Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2

Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.

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Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China

Viruses ◽

10.3390/v13071322 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1322

Author(s):

Ruiming Hu ◽

Leyi Wang ◽

Qingyun Liu ◽

Lin Hua ◽

Xi Huang ◽

...

Keyword(s):

Selection Pressure ◽

Pseudorabies Virus ◽

Viral Evolution ◽

Infectious Agent ◽

Genomic Diversity ◽

Whole Genome Sequence ◽

Evolutionary Constraint ◽

The Novel ◽

Novel Variants ◽

Pressure Analysis

Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and evolution is still limited. Here, we sequenced 54 genomes of novel PRV variants isolated in China from 2012 to 2017. Phylogenetic analysis revealed that China strains and US/Europe strains were classified into two separate genotypes. PRV strains isolated from 2012 to 2017 in China are highly related to each other and genetically close to classic China strains such as Ea, Fa, and SC. RDP analysis revealed 23 recombination events within novel PRV variants, indicating that recombination contributes significantly to the viral evolution. The selection pressure analysis indicated that most ORFs were under evolutionary constraint, and 19 amino acid residue sites in 15 ORFs were identified under positive selection. Additionally, 37 unique mutations were identified in 19 ORFs, which distinguish the novel variants from classic strains. Overall, our study suggested that novel PRV variants might evolve from classical PRV strains through point mutation and recombination mechanisms.

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Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients

10.1101/2020.09.04.282616 ◽

2020 ◽

Cited By ~ 1

Author(s):

Anthony Levasseur ◽

Jeremy Delerce ◽

Aurelia Caputo ◽

Ludivine Brechard ◽

Philippe Colson ◽

...

Keyword(s):

Stop Codon ◽

Genomic Diversity ◽

The Novel ◽

Viral Isolate ◽

Mutational Signatures ◽

Phylogenetic Origin ◽

Substitution Mutations ◽

Novel Coronavirus ◽

Shed Light ◽

French Cohort

ABSTRACTThe novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.

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Unlocking the genomic taxonomy of the Prochlorococcus collective

10.1101/2020.03.09.980698 ◽

2020 ◽

Cited By ~ 1

Author(s):

Diogo Tschoeke ◽

Livia Vidal ◽

Mariana Campeão ◽

Vinícius W. Salazar ◽

Jean Swings ◽

...

Keyword(s):

Genomic Data ◽

Genomic Diversity ◽

The Novel ◽

Ecological Attributes ◽

Pan Genome ◽

Ecological Literature ◽

Genomic Taxonomy ◽

Single Genus

ABSTRACTProchlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus and Riococcus. The novel genera have distinct genomic and ecological attributes.

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Mutational hotspots and conserved domains of SARS-CoV-2 genome in African population

Beni-Suef University Journal of Basic and Applied Sciences ◽

10.1186/s43088-021-00102-1 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Olabode E. Omotoso ◽

Ayoade D. Babalola ◽

Amira Matareek

Keyword(s):

Global Economy ◽

African Population ◽

The Novel ◽

Conserved Domains ◽

Nucleocapsid Proteins ◽

Genome Variability ◽

Promising Strategy ◽

Mutational Hotspots ◽

Novel Coronavirus ◽

Complete Protein

Abstract Background Since outbreak in December 2019, the highly infectious and pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over a million deaths globally. With increasing burden, the novel coronavirus has posed a dire threat to public health, social interaction, and global economy. Mutations in the SARS-CoV-2 genome are moderately evolving which might have contributed to its genome variability, transmission, replication efficiency, and virulence in different regions of the world. Results The present study elucidated the mutational landscape in the SARS-CoV-2 genome among the African populace, which may have contributed to the virulence, spread, and pathogenicity observed in the region. A total of 3045 SARS-CoV-2 complete protein sequences with the reference viral sequence (EPI_ISL_402124) were mined and analyzed. SARS-CoV-2 ORF1ab, spike, ORF3, ORF8, and nucleocapsid proteins were observed as mutational hotspots in the African population and may be of keen interest in understanding the viral host relationship, while there is conservation in the ORF6, ORF7a, ORF7b, ORF10, envelope, and membrane proteins. Conclusions The accumulation of moderate mutations (though slowly), in the SARS-CoV-2 genome as seen in this present study, could be a promising strategy to develop antiviral drugs or vaccines. These antiviral interventions should target viral conserved domains and host cellular proteins and/or receptors involved in viral invasion and replication to avoid a new viral wave due to drug resistance and vaccine evasion.

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Becoming a Crorepati: From Glocal TV Game to Grobal Fiction

Asiatische Studien – Études Asiatiques ◽

10.1515/asia-2019-0053 ◽

2020 ◽

Vol 73 (3) ◽

pp. 497-520

Author(s):

Nicola Pozza

Keyword(s):

Effective Means ◽

The Novel ◽

Cultural Products ◽

Slumdog Millionaire ◽

Interactive Nature ◽

Tv Show ◽

Shed Light ◽

The Way

AbstractNumerous studies have dealt with the process of globalization and its various cultural products. Three such cultural products illustrate this process: Vikas Swarup’s novel Q and A (2005), the TV quiz show Kaun banega crorepati? (Who Wants to Be a Millionaire?), and Danny Boyle’s film Slumdog Millionaire (2008). The novel, the TV show and the film have so far been studied separately. Juxtaposing and comparing Q and A, Kaun banega crorepati, and Slumdog Millionaire provides an effective means to shed light on the dialogic and interactive nature of the process of globalization. It is argued through this case study that an analysis of their place of production, language and content, helps clarify the derivative concepts of “glocalization” and “grobalization” with regard to the way(s) contemporary cultural products respond to globalization.

