Sequence Note: Identification of a New HIV-2 Subtype Based on Phylogenetic Analysis of Full-Length Genomic Sequence

Hepatitis A virus is known to cause acute hepatitis and has significant implications for public health throughout the world. In the Republic of Korea, the number of patients with hepatitis A virus infection has been increasing rapidly since 2006. In this study, the Kor-HAV-F strain was identified as subgenotype IIIA by RT-PCR, and its identity was confirmed by nucleotide sequencing and alignment analysis. Moreover, detailed phylogenetic analysis indicated that the Kor-HAV-F strain clustered into subgenotype IIIA, including strains isolated in Japan, Norway, and India. The entire amino acid sequence of the VP1 and 2A regions was compared with that of the reference strains isolated in various countries. We found 2 amino acid changes (T168A and L96P, resp.) in the VP1 and 2A regions, which had not been found in any other hepatitis A virus strain. To our knowledge, this study is the first to report the full-length sequence of a hepatitis A virus isolated in the Republic of Korea.

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Phylogenetic analysis of near full-length sequences of the Desmodus rotundus genetic lineage of rabies virus

Infection Genetics and Evolution ◽

10.1016/j.meegid.2020.104179 ◽

2020 ◽

Vol 80 ◽

pp. 104179

Author(s):

Angélica Cristine de Almeida Campos ◽

Camila Malta Romano ◽

Fernando Lucas Melo ◽

Danielle Bastos Araújo ◽

Elenice Maria Sequetin Cunha ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Rabies Virus ◽

Full Length ◽

Genetic Lineage ◽

Desmodus Rotundus

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Comparative analysis of the complete chloroplast genomic sequence and chemical components of Cinnamomum micranthum and Cinnamomum kanehirae

Holzforschung ◽

10.1515/hf-2016-0133 ◽

2017 ◽

Vol 71 (3) ◽

pp. 189-197 ◽

Cited By ~ 15

Author(s):

Chia-Chen Wu ◽

Fang-Hua Chu ◽

Cheng-Kuen Ho ◽

Chia-Hsuan Sung ◽

Shu-Hwa Chang

Keyword(s):

Phylogenetic Analysis ◽

Liquid Chromatography ◽

Comparative Analysis ◽

Chloroplast Genome ◽

Genomic Sequence ◽

Ultra Performance Liquid Chromatography ◽

Chemical Components ◽

Complete Chloroplast Genome ◽

Medicinal Fungus ◽

Indel Markers

Abstract Cinnamomum micranthum (Hayata) Hayata is a tree species that is often confused with Cinnamomum kanehirae Hayata, which is an endemic species in Taiwan and the sole natural host of the valuable medicinal fungus Antrodia cinnamomea. However, the two species are highly similar in morphology and difficult to distinguish based on traditional vegetative structures or wood anatomical methods. The aim of the present study was to identify of these two species by DNA and chemical analysis. The complete chloroplast genome of C. micranthum has been determined and compared with that of C. kanehirae. The leaf methanol extracts of these species were also analyzed by ultra-performance liquid chromatography (UPLC). The length of the C. micranthum chloroplast genome was 152675 bp, i.e. 25 bp shorter than that of C. kanehirae. In phylogenetic analysis, C. micranthum was more closely related to C. kanehirae than other six Lauracea species. Six validated insertion/deletions of bases in the DNA (InDels) are suitable for differentiation of the two species. Moreover, high amounts of linalool and sesamin were present in the leaves of C. kanehirae, but not in C. micranthum. Overall, this study provided new insight for distinguishing the two species on the basis of the chemical composition of the leaves and the InDel markers.

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Genetic characterization of a Marek’s disease virus strain isolated in Japan

Virology Journal ◽

10.1186/s12985-020-01456-1 ◽

2020 ◽

Vol 17 (1) ◽

Author(s):

Shiro Murata ◽

Yuka Machida ◽

Masayoshi Isezaki ◽

Naoya Maekawa ◽

Tomohiro Okagawa ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Disease Virus ◽

Genomic Sequence ◽

Marek's Disease Virus ◽

Marek's Disease ◽

Marek’S Disease Virus ◽

Marek’S Disease ◽

Coding Region ◽

Japanese Strain ◽

Genetic Characteristics

Abstract Background Marek’s disease virus (MDV) causes malignant lymphomas in chickens (Marek’s disease, MD). MD is currently controlled by vaccination; however, MDV strains have a tendency to develop increased virulence. Distinct diversity and point mutations are present in the Meq proteins, the oncoproteins of MDV, suggesting that changes in protein function induced by amino acid substitutions might affect MDV virulence. We previously reported that recent MDV isolates in Japan display distinct mutations in Meq proteins from those observed in traditional MDV isolates in Japan, but similar to those in MDV strains isolated from other countries. Methods To further investigate the genetic characteristics in Japanese field strains, we sequenced the whole genome of an MDV strain that was successfully isolated from a chicken with MD in Japan. A phylogenetic analysis of the meq gene was also performed. Results Phylogenetic analysis revealed that the Meq proteins in most of the Japanese isolates were similar to those of Chinese and European strains, and the genomic sequence of the Japanese strain was classified into the Eurasian cluster. Comparison of coding region sequences among the Japanese strain and MDV strains from other countries revealed that the genetic characteristics of the Japanese strain were similar to those of Chinese and European strains. Conclusions The MDV strains distributed in Asian and European countries including Japan seem to be genetically closer to each other than to MDV strains from North America. These findings indicate that the genetic diversities of MDV strains that emerged may have been dependent on the different vaccination-based control approaches.

