scholarly journals Genome evolution of SARS-CoV-2 and its virological characteristics

2020 ◽  
Vol 40 (1) ◽  
Author(s):  
So Nakagawa ◽  
Takayuki Miyazawa
Keyword(s):  
Genome Evolution ◽  
Genome Sequence ◽  
Causative Agent ◽  
Sequence Data ◽  
Genome Sequences ◽  
Genome Sequence Data ◽  
Global Prevalence ◽  
Horseshoe Bats

AbstractCoronavirus disease of 2019 (COVID-19), which originated in China in 2019, shows mild cold and pneumonia symptoms that can occasionally worsen and result in deaths. SARS-CoV-2 was reported to be the causative agent of the disease and was identified as being similar to SARS-CoV, a causative agent of SARS in 2003. In this review, we described the phylogeny of SARS-CoV-2, covering various related studies, in particular, focusing on viruses obtained from horseshoe bats and pangolins that belong to Sarbecovirus, a subgenus of Betacoronavirus. We also describe the virological characteristics of SARS-CoV-2 and compare them with other coronaviruses. More than 30,000 genome sequences of SARS-CoV-2 are available in the GISAID database as of May 28, 2020. Using the genome sequence data of closely related viruses, the genomic characteristics and evolution of SARS-CoV-2 were extensively studied. However, given the global prevalence of COVID-19 and the large number of associated deaths, further computational and experimental virological analyses are required to fully characterize SARS-CoV-2.

Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2742-2751 ◽  
Author(s):  
Henryk Urbanczyk ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Taxonomic Revision ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Sequence Data ◽  
The Family

Use of inadequate methods for classification of bacteria in the so-called Harveyi clade (family Vibrionaceae, Gammaproteobacteria) has led to incorrect assignment of strains and proliferation of synonymous species. In order to resolve taxonomic ambiguities within the Harveyi clade and to test usefulness of whole genome sequence data for classification of Vibrionaceae, draft genome sequences of 12 strains were determined and analysed. The sequencing included type strains of seven species: Vibrio sagamiensis NBRC 104589T, Vibrio azureus NBRC 104587T, Vibrio harveyi NBRC 15634T, Vibrio rotiferianus LMG 21460T, Vibrio campbellii NBRC 15631T, Vibrio jasicida LMG 25398T, and Vibrio owensii LMG 25443T. Draft genome sequences of strain LMG 25430, previously designated the type strain of [Vibrio communis], and two strains (MWB 21 and 090810c) from the ‘beijerinckii’ lineage were also determined. Whole genomes of two additional strains (ATCC 25919 and 200612B) that previously could not be assigned to any Harveyi clade species were also sequenced. Analysis of the genome sequence data revealed a clear case of synonymy between V. owensii and [V. communis], confirming an earlier proposal to synonymize both species. Both strains from the ‘beijerinckii’ lineage were classified as V. jasicida, while the strains ATCC 25919 and 200612B were classified as V. owensii and V. campbellii, respectively. We also found that two strains, AND4 and Ex25, are closely related to Harveyi clade bacteria, but could not be assigned to any species of the family Vibrionaceae. The use of whole genome sequence data for the taxonomic classification of the Harveyi clade bacteria and other members of the family Vibrionaceae is also discussed.

scholarly journals Returning genome sequences to research participants: Policy and practice

2017 ◽  
Vol 2 ◽  
pp. 15 ◽  
Author(s):  
Caroline F. Wright ◽  
Anna Middleton ◽  
Jeffrey C. Barrett ◽  
Helen V. Firth ◽  
David R. FitzPatrick ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Large Scale ◽  
Sequence Data ◽  
Careful Consideration ◽  
Unintended Consequences ◽  
Genome Sequences ◽  
Individual Genome ◽  
Entire Genome ◽  
Genome Sequence Data ◽  
Research Participants

Despite advances in genomic science stimulating an explosion of literature around returning health-related findings, the possibility of returning entire genome sequences to individual research participants has not been widely considered. Through direct involvement in large-scale translational genomics studies, we have identified a number of logistical challenges that would need to be overcome prior to returning individual genome sequence data, including verifying that the data belong to the requestor and providing appropriate informatics support. In addition, we identify a number of ethico-legal issues that require careful consideration, including returning data to family members, mitigating against unintended consequences, and ensuring appropriate governance. Finally, recognising that there is an opportunity cost to addressing these issues, we make some specific pragmatic suggestions for studies that are considering whether to share individual genomic datasets with individual study participants. If data are shared, research should be undertaken into the personal, familial and societal impact of receiving individual genome sequence data.

scholarly journals Genome Sequence Data of Six Isolates of Phytophthora capsici from Mexico

2019 ◽  
Vol 32 (10) ◽  
pp. 1267-1269 ◽  
Author(s):  
Alfredo Reyes-Tena ◽  
José C. Huguet-Tapia ◽  
Kurt H. Lamour ◽  
Erica M. Goss ◽  
Gerardo Rodríguez-Alvarado ◽  
...  
Keyword(s):  
Host Range ◽  
Genome Sequence ◽  
Plant Pathogen ◽  
Sequence Data ◽  
Phytophthora Capsici ◽  
Chili Pepper ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Sequence Data ◽  
Wide Host Range

Phytophthora capsici is an oomycete plant pathogen with a wide host range. Worldwide, P. capsici is known for causing the principal disease of chili pepper crops. Our goal was to expand the available genome resources for this diverse pathogen by generating whole-genome sequences for six isolates of P. capsici from Mexico.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Draft genome sequence data of the facultative, thermophilic, xylanolytic bacterium Paenibacillus sp. strain DA-C8

Data in Brief ◽  
2021 ◽  
Vol 35 ◽  
pp. 106784
Author(s):  
Chinda Chhe ◽  
Ayaka Uke ◽  
Sirilak Baramee ◽  
Umbhorn Ungkulpasvich ◽  
Chakrit Tachaapaikoon ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Genome Sequence Data ◽  
Paenibacillus Sp

scholarly journals Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

Data in Brief ◽  
2020 ◽  
Vol 33 ◽  
pp. 106416
Author(s):  
Asset Daniyarov ◽  
Askhat Molkenov ◽  
Saule Rakhimova ◽  
Ainur Akhmetova ◽  
Zhannur Nurkina ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data
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