Genomics beyond complete genomes

2022 ◽  
Vol 19 (1) ◽  
pp. 29-29
Author(s):  
Lin Tang
Keyword(s):  
Complete Genomes

scholarly journals Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
He-Teng Zhang ◽  
Hao Wang ◽  
Hai-Sheng Wu ◽  
Jian Zeng ◽  
Yan Yang
Keyword(s):  
Human Papillomavirus ◽  
Bacterial Community ◽  
Pregnant Women ◽  
Sequence Comparison ◽  
Pairwise Sequence Comparison ◽  
Vaginal Secretion ◽  
The Family ◽  
Complete Genomes ◽  
Different Types ◽  
Vaginal Tract

Abstract Background Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. Methods To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. Results Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. Conclusion Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.

scholarly journals Characterization of CRISPR Spacer and Protospacer Sequences in Paenibacillus larvae and Its Bacteriophages

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 459
Author(s):  
Casey Stamereilers ◽  
Simon Wong ◽  
Philippos K. Tsourkas
Keyword(s):  
Comparative Studies ◽  
Point Mutations ◽  
Paenibacillus Larvae ◽  
Bacterial Disease ◽  
American Foulbrood ◽  
Antibiotic Resistant ◽  
Future Studies ◽  
Complete Genomes ◽  
Point Of Reference

The bacterium Paenibacillus larvae is the causative agent of American foulbrood, the most devastating bacterial disease of honeybees. Because P. larvae is antibiotic resistant, phages that infect it are currently used as alternative treatments. However, the acquisition by P. larvae of CRISPR spacer sequences from the phages could be an obstacle to treatment efforts. We searched nine complete genomes of P. larvae strains and identified 714 CRISPR spacer sequences, of which 384 are unique. Of the four epidemiologically important P. larvae strains, three of these have fewer than 20 spacers, while one strain has over 150 spacers. Of the 384 unique spacers, 18 are found as protospacers in the genomes of 49 currently sequenced P. larvae phages. One P. larvae strain does not have any protospacers found in phages, while another has eight. Protospacer distribution in the phages is uneven, with two phages having up to four protospacers, while a third of phages have none. Some phages lack protospacers found in closely related phages due to point mutations, indicating a possible escape mechanism. This study serve a point of reference for future studies on the CRISPR-Cas system in P. larvae as well as for comparative studies of other phage–host systems.

scholarly journals Complete Genome Sequences of Six Novel Macaca mulatta Papillomavirus Types Isolated from Genital Sites of Rhesus Monkeys in Hong Kong SAR, China

2018 ◽  
Vol 7 (22) ◽  
Author(s):  
Teng Long ◽  
Po Yee Wong ◽  
Wendy C. S. Ho ◽  
Robert D. Burk ◽  
Paul K. S. Chan ◽  
...  
Keyword(s):  
Hong Kong ◽  
Macaca Mulatta ◽  
Complete Genome ◽  
Rhesus Monkeys ◽  
Genome Sequences ◽  
Content Type ◽  
Complete Genomes ◽  
Hong Kong Sar

The complete genomes of six Macaca mulatta papillomavirus types isolated from genital sites of rhesus monkeys were characterized, and less than 72% identity with the complete L1 genes of known papillomaviruses was found. Macaca mulatta papillomavirus type 2 (MmPV2), MmPV3, and MmPV6 cluster into the genus Alphapapillomavirus, and MmPV4, MmPV5, and MmPV7 cluster into the genus Gammapapillomavirus.

scholarly journals Genomics Analyses of GIV and GVI Noroviruses Reveal the Distinct Clustering of Human and Animal Viruses

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 204 ◽  
Author(s):  
Lauren Ford-Siltz ◽  
Lisa Mullis ◽  
Yasser Sanad ◽  
Kentaro Tohma ◽  
Cara Lepore ◽  
...  
Keyword(s):  
United States ◽  
Acute Gastroenteritis ◽  
Major Capsid Protein ◽  
Mammalian Species ◽  
The United States ◽  
Structural Proteins ◽  
Full Genome ◽  
Complete Genomes ◽  
Animal Strains ◽  
Canine Norovirus

Noroviruses are highly diverse viruses that are the major viral cause of acute gastroenteritis in humans. Although these viruses can infect multiple mammalian species, their potential for zoonosis is not well understood, especially within Genogroup IV (GIV), which contains viruses that infect humans, canines, and felines. The study of GIV viruses has been, in part, hindered by the limited number of complete genomes. Here, we developed a full-genome amplicon-based platform that facilitated the sequencing of canine noroviruses circulating in the United States. Eight novel nearly full-length canine norovirus genomes and two nearly complete VP1 sequences, including four GIV.2, three GVI.1, and three GVI.2 viruses, were successfully obtained. Only animal strains exhibited GVI/GIV chimeric viruses, demonstrating restrictions in norovirus recombination. Using genomic, phylogenetic, and structural analyses, we show that differences within the major capsid protein and the non-structural proteins of GIV and GVI noroviruses could potentially limit cross-species transmission between humans, canines, and felines.

scholarly journals In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

2016 ◽  
Vol 26 (9) ◽  
pp. 1257-1267 ◽  
Author(s):  
Igor Rodrigues Costa ◽  
Francisco Prosdocimi ◽  
W. Bryan Jennings
Keyword(s):  
In Silico ◽  
Complete Genomes

scholarly journals Sequences of Seven Complete Genomes of Human Parvovirus B19

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Yuhuan Qiu ◽  
Zehui Zhao ◽  
Jianming Qiu
Keyword(s):  
United States ◽  
Human Plasma ◽  
Parvovirus B19 ◽  
The United States ◽  
Human Parvovirus B19 ◽  
Genome Sequences ◽  
Complete Genomes ◽  
Inverted Terminal Repeats ◽  
Terminal Repeats

We are reporting the sequences of seven complete genomes of parvovirus B19, which were extracted from human plasma specimens collected in the United States. The seven B19 genome sequences, which are 5,596 nucleotides long and include the inverted terminal repeats (ITRs), share an identity of 96.73%.

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