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Isolation of an ovine genomic sequence containing the full-length angiotensin II type-1 receptor.

Endocrine Research ◽

10.3109/07435809809032619 ◽

1998 ◽

Vol 24 (3-4) ◽

pp. 387-390 ◽

Cited By ~ 1

Author(s):

Daniel S Millican ◽

Ian M Bird

Keyword(s):

Angiotensin Ii ◽

Genomic Sequence ◽

Full Length

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Sequencing and Phylogenetic Analysis of Near Full-Length HIV-1 Subtypes A, B, G and Unique Recombinant AC and AD Viral Strains Identified in South Africa

AIDS Research and Human Retroviruses ◽

10.1089/aid.2014.0230 ◽

2015 ◽

Vol 31 (4) ◽

pp. 412-420 ◽

Cited By ~ 6

Author(s):

Eduan Wilkinson ◽

Vera Holzmayer ◽

Graeme B. Jacobs ◽

Tulio de Oliveira ◽

Catherine A. Brennan ◽

...

Keyword(s):

South Africa ◽

Phylogenetic Analysis ◽

Full Length ◽

Hiv 1

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EFFICIENT ALGORITHMS AND SOFTWARE FOR DETECTION OF FULL-LENGTH LTR RETROTRANSPOSONS

Journal of Bioinformatics and Computational Biology ◽

10.1142/s021972000600203x ◽

2006 ◽

Vol 04 (02) ◽

pp. 197-216 ◽

Cited By ~ 20

Author(s):

ANANTHARAMAN KALYANARAMAN ◽

SRINIVAS ALURU

Keyword(s):

Genomic Sequence ◽

Linear Time ◽

Structural Characteristics ◽

Full Length ◽

Yeast Genome ◽

Structural Constraints ◽

Ltr Retrotransposons ◽

High Quality ◽

Robust Parameter ◽

And Performance

LTR retrotransposons constitute one of the most abundant classes of repetitive elements in eukaryotic genomes. In this paper, we present a new algorithm for detection of full-length LTR retrotransposons in genomic sequences. The algorithm identifies regions in a genomic sequence that show structural characteristics of LTR retrotransposons. Three key components distinguish our algorithm from that of current software — (i) a novel method that preprocesses the entire genomic sequence in linear time and produces high quality pairs of LTR candidates in run-time that is constant per pair, (ii) a thorough alignment-based evaluation of candidate pairs to ensure high quality prediction, and (iii) a robust parameter set encompassing both structural constraints and quality controls providing users with a high degree of flexibility. We implemented our algorithm into a software program called LTR_par, which can be run on both serial and parallel computers. Validation of our software against the yeast genome indicates superior results in both quality and performance when compared to existing software. Additional validations are presented on rice BACs and chimpanzee genome.

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Sequence and phylogenetic analysis of the SNF4/AMPK gamma subunit gene from Drosophila melanogaster

Genome ◽

10.1139/g99-059 ◽

1999 ◽

Vol 42 (6) ◽

pp. 1077-1087 ◽

Cited By ~ 1

Author(s):

Erin N Yoshida ◽

Bernhard F Benkel ◽

Ying Fong ◽

Donal A Hickey

Keyword(s):

Phylogenetic Analysis ◽

Drosophila Melanogaster ◽

Gene Family ◽

Genomic Sequence ◽

Sequence Similarity ◽

Energy Levels ◽

Metabolic Stress ◽

Gene Copy ◽

Gamma Subunit ◽

Snf1 Kinase

To optimize gene expression under different environmental conditions, many organisms have evolved systems which can quickly up- and down-regulate the activity of other genes. Recently, the SNF1 kinase complex from yeast and the AMP-activated protein kinase complex from mammals have been shown to represent homologous metabolic sensors that are key to regulating energy levels under times of metabolic stress. Using heterologous probing, we have cloned the Drosophila melanogaster homologue of SNF4, the noncatalytic effector subunit from this kinase complex. A sequence corresponding to the partial genomic sequence as well as the full-length cDNA was obtained, and shows that the D. melanogaster SNF4 is encoded in a 1944-bp cDNA representing a protein of 648 amino acids (aa). Southern analysis of Drosophila genomic DNA in concert with a survey of mammalian SNF4 ESTs indicates that in metazoans, SNF4 is a duplicated gene, and possibly even a larger gene family. We propose that one gene copy codes for a short (330 aa) protein, whereas the second locus codes for a longer version (<410 aa) that is extended at the carboxy terminus, as typified by the Drosophila homologue presented here. Phylogenetic analysis of yeast, invertebrate, and multiple mammalian isoforms of SNF4 shows that the gene duplication likely occurred early in the metazoan lineage, as the protein products of the different loci are relatively divergent. When the phylogeny was extended beyond the SNF4 gene family, SNF4 shares sequence similarity with other cystathionine-β-synthase domain-containing proteins, including IMP dehydrogenase and a variety of uncharacterized Methanococcus proteins.Key words: SNF4, AMPK gamma subunit, derepression, gene family, phylogeny.

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