Whole Genome Sequencing and the Zygomycota

Gryganskyi, Andrii P.; Muszewska, Anna

doi:10.4172/2165-8056.1000e116

Cited by 15 publications

(11 citation statements)

References 18 publications

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“…Thus, adopting and interpreting such data need the support of further studies to validate the proposed changes. Moreover, the use of these data does not exclude the possibility of genome duplication, even with the use of conservative orthologs, and issues related to ancient lineage sorting events (71). As DNA sequence technologies advance, new changes in the higher classification of these fungi are expected.…”

Section: Taxonomy and Phylogeny Entomophthorales: Traditional And Curmentioning

confidence: 99%

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Human Pathogenic Entomophthorales

Vilela

Mendoza

2018

Clin Microbiol Rev

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SUMMARYThe pathogenic entomophthoralean fungi cause infection in insects and mammalian hosts. and species can be found in soil and insect, reptile, and amphibian droppings in tropical and subtropical areas. The life cycles of these fungi occur in these environments where infecting sticky conidia are developed. The infection is acquired by insect bite or contact with contaminated environments through open skin. typically causes chronic rhinofacial disease in immunocompetent hosts, whereas some species can be found in immunocompromised patients. infection is restricted to subcutaneous tissues but may be involved in intestinal and disseminated infections. Its early diagnosis remains challenging due to clinical similarities to other intestinal diseases. Infected tissues characteristically display eosinophilic granulomas with the Splendore-Höeppli phenomenon. However, in immunocompromised patients, the above-mentioned inflammatory reaction is absent. Laboratory diagnosis includes wet mount, culture serological assays, and molecular methodologies. The management of entomophthoralean fungi relies on traditional antifungal therapies, such as potassium iodide (KI), amphotericin B, itraconazole, and ketoconazole, and surgery. These species are intrinsically resistant to some antifungals, prompting physicians to experiment with combinations of therapies. Research is needed to investigate the immunology of entomophthoralean fungi in infected hosts. The absence of an animal model and lack of funding severely limit research on these fungi.

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Section: Taxonomy and Phylogeny Entomophthorales: Traditional And Curmentioning

confidence: 99%

“…The Entomophthoramycota comprise around 280 species (63,71). Their detection in nature requires special methods; thus, their occurrence in these environments was seldom noted in early mycological studies (75).…”

Section: Biologymentioning

confidence: 99%

Human Pathogenic Entomophthorales

Vilela

Mendoza

2018

Clin Microbiol Rev

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“…However, unlike Dikarya for which genome data and phylogenomic analyses have transformed our understanding of phylogenetic relationships and evolutionary processes (e.g. Floudas et al 2012, Nagy et al 2014, Kohler et al 2015), genome data for zygomycetes have been sparse with respect to phylogenetic depth and breadth (Gryganskyi and Muszewska 2014). These gaps in our knowledge of zygomycete evolution have manifested in a poor understanding of the homology of numerous life history traits essential to Fungi.…”

Section: Introductionmentioning

confidence: 99%

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

et al. 2016

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Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.

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“…In genomic studies a major portion of study was focused on comparative genomics [1][2][3][4] and genome sequencing [5][6][7][8][9]. As soon as human genome project completed during 2003, there was an outburst in number of genome sequencing project was observed.…”

Section: Introductionmentioning

confidence: 99%

“…And also these methods were too much expensive as well as time consuming. And thus high throughput sequencing methods were taken into consideration [9][10][11][12][13][14]. Maxam-Gilbert sequencing method was one of the early DNA sequencing methods where any DNA sequence can be determined using synthetic location-specific primers during 1973.…”

Section: Introductionmentioning

confidence: 99%

A Review on New Horizons of Bioinformatics in Next Generation Sequencing, Viral and Cancer Genomics

Sharma¹

2016

Int J Biomed Data Min

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Genomics and molecular biology has always been a constant source of inspiration and motivational research for worldwide researchers in field of biology and biotechnology. These two fields have always generated a huge amount of data and in order to compile and analyze those, bioinformatics came into action during last decade. Implementation of bioinformatics has a clear intention of doing all these analysis of data in efficient and fast manner in order to cut down the expensive laboratory equipment, chemicals and most precious time. Mostly genomic data is composed of sequencing results at a higher scale and that is why manual curating and handling of these data is quite difficult. Supreme aim of this review is to make awareness about bioinformatics options in cancer genomics and viral genomics apart from next generation sequencing. Next generation sequencing or high throughput sequencing has helped a lot to replace old conventional method of sequencing and with the help of recent advances in technologies. These technologies are very efficient, fast and cheaper also as compare to conventional methods. Recently used methods were also discussed under appropriate headings. Role of bioinformatics is getting bigger and bigger in management and analysis of enormous amount of biological data generated through medical, biotechnological and clinical research globally. But we still need to understand challenges and limitation of bioinformatics as well as reliability.

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Whole Genome Sequencing and the Zygomycota

Cited by 15 publications

References 18 publications

Human Pathogenic Entomophthorales

Human Pathogenic Entomophthorales

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

A Review on New Horizons of Bioinformatics in Next Generation Sequencing, Viral and Cancer Genomics

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