[Carpesium sp.]

原著和名: [記載なし]科名: キク科 = Compositae採集地: 栃木県 日光市 東照宮裏〜雲竜入口 (下野 日光 東照宮裏〜雲竜入口)採集日: 1980/10/10採集者: 萩庭丈壽整理番号: JH027469国立科学博物館整理番号: TNS-VS-977469備考: DB作成協力会による補足あ

Additional file 4: Figure S2. of Common position of indels that cause deviations from canonical genome organization in different measles virus strains

Variability fingerprint constructed using 54 different complete measles genomic sequences. Legend: The variability of each genomic position is quantified by considering the number of different nucleotides that are found at that position (shown in white, light grey, dark grey or black). The rectangle indicates which fingerprint area depicts variability of non-coding region between M and F genes’ open reading frames (1012 nts). (TIF 501 kb

Supplementary Material for: Early Evolution of Human Respiratory Syncytial Virus ON1 Strains: Analysis of the Diversity in the C-Terminal Hypervariable Region of Glycoprotein Gene within the First 3.5 Years since Their Detection

<b><i>Objective:</i></b> Characterization of the phylogeny and diversity of human respiratory syncytial virus (HRSV) genotype ON1 that occurred during its early evolution (within the first 3.5 years since the detection of the first ON1 strains). ON1 strains have a 72-nucleotide-long in-frame duplication within the second hypervariable domain of the glycoprotein gene (HVR2). <b><i>Methods:</i></b> All available HVR2 sequences of strains belonging to the ON1 genotype published prior to June 20, 2014 were collected. Multiple sequence alignments, phylogeny, phylogeography, sequence clustering and putative protein analyses were performed. <b><i>Results:</i></b> The worldwide spread and diversification of ON1 strains are presented. Only in a minority of ON1 strains do the two replicas remain identical, and various ON1 strains possess common differences between the first and the second copy (segments A and B). Mutations of the progenitor sequence were more frequent in segment B, a higher overall diversity on the protein level and more putative glycosylation sites exist in segment B, and, unlike in segment A, positive selection acts on that protein region. <b><i>Conclusions:</i></b> The fast spread of the novel HRSV genotype ON1 has been accompanied by its rapid concurrent diversification. Differences in variability of the two replicas within HVR2 were detected, with C-terminal replica being more variable

Additional file 1: of Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene

Figure S1. Phylogenetic tree of RSV strains based on HVR2 genomic segment. Tree was generated using maximum-likelihood method, based on the General Time Reversible model and discrete gamma distributed rates across sites. The scale bar indicates the proportion of nucleotide substitutions per site. Numbers are percentages of bootstrap values determined for 1000 iterations, only values above 70% are shown. Strain designations are composed of NCBI GenBank acc. no., name and genotype. (PDF 54 kb

Additional file 2: of Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene

Table S1. Sequences identical at HVR2 or SHseg. (PDF 82 kb