scholarly journals Genetic characterization of the Wyeomyia group of orthobunyaviruses and their phylogenetic relationships

2012 ◽  
Vol 93 (5) ◽  
pp. 1023-1034 ◽  
Author(s):  
Rashmi Chowdhary ◽  
Craig Street ◽  
Amelia Travassos da Rosa ◽  
Marcio R. T. Nunes ◽  
Kok Keng Tee ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Whole Genome Sequence ◽  
Interferon Response ◽  
Sequence Information ◽  
History Of ◽  
Group Members ◽  
Genome Sequence Information ◽  
Genome Reassortment

Phylogenetic analyses can give new insights into the evolutionary history of viruses, especially of viruses with segmented genomes. However, sequence information for many viral families or genera is still limited and phylogenies based on single or short genome fragments can be misleading. We report the first genetic analysis of all three genome segments of Wyeomyia group viruses Wyeomyia, Taiassui, Macaua, Sororoca, Anhembi and Cachoeira Porteira (BeAr328208) in the genus Orthobunyavirus of the family Bunyaviridae. In addition, Tucunduba and Iaco viruses were identified as members of the Wyeomyia group. Features of Wyeomyia group members that distinguish them from other viruses in the Bunyamwera serogroup and from other orthobunyaviruses, including truncated NSs sequences that may not counteract the host’s interferon response, were characterized. Our findings also suggest genome reassortment within the Wyeomyia group, identifying Macaua and Tucunduba viruses as M-segment reassortants that, in the case of Tucunduba virus, may have altered pathogenicity, stressing the need for whole-genome sequence information to facilitate characterization of orthobunyaviruses and their phylogenetic relationships.

scholarly journals Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Takashi Gakuhari ◽  
Shigeki Nakagome ◽  
Simon Rasmussen ◽  
Morten E. Allentoft ◽  
Takehiro Sato ◽  
...  
Keyword(s):  
East Asia ◽  
Genome Sequence ◽  
Phylogenetic Analyses ◽  
Human Migration ◽  
Whole Genome Sequence ◽  
Migration Patterns ◽  
Asian Populations ◽  
Anatomically Modern Humans ◽  
History Of ◽  
Northeast Asian

AbstractAnatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is  characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

scholarly journals Expression and Characterization of a Dye-Decolorizing Peroxidase from Pseudomonas Fluorescens Pf0-1

Catalysts ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 463 ◽  
Author(s):  
Nikola Lončar ◽  
Natalija Drašković ◽  
Nataša Božić ◽  
Elvira Romero ◽  
Stefan Simić ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Pseudomonas Fluorescens ◽  
Alginate Beads ◽  
Sequence Information ◽  
Soluble Enzyme ◽  
Initial Activity ◽  
Alternative Substrate ◽  
65 H ◽  
Genome Sequence Information

The consumption of dyes is increasing worldwide in line with the increase of population and demand for clothes and other colored products. However, the efficiency of dyeing processes is still poor and results in large amounts of colored effluents. It is desired to develop a portfolio of enzymes which can be used for the treatment of colored wastewaters. Herein, we used genome sequence information to discover a dye-decolorizing peroxidase (DyP) from Pseudomonas fluorescens Pf-01. Two genes putatively encoding for DyPs were identified in the respective genome and cloned for expression in Escherichia coli, of which one (PfDyP B2) could be overexpressed as a soluble protein. PfDyP B2 shows some typical features known for DyPs which includes the ability to convert dyes at the expense of hydrogen peroxide. Interestingly, t-butyl hydroperoxide could be used as an alternative substrate to hydrogen peroxide. Immobilization of PfDyP B2 in calcium-alginate beads resulted in a significant increase in stability: PfDyP B2 retains 80% of its initial activity after 2 h incubation at 50 °C, while the soluble enzyme is inactivated within minutes. PfDyP B2 was also tested with aniline and ethyl diazoacetate as substrates. Based on GC-MS analyses, 30% conversion of the starting material was achieved after 65 h at 30 °C. Importantly, this is the first report of a DyP-catalyzed insertion of a carbene into an N-H bond.

