scholarly journals The Genome of Medicinal Leech (Whitmania pigra) and comparative genomic study for Exploration of Bioactive Ingredients

2020 ◽  
Author(s):  
Lei Tong ◽  
Shao-Xing Dai ◽  
De-Jun Kong ◽  
Peng-Peng Yang ◽  
Xin Tong ◽  
...  
Keyword(s):  
Gene Families ◽  
Bioactive Molecules ◽  
Comparative Genomic ◽  
Protein Coding ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Bioactive Ingredients ◽  
The Difference ◽  
Medicinal Leeches ◽  
Whitmania Pigra

Abstract BackgroundLeeches are classic annelids that have a huge diversity and closely related to people, especially medicinal leeches. Medicinal leeches have been widely utilized in medicine based on the pharmacological activities of their bioactive ingredients. Comparative genomic study of these leeches enables us to understand the difference among medicinal leeches and other leeches and facilitates the discovery of bioactive ingredients.ResultsIn this study, we reported the genome of Whitmania pigra and compared it with Hirudo medicinalis and Helobdella robusta. The assembled genome size of W. pigra is 177 Mbp, close to the estimated genome. Approximately about 23% of the genome was repetitive. A total of 26,743 protein-coding genes were subsequently predicted. W. pigra have 12346 (46%) and 10295 (38%) orthologous genes with H. medicinalis and H. robusta, respectively. About 20% and 24% genes in W. pigra showed syntenic arrangement with H. medicinalis and H. robusta, respectively, revealed by gene synteny analysis. Furthermore, W. pigra, H. medicinalis and H. robusta expanded different gene families enriched in different biological processes. By inspecting genome distribution and gene structure of hirudin, we identified a new hirudin gene g17108 (hirudin_2) with different cysteine pattern. Finally, we systematically explored and compared the active substances in the genomes of three leeches. The results showed that W. pigra and H. medicinalis exceed H. robusta in both kinds and gene number of active molecules.ConclusionsThis study reported the genome of W. pigra and compared it with other two leeches, which provides an important genome resource and new insight into the exploration and development of bioactive molecules of medicinal leeches.

scholarly journals The Genome of Medicinal Leech (Whitmania pigra) for Exploration of Bioactive Ingredients

2020 ◽  
Author(s):  
Lei Tong ◽  
Shao-Xing Dai ◽  
De-Jun Kong ◽  
Peng-Peng Yang ◽  
Xin Tong ◽  
...  
Keyword(s):  
Gene Families ◽  
Medicinal Leech ◽  
Bioactive Molecules ◽  
Protein Coding ◽  
Helobdella Robusta ◽  
Bioactive Ingredients ◽  
Medicinal Leeches ◽  
Whitmania Pigra ◽  
Insight Into ◽  
Active Substances

Abstract BackgroundLeeches are classic annelids that have a huge diversity and closely related to people, especially medicinal leeches. Medicinal leeches have been widely utilized in medicine based on the pharmacological activities of their bioactive ingredients. The discovery of bioactive ingredients is hindered heavily due to the lack of the genome of medicinal leeches.ResultsTo facilitate this discovery and the research of medicinal leeches, we reported the first genome of the medicinal leech (Whitmania pigra). The assembled genome size of W. pigra is 177 Mbp, close to the estimated genome. Approximately about 23% of the genome was repetitive. A total of 26,743 protein-coding genes were subsequently predicted. There are only 9799 (57%) orthologous genes between W. pigra and Helobdella robusta. And only 16% genes in W. pigra showed syntenic arrangement with H. robusta revealed by gene synteny analysis. Furthermore, W. pigra and H. robusta expanded different gene families enriched in the ‘calcium ion’ and ‘sodium ion’ related functions, respectively. By inspecting genome distribution and gene structure of hirudin, we identified a new hirudin gene g17108 (hirudin_2) with different cysteine pattern. At last, we systematically explored and compared the active substances in the genomes of two leeches. The results showed that W. pigra exceeds H. robusta in both kinds and gene number of active molecules.ConclusionsThis study reported the first genome of the medicinal leech (W. pigra), which provides an important genome resource and new insight into the exploration and development of bioactive molecules of medicinal leeches.

