From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs

AbstractPreeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.

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Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

Scientific Reports ◽

10.1038/s41598-021-94545-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tongqing Zhang ◽

Jiawen Yin ◽

Shengkai Tang ◽

Daming Li ◽

Xiankun Gu ◽

...

Keyword(s):

De Novo ◽

Corbicula Fluminea ◽

Gene Families ◽

Ruditapes Philippinarum ◽

Genomic Sequences ◽

Future Research ◽

Asian Clam ◽

Sequencing Technologies ◽

East And Southeast Asia ◽

Clam Corbicula

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

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CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

Bioinformatics ◽

10.1093/bioinformatics/btaa1047 ◽

2020 ◽

Author(s):

Matteo Chiara ◽

Federico Zambelli ◽

Marco Antonio Tangaro ◽

Pietro Mandreoli ◽

David S Horner ◽

...

Keyword(s):

Functional Annotation ◽

Ad Hoc ◽

State Of The Art ◽

Supplementary Information ◽

Genomic Sequences ◽

Supplementary Data ◽

Evolutionary Patterns ◽

Genomic Variants ◽

Art Methods ◽

Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

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ZayyuNet A unified deep learning model for the identification of epigenetic modifications using raw genomic sequences

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2021.3083789 ◽

2021 ◽

pp. 1-1

Author(s):

Zeeshan Abbas ◽

Hilal Tayara ◽

Kil Chong

Keyword(s):

Deep Learning ◽

Learning Model ◽

Epigenetic Modifications ◽

Genomic Sequences ◽

Deep Learning Model

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Amplification of human genomic sequences by human papillomaviruses universal consensus primers

Journal of Virological Methods ◽

10.1016/s0166-0934(00)00148-8 ◽

2000 ◽

Vol 87 (1-2) ◽

pp. 171-175 ◽

Cited By ~ 5

Author(s):

M.Encarnación Fernández-Contreras ◽

Cristina Sarriá ◽

Santiago Nieto ◽

Pedro A Lazo

Keyword(s):

Human Papillomaviruses ◽

Genomic Sequences ◽

Human Genomic ◽

Consensus Primers

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D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect

Molecules ◽

10.3390/molecules26092622 ◽

2021 ◽

Vol 26 (9) ◽

pp. 2622

Author(s):

Romina Oliva ◽

Abdul Rajjak Shaikh ◽

Andrea Petta ◽

Anna Vangone ◽

Luigi Cavallo

Keyword(s):

Three Dimensional ◽

Salt Bridge ◽

Structural Effect ◽

Host Cells ◽

Heptad Repeat ◽

Genomic Sequences ◽

Strong Interactions ◽

Virus Infectivity ◽

S Protein ◽

Global Threat

The crown of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constituted by its spike (S) glycoprotein. S protein mediates the SARS-CoV-2 entry into the host cells. The “fusion core” of the heptad repeat 1 (HR1) on S plays a crucial role in the virus infectivity, as it is part of a key membrane fusion architecture. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On 15 February 2021, from the SARS-CoV-2 genomic sequences in the GISAID resource, we collected 415,673 complete S protein sequences and identified all the mutations occurring in the HR1 fusion core. This is a 21-residue segment, which, in the post-fusion conformation of the protein, gives many strong interactions with the heptad repeat 2, bringing viral and cellular membranes in proximity for fusion. We investigated the frequency and structural effect of novel mutations accumulated over time in such a crucial region for the virus infectivity. Three mutations were quite frequent, occurring in over 0.1% of the total sequences. These were S929T, D936Y, and S949F, all in the N-terminal half of the HR1 fusion core segment and particularly spread in Europe and USA. The most frequent of them, D936Y, was present in 17% of sequences from Finland and 12% of sequences from Sweden. In the post-fusion conformation of the unmutated S protein, D936 is involved in an inter-monomer salt bridge with R1185. We investigated the effect of the D936Y mutation on the pre-fusion and post-fusion state of the protein by using molecular dynamics, showing how it especially affects the latter one.

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Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea

Viruses ◽

10.3390/v13050847 ◽

2021 ◽

Vol 13 (5) ◽

pp. 847

Author(s):

Kyungmin Park ◽

Seung-Ho Lee ◽

Jongwoo Kim ◽

Jingyeong Lee ◽

Geum-Young Lee ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Republic Of Korea ◽

Hantaan Virus ◽

Genomic Sequences ◽

Whole Genome ◽

Nanopore Sequencing ◽

Apodemus Agrarius ◽

Copy Numbers ◽

Nanopore Sequencer

Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.

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