scholarly journals Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

GigaScience ◽  
2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Gaik Tamazian ◽  
Pavel Dobrynin ◽  
Ksenia Krasheninnikova ◽  
Aleksey Komissarov ◽  
Klaus-Peter Koepfli ◽  
...  
Keyword(s):  
Genome Arrangement

scholarly journals Unique Genome Arrangement of an Ovine Adenovirus: Identification of New Proteins and Proteinase Cleavage Sites

Virology ◽  
1996 ◽  
Vol 220 (1) ◽  
pp. 186-199 ◽  
Author(s):  
SUDHANSHU VRATI ◽  
D.E. BROOKES ◽  
P. STRIKE ◽  
A. KHATRI ◽  
D.B. BOYLE ◽  
...  
Keyword(s):  
Cleavage Sites ◽  
Genome Arrangement

scholarly journals A Single Chromosome Strain of S. cerevisiae Exhibits Diminished Ethanol Metabolism and Tolerance

2020 ◽  
Author(s):  
Tyler W. Doughty ◽  
Rosemary Yu ◽  
Lucy Fang-I Chao ◽  
Zhongjun Qin ◽  
Verena Siewers ◽  
...  
Keyword(s):  
Carbon Source ◽  
Reference Strain ◽  
Biomass Concentration ◽  
Biomass Accumulation ◽  
Ethanol Metabolism ◽  
Large Chromosome ◽  
Lag Phase ◽  
Diauxic Shift ◽  
Single Chromosome ◽  
Genome Arrangement

AbstractThis study characterized the growth, metabolism, and transcriptional profile of a S. cerevisiae strain with a single large chromosome that was constructed via successive chromosomal fusions. The single chromosome strain exhibited a longer lag phase, increased doubling time, and lower final biomass concentration compared with a wildtype strain when grown on YPD. These phenotypes were amplified when ethanol was added to the medium or used as the sole carbon source. RNAseq analysis showed diminished induction of genes involved in diauxic shift, ethanol metabolism, fatty-acid ß-oxidation, and methylglyoxal catabolism during growth on ethanol compared to the reference strain. Enzyme-constrained metabolic modeling predicted that decreased flux through these poorly induced enzymes results in diminished ATP formation and decreased biomass accumulation observed. Together, these observations suggest that switch-like control of carbon source dependent gene expression in S. cerevisiae requires genome arrangement into multiple chromosomes.

scholarly journals Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species

2019 ◽  
Vol 20 (5) ◽  
pp. 1045 ◽  
Author(s):  
Xiaoqin Li ◽  
Yunjuan Zuo ◽  
Xinxin Zhu ◽  
Shuai Liao ◽  
Jinshuang Ma
Keyword(s):  
Genomic Structure ◽  
Gc Content ◽  
Medicinal Species ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Aristolochic Acids ◽  
Chloroplast Genomes ◽  
The Family ◽  
Cp Genome ◽  
Genome Arrangement

Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods.

scholarly journals Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1301
Author(s):  
Kate Van Brussel ◽  
Xiuwan Wang ◽  
Mang Shi ◽  
Maura Carrai ◽  
Jun Li ◽  
...  
Keyword(s):  
Large Scale ◽  
Mammalian Species ◽  
Open Reading Frames ◽  
Virus Infections ◽  
Molecular Surveillance ◽  
Definitive Evidence ◽  
A Genome ◽  
Faecal Samples ◽  
Feline Parvovirus ◽  
Genome Arrangement

Astroviruses, isolated from numerous avian and mammalian species including humans, are commonly associated with enteritis and encephalitis. Two astroviruses have previously been identified in cats, and while definitive evidence is lacking, an association with enteritis is suggested. Using metagenomic next-generation sequencing of viral nucleic acids from faecal samples, we identified two novel feline astroviruses termed Feline astrovirus 3 and 4. These viruses were isolated from healthy shelter-housed kittens (Feline astrovirus 3; 6448 bp) and from a kitten with diarrhoea that was co-infected with Feline parvovirus (Feline astrovirus 4, 6549 bp). Both novel astroviruses shared a genome arrangement of three open reading frames (ORFs) comparable to that of other astroviruses. Phylogenetic analysis of the concatenated ORFs, ORF1a, ORF1b and capsid protein revealed that both viruses were phylogenetically distinct from other feline astroviruses, although their precise evolutionary history could not be accurately determined due to a lack of resolution at key nodes. Large-scale molecular surveillance studies of healthy and diseased cats are needed to determine the pathogenicity of feline astroviruses as single virus infections or in co-infections with other enteric viruses.

scholarly journals Divergence and Mosaicism among Virulent Soil Phages of the Burkholderia cepacia Complex

