OBM Genetics is an international Open Access journal published quarterly online by LIDSEN Publishing Inc. It accepts papers addressing basic and medical aspects of genetics and epigenetics and also ethical, legal and social issues. Coverage includes clinical, developmental, diagnostic, evolutionary, genomic, mitochondrial, molecular, oncological, population and reproductive aspects. It publishes a variety of article types (Original Research, Review, Communication, Opinion, Comment, Conference Report, Technical Note, Book Review, etc.). There is no restriction on the length of the papers and we encourage scientists to publish their results in as much detail as possible.

Publication Speed (median values for papers published in 2023): Submission to First Decision: 5.1 weeks; Submission to Acceptance: 17.0 weeks; Acceptance to Publication: 7 days (1-2 days of FREE language polishing included)

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Special Issue

Pneumocystis: A Model of Adaptive Coevolution

Submission Deadline: October 31, 2018 (Closed) Submit Now

Guest Editors

Andrés Moya

Prof. of Genetics, Institute of Integrative Systems Biology (University of Valencia), FISABIO Foundation for Biomedical Research and CIBER in Epidemiology and Public Health (CIBERESP), Spain

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Research Interests: genome evolution, symbiosis, microbiome

Enrique J.Calderón

Associate Prof. of Medicine, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, and Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Spain

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Research Interests: Infectious diseases, Pneumcystosis

Luis Delaye

Prof. of Bioinformatics, CINVESTAV Irapuato, México

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Research Interests: molecular evolution, phylogenetic inference

About This Topic

Pneumocystis organisms, which were first reported and named Pneumocystis carinii at the beginning of the last century, were long considered as protozoans and a single species based on morphologic features and the resistance to classical antifungal agents. The lack of a continuous in vitro system was a major obstacle to Pneumocystis research and these organisms were largely ignored until the dramatic increase in the incidence of Pneumocystis pneumonia that occurred with the emergence of the human immunodeficiency virus (HIV) pandemic, which made pneumocystosis a major medical and public health problem in the 1980s. However, this obvious pathogenic Pneumocystis–host interaction is only the tip of the iceberg, and recent findings suggest that the vast majority of mammal–Pneumocystis interactions led to relatively benign colonization, rather than pneumonia.

Molecular and biochemical studies have provided clear evidence for the placement of Pneumocystis with fungi, and based on genomic or phenotypic divergence, multiple Pneumocystis species have been recognized. Genetic data, in addition, suggested that speciation in the group resulted from long genetic isolation and co-evolution in parallel with mammal species.

In this special issue of OBM Genetics, we present the state-of-the art of the genetics and the coevolution of Pneumocystis in different mammalian species in a broad perspective, although with a particular emphasis on the human host. Reviews and methodological papers related with the topic are also welcome.

Planned Papers

Title: Dihydropteroate synthase (DHPS) polymorphisms in Pneumocystis jirovecii
Authors: Carmen de la Horra, Vicente Friaza, Rubén Morilla, María Mercedes Panizo, Yaxsier de Armas, Gustavo Wissmann, Enrique J. Calderón

Manuscript Submission Information

Manuscripts should be submitted through the LIDSEN Submission System. Detailed information on manuscript preparation and submission is available in the Instructions for Authors. All submitted articles will be thoroughly refereed through a single-blind peer-review process and will be processed following the Editorial Process and Quality Control policy. Upon acceptance, the article will be immediately published in a regular issue of the journal and will be listed together on the special issue website, with a label that the article belongs to the Special Issue. LIDSEN distributes articles under the Creative Commons Attribution (CC BY 4.0) License in an open-access model. The authors own the copyright to the article, and the article can be free to access, distribute, and reuse provided that the original work is correctly cited.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). Research articles and review articles are highly invited. Authors are encouraged to send the tentative title and abstract of the planned paper to the Editorial Office (genetics@lidsen.com) for record. If you have any questions, please do not hesitate to contact the Editorial Office.

Welcome your submission!


