First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First–Third Centuries AD)

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.

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Genetic characterization of skull base chondrosarcomas

Journal of Neurosurgery ◽

10.3171/2014.12.jns142059 ◽

2015 ◽

Vol 123 (4) ◽

pp. 1036-1041 ◽

Cited By ~ 9

Author(s):

Hiroki Kanamori ◽

Yohei Kitamura ◽

Tokuhiro Kimura ◽

Kazunari Yoshida ◽

Hikaru Sasaki

Keyword(s):

Skull Base ◽

Case Series ◽

Bone Neoplasms ◽

Comparative Genomic ◽

Whole Genome ◽

Whole Genome Analysis ◽

Genetic Characteristics ◽

Genome Study ◽

Skull Base Chordomas

OBJECT Although chondrosarcomas rarely arise in the skull base, chondrosarcomas and chordomas are the 2 major malignant bone neoplasms occurring at this location. The distinction of these 2 tumors is important, but this distinction is occasionally problematic because of radiological and histological overlap. Unlike chordoma and extracranial chondrosarcoma, no case series presenting a whole-genome analysis of skull base chondrosarcomas (SBCSs) has been reported. The goal of this study is to clarify the genetic characteristics of SBCSs and contrast them with those of chordomas. METHODS The authors analyzed 7 SBCS specimens for chromosomal copy number alterations (CNAs) using comparative genomic hybridization (CGH). They also examined IDH1 and IDH2 mutations and brachyury expression. RESULTS In CGH analyses, the authors detected CNAs in 6 of the 7 cases, including chromosomal gains of 8q21.1, 19, 2q22-q32, 5qcen-q14, 8q21-q22, and 15qcen-q14. Mutation of IDH1 was found with a high frequency (5 of 7 cases, 71.4%), of which R132S was most frequently mutated. No IDH2 mutations were found, and immunohistochemical staining for brachyury was negative in all cases. CONCLUSIONS To the best of the authors' knowledge, this is the first whole-genome study of an SBSC case series. Their findings suggest that these tumors are molecularly consistent with a subset of conventional central chondrosarcomas and different from skull base chordomas.

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First isolation and characterization of Brucella suis from yak

Genome ◽

10.1139/gen-2019-0101 ◽

2020 ◽

Vol 63 (8) ◽

pp. 397-405

Author(s):

Xiaowen Yang ◽

Ning Wang ◽

Xiaofang Cao ◽

Pengfei Bie ◽

Zhifeng Xing ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Health And Safety ◽

Host Cells ◽

Whole Genome ◽

Genetic Characteristics ◽

Qinghai Province ◽

Isolation And Characterization ◽

Smooth Strain

Brucella spp., facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonosis, affect public health and safety. A Brucella strain was isolated from yak in Qinghai Province. To detect whether this isolate could cause an outbreak of brucellosis and to reveal its genetic characteristics, several typing and whole-genome sequencing methods were applied to identify its species and genetic characteristics. Phylogenetic analysis based on MLVA and whole-genome sequencing revealed the genetic characteristics of the isolated strain. The results showed that the isolated strain is a B. suis biovar 1 smooth strain, and this isolate was named B. suis QH05. The results of comparative genomics and MLVA showed that B. suis QH05 is not a vaccine strain. Comparison with other B. suis strains isolated from humans and animals indicated that B. suis QH05 may be linked to specific animal and human sources. In conclusion, B. suis QH05 does not belong to the Brucella epidemic species in China, and as the first isolation of B. suis from yak, this strain expands the host range of B. suis.

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Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽

10.3390/v12020183 ◽

2020 ◽

Vol 12 (2) ◽

pp. 183 ◽

Cited By ~ 11

Author(s):

Tohru Suzuki ◽

Yoshihiro Otake ◽

Satoko Uchimoto ◽

Ayako Hasebe ◽

Yusuke Goto

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Molecular Characterization ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Wild Ruminant ◽

Genome Sequence Analysis ◽

Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

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DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells

Nucleic Acids Research ◽

10.1093/nar/gkz717 ◽

2019 ◽

Vol 47 (19) ◽

pp. e122-e122

Author(s):

Ramya Viswanathan ◽

Elsie Cheruba ◽

Lih Feng Cheow

Keyword(s):

Dna Methylation ◽

Restriction Enzyme ◽

Copy Number ◽

Dna Analysis ◽

Whole Genome Amplification ◽

Single Cells ◽

Whole Genome ◽

Copy Number Alterations ◽

Genome Wide

Abstract Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of complex cell populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single-cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.