2006 ◽  
Vol 188 (1) ◽  
pp. 255-268 ◽  
Author(s):  
Elizabeth J. Summer ◽  
Carlos F. Gonzalez ◽  
Morgan Bomer ◽  
Thomas Carlile ◽  
Addie Embry ◽  
...  
Keyword(s):  
Burkholderia Cepacia ◽  
Sequence Divergence ◽  
Burkholderia Cepacia Complex ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Lambda Repressor ◽  
Host Lysis ◽  
Defective Prophage ◽  
Neutral Genetic Drift ◽  
Genome Arrangement

ABSTRACT We have determined the genomic sequences of four virulent myophages, Bcep1, Bcep43, BcepB1A, and Bcep781, whose hosts are soil isolates of the Burkholderia cepacia complex. Despite temporal and spatial separations between initial isolations, three of the phages (Bcep1, Bcep43, and Bcep781, designated the Bcep781 group) exhibit 87% to 99% sequence identity to one another and most coding region differences are due to synonymous nucleotide substitutions, a hallmark of neutral genetic drift. Phage BcepB1A has a very different genome organization but is clearly a mosaic with respect to many of the genes of the Bcep781 group, as is a defective prophage element in Photorhabdus luminescens. Functions were assigned to 27 out of 71 predicted genes of Bcep1 despite extreme sequence divergence. Using a lambda repressor fusion technique, 10 Bcep781-encoded proteins were identified for their ability to support homotypic interactions. While head and tail morphogenesis genes have retained canonical gene order despite extreme sequence divergence, genes involved in DNA metabolism and host lysis are not organized as in other phages. This unusual genome arrangement may contribute to the ability of the Bcep781-like phages to maintain a unified genomic type. However, the Bcep781 group phages can also engage in lateral gene transfer events with otherwise unrelated phages, a process that contributes to the broader-scale genomic mosaicism prevalent among the tailed phages.

scholarly journals Complete genome sequence of a novel secovirid infecting cassava in the Americas

2022 ◽  
Author(s):  
Ana M. Leiva ◽  
Jenyfer Jimenez ◽  
Hector Sandoval ◽  
Shirley Perez ◽  
Wilmer J. Cuellar
Keyword(s):  
Amino Acids ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Field Isolate ◽  
Viral Genomes ◽  
Oxford Nanopore ◽  
Replication Block ◽  
Genome Arrangement

AbstractWe report the complete genome sequence of a field isolate of a novel bipartite secovirid infecting cassava in Colombia, provisionally named "cassava torrado-like virus" (CsTLV). The genome sequence was obtained using Oxford Nanopore Technology, and the 5’ ends were confirmed by RACE. The RNA1 is 7252 nucleotides (nt) long, encoding a polyprotein of 2336 amino acids (aa) containing the typical “replication block”, conserved torradovirus motifs, and a Maf/Ham1 domain, which is not commonly found in viral genomes. The RNA2 is 4469 nt long and contains two overlapping ORFs encoding proteins of 226 and 1179 aa, showing the characteristic genome arrangement of members of the genus Torradovirus.

scholarly journals Comparative Analysis of Chloroplast Genomes of Seven Chaetoceros Species Revealed Variation Hotspots and Speciation Time

2021 ◽  
Vol 12 ◽  
Author(s):  
Qing Xu ◽  
Zongmei Cui ◽  
Nansheng Chen
Keyword(s):  
Divergence Time ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Time Estimation ◽  
Divergence Time Estimation ◽  
Chloroplast Genomes ◽  
Diatom Genus ◽  
The Common ◽  
Genome Arrangement ◽  
Global Carbon

Chaetoceros is a species-rich diatom genus with broad distribution and plays an important role in global carbon cycle and aquatic ecosystems. However, genomic information of Chaetoceros species is limited, hindering advanced researches on Chaetoceros biodiversity and their differential impact on ecology. In this study, we constructed full-length chloroplast genomes (cpDNAs) for seven Chaetoceros species, including C. costatus, C. curvisetus, C. laevisporus, C. muelleri, C. pseudo-curvisetus, C. socialis, and C. tenuissimus. All of these cpDNAs displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The sizes of these cpDNAs were similar, ranging from 116,421 to 119,034 bp in size, and these cpDNAs also displayed similar GC content, ranging from 30.26 to 32.10%. Despite extensive synteny conservation, discrete regions showed high variations. Divergence time estimation revealed that the common ancestor of Chaetoceros species, which formed a monophyletic clade at approximately 58 million years ago (Mya), split from Acanthoceras zachariasii at about 70 Mya. The availability of cpDNAs of multiple Chaetoceros species provided valuable reference sequences for studying evolutionary relationship among Chaetoceros species, as well as between Chaetoceros species and other diatom species.

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