scholarly journals Functional genomics of pathogenic bacteria

2002 ◽  
Vol 357 (1417) ◽  
pp. 109-116 ◽  
Author(s):  
E. R. Moxon ◽  
D. W. Hood ◽  
N. J. Saunders ◽  
E. K. H. Schweda ◽  
J. C. Richards
Keyword(s):  
Pathogenic Bacteria ◽  
Whole Genome Sequence ◽  
Sequence Information ◽  
Microbial Diseases ◽  
Mortality And Morbidity ◽  
Automated Dna Sequencing ◽  
Genome Sequence Information ◽  
Pathogenic Microbes

Microbial diseases remain the commonest cause of global mortality and morbidity. Automated–DNA sequencing has revolutionized the investigation of pathogenic microbes by making the immense fund of information contained in their genomes available at reasonable cost. The challenge is how this information can be used to increase current understanding of the biology of commensal and virulence behaviour of pathogens with particular emphasis on in vivo function and novel approaches to prevention. One example of the application of whole–genome–sequence information is afforded by investigations of the pathogenic role of Haemophilus influenzae lipopolysaccharide and its candidacy as a vaccine.

scholarly journals A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Russell J. S. Orr ◽  
Marianne N. Haugen ◽  
Björn Berning ◽  
Philip Bock ◽  
Robyn L. Cumming ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Mitochondrial Genomes ◽  
Sequence Information ◽  
A Genome ◽  
Ribosomal Operon ◽  
History Of ◽  
Genome Skimming ◽  
Phylogenetic Hypotheses ◽  
Cheilostome Bryozoans

Abstract Background Understanding the phylogenetic relationships among species is one of the main goals of systematic biology. Simultaneously, credible phylogenetic hypotheses are often the first requirement for unveiling the evolutionary history of traits and for modelling macroevolutionary processes. However, many non-model taxa have not yet been sequenced to an extent such that statistically well-supported molecular phylogenies can be constructed for these purposes. Here, we use a genome-skimming approach to extract sequence information for 15 mitochondrial and 2 ribosomal operon genes from the cheilostome bryozoan family, Adeonidae, Busk, 1884, whose current systematics is based purely on morphological traits. The members of the Adeonidae are, like all cheilostome bryozoans, benthic, colonial, marine organisms. Adeonids are also geographically widely-distributed, often locally common, and are sometimes important habitat-builders. Results We successfully genome-skimmed 35 adeonid colonies representing 6 genera (Adeona, Adeonellopsis, Bracebridgia, Adeonella, Laminopora and Cucullipora). We also contributed 16 new, circularised mitochondrial genomes to the eight previously published for cheilostome bryozoans. Using the aforementioned mitochondrial and ribosomal genes, we inferred the relationships among these 35 samples. Contrary to some previous suggestions, the Adeonidae is a robustly supported monophyletic clade. However, the genera Adeonella and Laminopora are in need of revision: Adeonella is polyphyletic and Laminopora paraphyletically forms a clade with some Adeonella species. Additionally, we assign a sequence clustering identity using cox1 barcoding region of 99% at the species and 83% at the genus level. Conclusions We provide sequence data, obtained via genome-skimming, that greatly increases the resolution of the phylogenetic relationships within the adeonids. We present a highly-supported topology based on 17 genes and substantially increase availability of circularised cheilostome mitochondrial genomes, and highlight how we can extend our pipeline to other bryozoans.

scholarly journals The evolutionary history of polycotylid plesiosaurians

2018 ◽  
Vol 5 (3) ◽  
pp. 172177 ◽  
Author(s):  
V. Fischer ◽  
R. B. J. Benson ◽  
P. S. Druckenmiller ◽  
H. F. Ketchum ◽  
N. Bardet
Keyword(s):  
Early Cretaceous ◽  
Late Cretaceous ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Neck Length ◽  
Ecological Release ◽  
Holotype Specimen ◽  
Low Diversity ◽  
History Of

