TY  - JOUR
A1  - Gupta, Shishir K.
A1  - Srivastava, Mugdha
A1  - Osmanoglu, Özge
A1  - Xu, Zhuofei
A1  - Brakhage, Axel A.
A1  - Dandekar, Thomas
T1  - Aspergillus fumigatus versus genus Aspergillus: conservation, adaptive evolution and specific virulence genes
JF  - Microorganisms
N2  - Aspergillus is an important fungal genus containing economically important species, as well as pathogenic species of animals and plants. Using eighteen fungal species of the genus Aspergillus, we conducted a comprehensive investigation of conserved genes and their evolution. This also allows us to investigate the selection pressure driving the adaptive evolution in the pathogenic species A. fumigatus. Among single-copy orthologs (SCOs) for A. fumigatus and the closely related species A. fischeri, we identified 122 versus 50 positively selected genes (PSGs), respectively. Moreover, twenty conserved genes of unknown function were established to be positively selected and thus important for adaption. A. fumigatus PSGs interacting with human host proteins show over-representation of adaptive, symbiosis-related, immunomodulatory and virulence-related pathways, such as the TGF-β pathway, insulin receptor signaling, IL1 pathway and interfering with phagosomal GTPase signaling. Additionally, among the virulence factor coding genes, secretory and membrane protein-coding genes in multi-copy gene families, 212 genes underwent positive selection and also suggest increased adaptation, such as fungal immune evasion mechanisms (aspf2), siderophore biosynthesis (sidD), fumarylalanine production (sidE), stress tolerance (atfA) and thermotolerance (sodA). These genes presumably contribute to host adaptation strategies. Genes for the biosynthesis of gliotoxin are shared among all the close relatives of A. fumigatus as an ancient defense mechanism. Positive selection plays a crucial role in the adaptive evolution of A. fumigatus. The genome-wide profile of PSGs provides valuable targets for further research on the mechanisms of immune evasion, antimycotic targeting and understanding fundamental virulence processes.
KW  - molecular evolution
KW  - phylogenetic analysis
KW  - adaptation
KW  - recombination
KW  - positive selection
KW  - human pathogenic fungi
KW  - genus Aspergillus
KW  - Aspergillus fumigatus
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-246318
SN  - 2076-2607
VL  - 9
IS  - 10
ER  - 
TY  - JOUR
A1  - Gupta, Shishir K.
A1  - Minocha, Rashmi
A1  - Thapa, Prithivi Jung
A1  - Srivastava, Mugdha
A1  - Dandekar, Thomas
T1  - Role of the pangolin in origin of SARS-CoV-2: an evolutionary perspective
JF  - International Journal of Molecular Sciences
N2  - After the recent emergence of SARS-CoV-2 infection, unanswered questions remain related to its evolutionary history, path of transmission or divergence and role of recombination. There is emerging evidence on amino acid substitutions occurring in key residues of the receptor-binding domain of the spike glycoprotein in coronavirus isolates from bat and pangolins. In this article, we summarize our current knowledge on the origin of SARS-CoV-2. We also analyze the host ACE2-interacting residues of the receptor-binding domain of spike glycoprotein in SARS-CoV-2 isolates from bats, and compare it to pangolin SARS-CoV-2 isolates collected from Guangdong province (GD Pangolin-CoV) and Guangxi autonomous regions (GX Pangolin-CoV) of South China. Based on our comparative analysis, we support the view that the Guangdong Pangolins are the intermediate hosts that adapted the SARS-CoV-2 and represented a significant evolutionary link in the path of transmission of SARS-CoV-2 virus. We also discuss the role of intermediate hosts in the origin of Omicron.
KW  - COVID-19
KW  - SARS-CoV-2
KW  - origin
KW  - evolution
KW  - intermediate host
KW  - pangolin
KW  - mutation
KW  - recombination
KW  - adaptation
KW  - transmission
KW  - comparative sequence analysis
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285995
SN  - 1422-0067
VL  - 23
IS  - 16
ER  -