Open Access Original Research

Genes Coding for GPI Biosynthesis in Pneumocystis Experienced Relaxed Selection: A Follow-up Study

Received: 05 May 2019;  Published: 11 July 2019;  doi: 10.21926/obm.genet.1903083


Background: Phylogenetic analyses shows that Pneumocystis species have coevolved with their mammalian hosts for millions of years. As a result, infection by Pneumocystis is species specific (i.e. a given Pneumocystis species can infect only a single species of host). This specificity suggests the existence of a Red-Queen dynamic between Pneumo [...]
Open Access Review

Airborne Interindividual Transmission of Pneumocystis jirovecii

Received: 17 December 2018;  Published: 22 May 2019;  doi: 10.21926/obm.genet.1902080


Pneumocystis pneumonia (PCP) is still the most frequent AIDS-defining disease in developed countries and also concerns patients with other immunodeficiencies not associated with HIV. Experimental studies on rodent models carried out in the early eighties have showed that Pneumocystis sp. can be transmitted by the airborne route. Unfortunatel [...]
Open Access Review

Pneumocystis Species Co-evolution: State-of-the-Art Review

Received: 22 February 2019;  Published: 15 May 2019;  doi: 10.21926/obm.genet.1902078


At the end of the 20th century, the notion of a unique species in the genus Pneumocystis (i.e. Pneumocystis carinii) was challenged and our understanding of the natural history of pneumocystosis was drastically changed. It is now accepted that the Pneumocystis genus comprises multiple stenoxenic biological entities that are widely distributed [...]
Open Access Research Article

New DNA Extraction Method for the Detection of Pneumocystis in Lung Tissue Samples of Colonized Individuals

Received: 30 January 2019;  Published: 18 March 2019;  doi: 10.21926/obm.genet.1901066


Background: Pneumocystis jirovecii colonization in patients is associated with a low organism burden, which supports the need to use highly sensitive molecular techniques, such as nested-PCR to determine the presence of the organism. However, few studies have considered the effect of nucleic acid extraction methods on the detection of P. jirov [...]
Open Access Review

Genotyping Pneumocystis jirovecii: Impacting Our Understanding of Interhuman Transmission

Received: 04 December 2018;  Published: 17 January 2019;  doi: 10.21926/obm.genet.1901060


Pneumocystis jirovecii is an atypical fungus transmitted via interhuman airborn contact. This fungus is exclusively associated with humans and almost each individual has encountered it at least once before reaching the age of two. Pneumocystis jirovecii can be responsible for spontaneously resolutive symptoms in infants and for severe pneumoc [...]
Open Access Review

Pneumocystis as a Co-Factor in Pulmonary Diseases

Received: 02 November 2018;  Published: 27 December 2018;  doi: 10.21926/obm.genet.1804057


Pneumocystis causes life-threatening pneumonia in immunocompromised populations. More recently it has been implicated as a co-factor in a number of chronic lung diseases including chronic obstructive pulmonary disease (COPD), severe asthma, and cystic fibrosis. In this review, we will examine the current literature regarding Pneumocystis and [...]
Open Access Review

Reminiscence from Half a Century of Anti-Pneumocystis Drug Discovery and Development

Received: 12 September 2018;  Published: 06 December 2018;  doi: 10.21926/obm.genet.1804052


Experiences with Pneumocystis carinii and Pneumocystis jirovecii over the past one-half century are recounted. Circumstances threatening the lives of children with fatal Pneumocystis pneumonia (PCP) in 1969 led to discovery of the anti-P. carinii activity of trimethoprim-sulfamethoxazole in the laboratory. This was followed by clinical trials [...]
Open Access Review

Pneumocystis jirovecii Pneumonia: Current Advances in Laboratory Diagnosis

Received: 21 August 2018;  Published: 13 November 2018;  doi: 10.21926/obm.genet.1804049


Pneumocystis jirovecii pneumonia (PcP) remains a major cause of respiratory illness among immunocompromised patients. PcP is difficult to diagnose, in particular in non-HIV-infected patients due to the lack of specific clinical data associated. Since P. jirovecii could not be cultivated for many years, microscopic visualization of cystic [...]
Open Access Review

The Relationship between Pneumocystis Infection in Animal and Human Hosts, and Climatological and Environmental Air Pollution Factors: A Systematic Review

Received: 14 September 2018;  Published: 25 October 2018;  doi: 10.21926/obm.genet.1804045


Background: Over the past decade, there has been rising interest in the interaction of Pneumocystis with the environment. This interest has arisen in part from the demonstration that environmental factors have important effects on the viability and transmission of microbes, including Pneumocystis. Environmental factors include climatological [...]