: Methdology article

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  25. Babesia ovata, belonging to the phylum Apicomplexa, is an infectious parasite of bovids. It is not associated with the manifestation of severe symptoms, in contrast to other types of b...

    Authors: Junya Yamagishi, Masahito Asada, Hassan Hakimi, Takeshi Q. Tanaka, Chihiro Sugimoto and Shin-ichiro Kawazu

    Citation: BMC Genomics 2017 18:832

    Content type: Research article

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  26. Yeast infections are often connected with formation of biofilms that are extremely difficult to eradicate. An excellent model system for deciphering multifactorial determinants of yeast biofilm development is ...

    Authors: Jana Maršíková, Derek Wilkinson, Otakar Hlaváček, Gregor D. Gilfillan, Alexandru Mizeranschi, Timothy Hughes, Markéta Begany, Stanislava Rešetárová, Libuše Váchová and Zdena Palková

    Citation: BMC Genomics 2017 18:814

    Content type: Research article

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  27. Flagella have been lost in the vegetative phase of the diatom life cycle, but they are still present in male gametes of centric species, thereby representing a hallmark of sexual reproduction. This process, be...

    Authors: Deepak Nanjappa, Remo Sanges, Maria I. Ferrante and Adriana Zingone

    Citation: BMC Genomics 2017 18:813

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:793

    Content type: Methodology article

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

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

    Citation: BMC Genomics 2017 18:787

    Content type: Software

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

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

    Citation: BMC Genomics 2017 18:779

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:769

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:764

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:737

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:736

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:734

    Content type: Research article

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  36. Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate ada...

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

    Citation: BMC Genomics 2017 18:729

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:701

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:674

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:668

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:667

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:656

    Content type: Research article

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  42. Fungal pathogens of plants produce diverse repertoires of secondary metabolites, which have functions ranging from iron acquisition, defense against immune perturbation, to toxic assaults on the host. The whea...

    Authors: Timothy Cairns and Vera Meyer

    Citation: BMC Genomics 2017 18:631

    Content type: Research article

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  43. The effects of long-term environmental adaptation and the implications of major cellular malfunctions are still poorly understood for non-model but biotechnologically relevant species. In this study we perform...

    Authors: Josef W. Moser, Iain B. H. Wilson and Martin Dragosits

    Citation: BMC Genomics 2017 18:597

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:540

    Content type: Research article

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

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

    Citation: BMC Genomics 2017 18:501

    Content type: Research article

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  46. The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigene...

    Authors: Olivier Arnaiz, Erwin Van Dijk, Mireille Bétermier, Maoussi Lhuillier-Akakpo, Augustin de Vanssay, Sandra Duharcourt, Erika Sallet, Jérôme Gouzy and Linda Sperling

    Citation: BMC Genomics 2017 18:483

    Content type: Methodology article

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