![]() ![]() The sediment isolate from Xe Bangnouan, Laos, is more closely related to the sediment isolate from the Mekong River than to the corresponding water isolate ( Fig. 1). ![]() One clade includes isolates from or around Vientiane, Laos (city and province), whereas the other consists of isolates from further south. The six main branches of the tree correspond to the sequence types and are geographically clustered in two different clades. Then, we built a maximum likelihood tree using RAxML 8.2.11 ( 16) with a general time-reversible nucleotide substitution model including 1,000 bootstraps ( Fig. 1). pseudomallei MSHR4503 ( 15) as the reference. To unravel the phylogenetic relationship of the isolates, we first constructed a core single nucleotide polymorphism genome alignment using Snippy 4.4.3 with B. ![]() Sequence type 54 (ST54) (two isolates) was previously described and is common in neighboring Thailand ( 14). The 16 isolates were found to belong to 6 different sequence types using the multilocus sequence typing pipeline ( 12, 13), 5 of which were new. ![]() A summary of the assembly results is provided in Table 1. Default settings were used for all software unless otherwise specified. The genomes were annotated automatically using the NCBI Prokaryotic Annotation Pipeline 4.11 ( 11). The quality and completeness of the de novo-assembled genomes were accessed using BUSCO 3.0.1 (lineage, Betaprotebacteria odb9) ( 9), and basic assembly statistics were compared using QUAST 4.6.3 ( 10). Finally, contaminants were removed manually using a BLAST search against the NCBI nucleotide database. Scaffolds of <200 bp or with low coverage were removed. Pilon 1.22 ( 8) was applied to improve the quality of the draft assemblies. Reads were quality trimmed using Trimmomatic 0.36 (slidingwindow:4: 8, minlen:127) ( 6) and assembled using SPAdes 3.11.1 (-careful, -mismatch-correction, -k 21, 33, 55, 77, 99, 127 bp) ( 7). After storage at −80☌ and pure culture on nutrient agar in air at 37☌ for 24 h, genomic DNA was extracted using the Qiagen DNeasy blood and tissue kit and submitted to Microsynth AG (Balgach, Switzerland) for Nextera XT library preparation and sequencing using an Illumina NextSeq 500 instrument (paired-end, 150-bp reads). pseudomallei isolates from 14 filtered water samples and two sediment samples from rivers in Laos, cultured and confirmed as previously described ( 5). pseudomallei and their functions ( 3, 4). pseudomallei isolates contribute to research on links between environment-associated and disease-associated genes of B. Survival and replication in various ecological niches and within hosts is possibly enabled by the large and highly variable accessory genome of B. N.Burkholderia pseudomallei causes the human infectious disease melioidosis and is found in tropical and subtropical soils and freshwater ( 1). Result.var=match.out, omnibus.var=match.out, Idvar="seriali", timevar="year_2", intvar="treated", When I run the following code: cov.var <- c("age", "sex", "ethgr2", "hh_size", "country_4", I think I have set up the data exactly as the tutorial describes, giving the ID variable, a time variable (which is numerical) and a binary treatment variable. Can anyone help me figure out why I get an error code with the microsynth function? ![]()
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