Polycotylidae is a clade of plesiosaurians that appeared during the Early Cretaceous and became speciose and abundant early in the Late Cretaceous. However, this radiation is poorly understood. Thililua longicollis from the Middle Turonian of Morocco is an enigmatic taxon possessing an atypically long neck and, as originally reported, a series of unusual cranial features that cause unstable phylogenetic relationships for polycotylids. We reinterpret the holotype specimen of Thililua longicollis and clarify its cranial anatomy. Thililua longicollis possesses an extensive, foramina-bearing jugal, a premaxilla–parietal contact and carinated teeth. Phylogenetic analyses of a new cladistic dataset based on first-hand observation of most polycotylids recover Thililua and Mauriciosaurus as successive lineages at the base of the earliest Late Cretaceous polycotyline radiation. A new dataset summarizing the Bauplan of polycotylids reveals that their radiation produced an early burst of disparity during the Cenomanian–Turonian interval, with marked plasticity in relative neck length, but this did not arise as an ecological release following the extinction of ichthyosaurs and pliosaurids. This disparity vanished during and after the Turonian, which is consistent with a model of ‘early experimentation/late constraint’. Two polycotylid clades, Occultonectia clade nov. and Polycotylinae, survived up to the Maastrichtian, but with low diversity.

Phylogenetic relationships among Elymus and related diploid genera (Triticeae: Poaceae) based on nuclear rDNA ITS sequences

Biologia ◽  
2015 ◽  
Vol 70 (2) ◽  
Author(s):  
Gang Gao ◽  
Jia-bin Deng ◽  
Xue-mei Gou ◽  
Qian Wang ◽  
Chun-bang Ding ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Its Sequences ◽  
Neighbor Joining ◽  
Rdna Its ◽  
Genome Donor ◽  
Rdna Its Sequences ◽  
History Of ◽  
Elymus Species

AbstractTo investigate the phylogenetic relationships among Elymus and related diploid genera, the genome donor of Elymus, and the evolutionary history of polyploid Elymus species, nuclear ribosomal internal transcribed spacer (ITS) sequences were analyzed for 10 Elymus species, together with 17 diploid taxa from 5 monogenomic genera. The phylogenetic analyses (Neighbor-Joining) supported two major clades (St and H). Sequence diversity and genealogical analysis suggested that (1) Elymus species were unambiguously closely related to Pseudoroegeria; (2) Pse. stipifolia might be serve as the St genome donor of polyploid Elymus species; (3) the Y genome might be originated from ancestral lineage of Pseudoroegneria (St); (4) the ITS sequences of Elymus were evolutionarily distinct and may clarify parental lineages and phylogenetic relationships in Elymus.

Whole genome genetic-typing in yeast using high-density oligonucleotide arrays

Parasitology ◽  
1999 ◽  
Vol 118 (7) ◽  
pp. 73-80 ◽  
Author(s):  
E. A. WINZELER ◽  
B. LEE ◽  
J. H. McCUSKER ◽  
R. W. DAVIS
Keyword(s):  
New Technologies ◽  
High Density ◽  
Open Reading Frames ◽  
Sequence Information ◽  
Oligonucleotide Arrays ◽  
Genome Sequence Information ◽  
Genome Content ◽  
Reading Frames ◽  
Lower Copy

Genome sequence information in combination with new technologies has allowed researchers to approach genetic problems in new ways. High-density oligonucleotide arrays were used to probe the genome content of the yeast Saccharomyces cerevisiae. We show that these arrays, containing oligonucleotides complementary to the sequenced strain of S. cerevisiae, can be used to identify open reading frames that are missing or present in higher or lower copy number in related isolates of S. cerevisiae. We apply this method to the characterization of the genome of a strain derived from a clinical isolate of S. cerevisiae. Our results show that the telomeres are the regions with the most variability between the two strains.

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