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Full Genomic Characterization of a Lentogenic Newcastle Disease Virus Isolated from Farm-Reared Ostriches (Struthio camelus) in Northwest China

Genome Announcements ◽

10.1128/genomea.01590-16 ◽

2017 ◽

Vol 5 (6) ◽

Cited By ~ 2

Author(s):

Shanhui Ren ◽

Chongyang Wang ◽

Xiaolong Gao ◽

Xue Zhang ◽

Xiangwei Wang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Newcastle Disease Virus ◽

Disease Virus ◽

Newcastle Disease ◽

Northwest China ◽

Whole Genome Sequence ◽

Whole Genome ◽

Struthio Camelus ◽

Genomic Characterization

ABSTRACT To our knowledge, our study is the first to report the whole-genome sequence of an ostrich-origin Newcastle disease virus (NDV) isolate, abbreviated as Ostrich/SX-01/06. Phylogenetic analysis revealed that this isolate belongs to the subgenotype c in class II. The identification of the complete genome will provide useful information regarding ostrich diseases, especially NDV.

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Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

Foods ◽

10.3390/foods10112637 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2637

Author(s):

Jolien D’aes ◽

Marie-Alice Fraiture ◽

Bert Bogaerts ◽

Sigrid C. J. De Keersmaecker ◽

Nancy H. C. Roosens ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetically Modified ◽

Added Value ◽

Phylogenomic Analysis ◽

Whole Genome ◽

Antimicrobial Resistance Genes ◽

Long Read ◽

Genomic Characterization

Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.

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One year of SARS-CoV-2: Genomic characterization of COVID-19 outbreak in Qatar

10.1101/2021.05.19.21257433 ◽

2021 ◽

Author(s):

Fatiha M. Benslimane ◽

Hebah A. AlKhatib ◽

Ola Al-Jamal ◽

Dana Albatesh ◽

Sonia Boughattas ◽

...

Keyword(s):

International Travel ◽

Genomic Diversity ◽

Whole Genome ◽

Genome Sequences ◽

Short Period ◽

National Response ◽

Genomic Characterization ◽

One Year ◽

Local Transmission

The state of Qatar has emerged as a major transit hub connecting all parts of the globe, making it as a hotspot for infectious disease introduction and providing an ideal setting to monitor the emergence and spread of variants. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population's genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number in the mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. This raises the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor SARS-CoV-2 profile and re-emergence in Qatar.

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Whole-Genome Mate-Pair Sequencing (MPseq) Improves Genomic Characterization of Patients with Hematologic Malignancies

Cancer Genetics ◽

10.1016/j.cancergen.2016.04.036 ◽

2016 ◽

Vol 209 (6) ◽

pp. 294-295

Author(s):

Stephanie A. Smoley ◽

Sarah H. Johnson ◽

George Vasmatzis ◽

Hutton M. Kearney ◽

Rhett P. Ketterling ◽

...

Keyword(s):

Hematologic Malignancies ◽

Whole Genome ◽

Mate Pair ◽

Genomic Characterization

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Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020

Viruses ◽

10.3390/v13102041 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2041

Author(s):

Hai-Quynh Do ◽

Van-Giap Nguyen ◽

Chul-Un Chung ◽

Yong-Shin Jeon ◽

Sook Shin ◽

...

Keyword(s):

New Species ◽

Bioinformatics Analysis ◽

Whole Genome Sequence ◽

In Silico Prediction ◽

Genetic Characteristics ◽

Genomic Characterization ◽

Eptesicus Serotinus ◽

A New Species ◽

Generation Sequencing

Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.

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