Escherichia coli serotype O157:H7 strain B6914-MS1 is an isolate from the Centers for Disease Control and Prevention that is missing both Shiga toxin genes and has been used extensively in applied research studies. Here we report the genome sequence of strain B6914-ARS, a B6914-MS1 clone that has unique biofilm properties.
Lactobacillus salivarius BCRC 14759 has been identified as a high-exopolysaccharide-producing strain with potential as a probiotic or fermented dairy product. Here, we report the genome sequences of L. salivarius BCRC 14759 and the comparable strain BCRC 12574, isolated from human saliva. The PacBio RSII sequencing platform was used to obtain high-quality assemblies for characterization of this probiotic candidate. Copyright © 2017 Chiu et al.
We provide complete circularized genome sequences of two mosquito-derived Elizabethkingia anophelis strains with draft sequences currently in the public domain (R26 and Ag1), and two novel E. anophelis strains derived from a different mosquito species, Anopheles sinensis (AR4-6 and AR6-8). The genetic similarity of all four mosquito-derived strains is remarkable.
Satsuma (Citrus unshiu Marc.) is one of the most abundantly produced mandarin varieties of citrus, known for its seedless fruit production and as a breeding parent of citrus. De novo assembly of the heterozygous diploid genome of Satsuma (“Miyagawa Wase”) was conducted by a hybrid assembly approach using short-read sequences, three mate-pair libraries, and a long-read sequence of PacBio by the PLATANUS assembler. The assembled sequence, with a total size of 359.7 Mb at the N50 length of 386,404 bp, consisted of 20,876 scaffolds. Pseudomolecules of Satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of Clementine, pummelo, and sweet orange. Gene prediction by modeling with MAKER-P proposed 29,024 genes and 37,970 mRNA; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. BUSCO scores for the assembled scaffold and predicted transcripts, and another analysis by BAC end sequence mapping indicated the assembled genome consistency was close to those of the haploid Clementine, pummel, and sweet orange genomes. The number of repeat elements and long terminal repeat retrotransposon were comparable to those of the seven citrus genomes; this suggested no significant failure in the assembly at the repeat region. A resequencing application using the assembled sequence confirmed that both kunenbo-A and Satsuma are offsprings of Kishu, and Satsuma is a back-crossed offspring of Kishu. These results illustrated the performance of the hybrid assembly approach and its ability to construct an accurate heterozygous diploid genome.
[Objective] The aim of this study was to study the diversity of lipolytic enzymes in Stenotrophomonas maltophilia OUC_Est10. [Methods] Ion exchange chromatography, genome sequencing and heterologous expression were used to study the diversity of lipolytic enzymes in Stenotrophomonas maltophilia OUC_Est10. [Results] Stenotrophomonas maltophilia OUC_Est10 could secret a wide range of lipolytic enzymes (lipases and esterases) as revealed by ion exchange chromatography. The complete genome is of 4668743 bp in length, with an average GC content of 66.25%. Genome annotation indicated the presence of 33 candidate genes whose products possess the predicted lipolytic enzyme activities. Analysis of catalytic features was carried out by expressing five putative lipolytic enzyme genes, and lipolytic enzymes in OUC_Est10 had different catalytic properties. [Conclusion] We proved that Stenotrophomonas maltophilia OUC_Est10 was a good candidate to produce diverse lipolytic enzymes, with potential applications in various fields.
We report here the complete genome sequence of the facultative predatory bacterium Ensifer adhaerens strain Casida A. The genome was assembled into three circular contigs, with a main chromosome as well as two large secondary replicons, that totaled 7,267,502 bp with 6,641 predicted open reading frames. Copyright © 2017 Williams et al.
Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT) technology and are the first complete genome sequences reported for B. thermosphacta.