scholarly journals Shedding light on the bacterial resistance to toxic UV filters: a comparative genomic study

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12278
Author(s):  
Clément Lozano ◽  
Philippe Lebaron ◽  
Sabine Matallana-Surget
Keyword(s):  
Bacterial Resistance ◽  
Pairwise Comparison ◽  
Resistant Bacteria ◽  
Comparative Genomic ◽  
Uv Filters ◽  
Resistant Species ◽  
Genomic Study ◽  
Marine Biomass ◽  
Comparative Genomic Study ◽  
The Difference

UV filters are toxic to marine bacteria that dominate the marine biomass. Ecotoxicology often studies the organism response but rarely integrates the toxicity mechanisms at the molecular level. In this study, in silico comparative genomics between UV filters sensitive and resistant bacteria were conducted in order to unravel the genes responsible for a resistance phenotype. The genomes of two environmentally relevant Bacteroidetes and three Firmicutes species were compared through pairwise comparison. Larger genomes were carried by bacteria exhibiting a resistant phenotype, favoring their ability to adapt to environmental stresses. While the antitoxin and CRISPR systems were the only distinctive features in resistant Bacteroidetes, Firmicutes displayed multiple unique genes that could support the difference between sensitive and resistant phenotypes. Several genes involved in ROS response, vitamin biosynthesis, xenobiotic degradation, multidrug resistance, and lipophilic compound permeability were shown to be exclusive to resistant species. Our investigation contributes to a better understanding of UV filters resistance phenotypes, by identifying pivotal genes involved in key pathways.

scholarly journals Complete Genome Sequence of Streptococcus mutans Strain MD, Which Produces Highly Potent Mutacins

2020 ◽  
Vol 9 (33) ◽  
Author(s):  
Saswati Biswas ◽  
Indranil Biswas
Keyword(s):  
Streptococcus Mutans ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Comparative Genomic ◽  
Content Type ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Genome Information

ABSTRACT Here, we report the complete genome sequence of Streptococcus mutans strain MD, which produces potent mutacins capable of inhibiting streptococci. MD is a relatively uncharacterized strain whose genome information was unavailable. This study provides useful information for comparative genomic study and for understanding the repertoire of mutacins in S. mutans.

scholarly journals PanFunPro: PAN-genome analysis based on FUNctional PROfiles

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 265 ◽  
Author(s):  
Oksana Lukjancenko ◽  
Martin Christen Thomsen ◽  
Mette Voldby Larsen ◽  
David Wayne Ussery
Keyword(s):  
Genome Analysis ◽  
Markov Models ◽  
Epidemiological Studies ◽  
Comparative Genomic ◽  
Functional Domain ◽  
Homologous Proteins ◽  
Pan Genome ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Functional Profiles

PanFunPro is a tool for pan-genome analysis that integrates functional domains from three Hidden Markov Models (HMM) collections, and uses this information to group homologous proteins into families based on functional domain content. We use PanFunPro to compare a set of Lactobacillus and Streptococcus genomes. The example demonstrates that this method can provide analysis of differences and similarities in protein content within user-defined sets of genomes. PanFunPro can find various applications in a comparative genomic study, starting with the basic comparison of newly sequenced isolates to already existing strains, and an estimation of shared and specific genomic content. Furthermore, it can potentially be used in the determination of target sequences for in silico bacterial identification, as well as for epidemiological studies.

scholarly journals Stable Positions of Epigenetically Inherited Centromeres in the Emerging Fungal Pathogen Candida auris and Its Relatives

mBio ◽  
2021 ◽  
Author(s):  
Laura N. Rusche
Keyword(s):  
Fungal Pathogen ◽  
Evolutionary History ◽  
Comparative Genomic ◽  
Candida Auris ◽  
Content Type ◽  
Genomic Study ◽  
Comparative Genomic Study