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Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0009665 ◽

2021 ◽

Vol 15 (8) ◽

pp. e0009665

Author(s):

Shuai Xu ◽

Zhenpeng Li ◽

Yuanming Huang ◽

Lichao Han ◽

Yanlin Che ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Trees ◽

Gene Families ◽

Single Copy ◽

Taxonomic Classification ◽

Genomic Diversity ◽

Evolutionary Relationships ◽

Taxonomic Structure ◽

Pan Genome ◽

Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

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Sorghum pan-genome explores the functional utility to accelerate the genetic gain

10.1101/2021.02.02.429137 ◽

2021 ◽

Author(s):

Pradeep Ruperao ◽

Nepolean Thirunavukkarasu ◽

Prasad Gandham ◽

Sivasubramani S. ◽

Govindaraj M ◽

...

Keyword(s):

Genetic Gain ◽

Core Genome ◽

Agronomic Traits ◽

Crop Improvement ◽

Genomic Diversity ◽

Pan Genome ◽

Genome Association ◽

Reference Genomes ◽

Insight Into ◽

Variable Genes

AbstractSorghum (Sorghum bicolor L.) is one of the most important food crops in the arid and rainfed production ecologies. It is a part of resilient farming and is projected as a smart crop to overcome the food and nutritional challenges in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.

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Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds

Frontiers in Microbiology ◽

10.3389/fmicb.2021.677558 ◽

2021 ◽

Vol 12 ◽

Author(s):

Carlos Caicedo-Montoya ◽

Monserrat Manzo-Ruiz ◽

Rigoberto Ríos-Estepa

Keyword(s):

Comparative Genomics ◽

Sequence Similarity ◽

Experimental Studies ◽

Gene Clusters ◽

Antibiotic Activity ◽

Genomic Diversity ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Genus Streptomyces ◽

Pan Genome

Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.

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The Whole-Genome Sequence of the Novel Yeast Species Metschnikowia persimmonesis Isolated from Medicinal Plant Diospyros kaki Thunb

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab246 ◽

2021 ◽

Author(s):

Endang Rahmat ◽

Inkyu Park ◽

Youngmin Kang

Keyword(s):

Gc Content ◽

Whole Genome Sequence ◽

Diospyros Kaki ◽

Whole Genome ◽

The Novel ◽

Data Set ◽

Draft Assembly ◽

Future Possibility ◽

Complete Set ◽

New Yeast

Abstract The new yeast Metschnikowia persimmonesis KCTC 12991BP (KIOM G15050 strain) exhibits strong antimicrobial activity against some pathogens. This activity may be related to the medicinal profile of secondary metabolites that could be found in the genome of this species. Therefore, to explore its future possibility of producing some beneficial activities, including medicinal ability, we report high quality whole-genome assembly of M. persimmonesis produced by PacBio RSII sequencer. The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set. The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7,029 genes and 6,939 functionally annotated proteins. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), M. persimmonesis was proved to a novel species within the Metschnikowia genus. This finding is expected to significantly contribute to the discovery of high-value natural products from M. persimmonesis as well as for genome biology and evolution comparative analysis within Metschnikowia species.

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Firefly genomes illuminate parallel origins of bioluminescence in beetles

10.1101/237586 ◽

2017 ◽

Cited By ~ 1

Author(s):

Timothy R. Fallon ◽

Sarah E. Lower ◽

Ching-Ho Chang ◽

Manabu Bessho-Uehara ◽

Gavin J. Martin ◽

...

Keyword(s):

Firefly Luciferase ◽

Chemical Defenses ◽

Photinus Pyralis ◽

Click Beetles ◽

Origin And Evolution ◽

The North ◽

Click Beetle ◽

Light Organs ◽

The Caribbean ◽

Shed Light

AbstractFireflies and their fascinating luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of their bioluminescence remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North AmericanPhotinus pyralisand JapaneseAquatica lateralis.We also sequenced the genome of a related click-beetle, the CaribbeanIgnelater luminosus,with bioluminescent biochemistry near-identical to fireflies, but anatomically unique light organs, suggesting the intriguing but contentious hypothesis of parallel gains of bioluminescence. Our analyses support two independent gains of bioluminescence between fireflies and click-beetles, and provide new insights into the genes, chemical defenses, and symbionts that evolved alongside their luminous lifestyle.One Sentence Summary:Comparative analyses of the first linkage-group-resolution genomes of fireflies and related bioluminescent beetles address long-standing questions of the origin and evolution of bioluminescence and its associated traits.

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