genomic characterization
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Pedosphere ◽  
2022 ◽  
Vol 32 (3) ◽  
pp. 495-502
João Pedro Rueda FURLAN ◽  
Inara Fernanda Lage GALLO ◽  
Eliana Guedes STEHLING

Cheng-He Sun ◽  
Ya-Nan Zhang ◽  
Xiao-Shu Zeng ◽  
Da-Wei Liu ◽  
Qi Huang ◽  

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 136
Flavio De Angelis ◽  
Marco Romboni ◽  
Virginia Veltre ◽  
Paola Catalano ◽  
Cristina Martínez-Labarga ◽  

This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first–third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops.

2022 ◽  
Vol 12 ◽  
Dong Zhang ◽  
Yiliang He ◽  
Karina Yew-Hoong Gin

Cyanobacteria are one of the dominant autotrophs in tropical freshwater communities, yet phages infecting them remain poorly characterized. Here we present the characterization of cyanophage S-SRP02, isolated from a tropical freshwater lake in Singapore, which infects Synechococcus sp. Strain SR-C1 isolated from the same lake. S-SRP02 represents a new evolutionary lineage of cyanophage. Out of 47 open reading frames (ORFs), only 20 ORFs share homology with genes encoding proteins of known function. There is lack of auxiliary metabolic genes which was commonly found as core genes in marine cyanopodoviruses. S-SRP02 also harbors unique structural genes highly divergent from other cultured phages. Phylogenetic analysis and viral proteomic tree further demonstrate the divergence of S-SRP02 from other sequenced phage isolates. Nonetheless, S-SRP02 shares synteny with phage genes of uncultured phages obtained from the Mediterranean Sea deep chlorophyll maximum fosmids, indicating the ecological importance of S-SRP02 and its related viruses. This is further supported by metagenomic mapping of environmental viral metagenomic reads onto the S-SRP02 genome.

Celia Boukadida ◽  
Blanca Taboada ◽  
Marina Escalera-Zamudio ◽  
Pavel Isa ◽  
José Ernesto Ramírez-González ◽  

The genetic association of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with different clinical conditions remains unclear and needs further investigation. In this study, we characterized 57 complete SARS-CoV-2 genomes from patients in Mexico with distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased.

Jonathan Lombardino ◽  
Swati Bijlani ◽  
Nitin K. Singh ◽  
Jason M. Wood ◽  
Richard Barker ◽  

Sphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth.

2022 ◽  
Vol 8 (1) ◽  
pp. 66
Ceth W. Parker ◽  
Marcus de Melo Teixeira ◽  
Nitin K. Singh ◽  
Huzefa A. Raja ◽  
Kristof B. Cank ◽  

A fungal strain (FJII-L10-SW-P1) was isolated from the Mars 2020 spacecraft assembly facility and exhibited biofilm formation on spacecraft-qualified Teflon surfaces. The reconstruction of a six-loci gene tree (ITS, LSU, SSU, RPB1 and RPB2, and TEF1) using multi-locus sequence typing (MLST) analyses of the strain FJII-L10-SW-P1 supported a close relationship to other known Parengyodontium album subclade 3 isolates while being phylogenetically distinct from subclade 1 strains. The zig-zag rachides morphology of the conidiogenous cells and spindle-shaped conidia were the distinct morphological characteristics of the P. album subclade 3 strains. The MLST data and morphological analysis supported the conclusion that the P. album subclade 3 strains could be classified as a new species of the genus Parengyodontium and placed in the family Cordycipitaceae. The name Parengyodontium torokii sp. nov. is proposed to accommodate the strain, with FJII-L10-SW-P1 as the holotype. The genome of the FJII-L10-SW-P1 strain was sequenced, annotated, and the secondary metabolite clusters were identified. Genes predicted to be responsible for biofilm formation and adhesion to surfaces were identified. Homology-based assignment of gene ontologies to the predicted proteome of P. torokii revealed the presence of gene clusters responsible for synthesizing several metabolic compounds, including a cytochalasin that was also verified using traditional metabolomic analysis.

Ramya Ramadoss ◽  
Fajer Al-Marzooqi ◽  
Basem Shomar ◽  
Valentin Alekseevich Ilyin ◽  
Annette Shoba Vincent

We report the genome sequences of Escherichia phage C600M2 (length, 88,162 bp; G+C content, 38.98%) and Escherichia phage CL1 (length, 87,820 bp; G+C content, 41.32%), which were isolated from a wastewater treatment plant in Qatar. Both Escherichia phage C600M2 and Escherichia phage CL1 genomes contain 128 protein-coding genes and 26 tRNAs.

David A. Read ◽  
Genevieve D. Thompson ◽  
Nathan Le Cordeur ◽  
Dirk Swanevelder ◽  
Gerhard Pietersen

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