Candida auris is an emerging fungal pathogen that is thermotolerant and often resistant to standard antifungal treatments. To trace its evolutionary history, the Sanyal lab conducted a comparative genomic study focusing on the positions of centromeres in C. auris and eight other species from the Clavispora / Candida clade of yeasts (A.

scholarly journals Association of Sequence types, Antimicrobial Resistance and Virulence Genes in India isolates of Klebsiella pneumoniae: A Comparative Genomics Study

2021 ◽  
Author(s):  
Abhirami Krishnamoorthy Sundaresan ◽  
Keerthana Vincent ◽  
Ganesh Babu Malli Mohan ◽  
Jayapradha Ramakrishnan
Keyword(s):  
Comparative Genomics ◽  
Klebsiella Pneumoniae ◽  
Virulence Genes ◽  
Respiratory Infections ◽  
Comparative Genomic ◽  
Clinical Strains ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Phylogenetic Evolution ◽  
Tract Infections

Abstract Klebsiella pneumoniae is an important ESKAPE pathogen that causes sepsis, urinary tract infections, peritonitis, intraabdominal abscesses and upper respiratory infections. The strains exhibiting multidrug resistance and hypervirulence are priority pathogens for which immediate treatment and dissemination prevention strategies are required. The hypervirulent drug resistant K. pneumoniae is associated with high mortality rates. Numbers of environmental strains also have acquired virulence genes. Hence to gain a better understanding of the spread of antimicrobial resistant genes across the country over 10 years and to delineate environmental and clinical K. pneumoniae, a comparative genomics investigation was made. This is the first comparative genomic study using India isolates of K. pneumoniae, which includes publicly available WGS of 144 clinical and 9 environmental strains collected during 2010–2020. The blaCTX-M-15 was widely distributed in clinical isolates since 2013 and increased over time from 5 % to 30 %. The co-existence of blaNDM and blaOXA was observed in 22 % of clinical strains. Diverse serotypes were found among the 153 K. pneumoniae isolates, of which, K51 (28%) and K64 (21.56%) were majorly found. Most of the K51 isolates belong to ST231 (93.02 %). And more than 50% of KL51 strains were found to have both rmpA and magA. The number of associated virulence genes (rmpA, magA, entB, ybtS, iutA, alls,) appeared to be higher in ST231-KL51 and ST23-KL1 isolates. Of greatest concern, these virulence genes are observed in environmental strains aswell. More than 97% of clinical strains have yersinibactin (ybtS), aerobactin (iutA) genes. Importantly, 98% of ESBL and 62% of carbapenamasen isolates harboured ybtS, iutA and rmpA, magA respectively. The IncF conjugative plasmids are predominant in K. pneumoniae, which contribute to the spread of AMR, and virulence genes. The increasing trend in hypervirulent strains was observed from 2017. The phylogenetic analysis separates the environmental from clinical strains and is characterized by uncommon STs and serotypes. Thus, the study illustrates the K. pneumoniae genomic surveillance in India representing the phylogenetic evolution, STs, AMR, virulence, serotype to provide more attention for immediate treatment and preventing the dissemination of K. pneumoniae.

scholarly journals Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0258019
Author(s):  
Ishtiaque Ahammad ◽  
Mohammad Uzzal Hossain ◽  
Anisur Rahman ◽  
Zeshan Mahmud Chowdhury ◽  
Arittra Bhattacharjee ◽  
...  
Keyword(s):  
Average Rate ◽  
Spike Protein ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Dynamic Nature ◽  
Genomic Study ◽  
The World ◽  
Comparative Genomic Study ◽  
Second Wave ◽  
Successful Prevention

As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomesequences have been deposited in the GISAID database from Bangladesh which were extracted and categorized into two waves. By analyzing these genome sequences, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country.

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