Long read technologies have revolutionized de novo genome assembly by generating contigs orders of magnitude longer than that of short read assemblies. Although assembly contiguity has increased, it usually does not reconstruct a full chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To increase the contiguity of the assembly to the chromosome level, different strategies are used which exploit long range contact information between chromosomes in the genome.We develop a scalable and computationally efficient scaffolding method that can boost the assembly contiguity to a large extent using genome-wide chromatin interaction data such as Hi-C.we demonstrate an algorithm that uses Hi-C data for longer-range scaffolding of de novo long read genome assemblies. We tested our methods on the human and goat genome assemblies. We compare our scaffolds with the scaffolds generated by LACHESIS based on various metrics.Our new algorithm SALSA produces more accurate scaffolds compared to the existing state of the art method LACHESIS.
The PacBio RS II provides for single molecule, real-time DNA technology to sequence genomes and detect DNA modifications. The starting point for high-quality sequence production is high molecular weight genomic DNA. To automate the library preparation process, there must be high-throughput methods in place to assess the genomic DNA, to ensure the size and amounts of the sheared DNA fragments and final library.The library construction automation was accomplished using the Agilent NGS workstation with Bravo accessories for heating, shaking, cooling, and magnetic bead manipulations for template purification. The quality control methods from gDNA input to final library using the Agilent Bioanalyzer System and Agilent TapeStation System were evaluated.Automated protocols of PacBio 10 kb library preparation produced libraries with similar technical performance to those generated manually. The TapeStation System proved to be a reliable method that could be used in a 96-well plate format to QC the DNA equivalent to the standard Bioanalyzer System results. The DNA Integrity Number that is calculated in the TapeStation System software upon analysis of genomic DNA is quite helpful to assure that the starting genomic DNA is not degraded. In this respect, the gDNA assay on the TapeStation System is preferable to the DNA 12000 assay on the Bioanalyzer System, which cannot run genomic DNA, nor can the Bioanalyzer work directly from the 96-well plates.
Peter Raven, in 1963, included two fern taxa of the genus Botrychium in his list of plant species exhibiting American amphitropical bipolar disjunctions. He attributed the southern hemisphere occurrences to post-Pleistocene long-distance dispersal from counterparts in the northern hemisphere, probably assisted by annual bird migrations between the disjunct areas. Using genetic evidence gathered through worldwide analyses of phylogenetic relationship in Botrychium, we now review and reconsider Raven’s conclusions. Genetic similarities indicate that South American Botrychium dusenii is an allotetraploid taxon closely related to B. spathulatum, a North American endemic, and that B. lunaria in New Zealand possesses a genotype identical to that of a taxon in North America derived through introgressive hybridization between B. lunaria and an endemic North American species, B. neolunaria. Both North American counterparts exhibit Raven’s characteristics of bipolar disjuncts in their occurrence in mountain and coastal meadows, copious production of small propagules (spores in Botrychium), occurrence in habitats frequented by transpolar bird migrants, and ability to found new colonies through inbreeding. We discuss these characteristics in Botrychium and relative to other ferns and suggest further studies on Botrychium and related taxa to address questions of time, number, and mode of bipolar dispersals.© 2017 Botanical Society of America.
Bacillus velezensis YJ11-1-4 is a strain that exhibits broad-spectrum antimicrobial activity against various pathogens. It was isolated from doenjang, a traditional Korean fermented soybean paste. The genome comprises a single circular chromosome of 4,006,637 bp with 46.42% G+C content without plasmids. Copyright © 2017 Lee et al.
Acetobacter pomorum Oregon-R-modENCODE strain BDGP5 was isolated from Drosophila melanogaster for functional host-microbe interaction studies. The complete genome is composed of a single chromosomal circle of 2,848,089 bp, with a G+C content of 53% and three plasmids of 131,455 bp, 19,216 bp, and 9,160 bp. Copyright © 2017 Wan et al.
Bacillus vallismortis NBIF-001, a Gram-positive bacterium, was isolated from soil in Shangri-La, China. Here, we provide the complete genome sequence of this bacterium, which has a 3,929,787-bp-long genome, including 4,030 protein-coding genes and 195 RNA genes. This strain possesses a number of genes encoding virulence factors of pathogens. Copyright © 2017 Liu et al.
Clostridial neurotoxins, including botulinum and tetanus neurotoxins, are among the deadliest known bacterial toxins. Until recently, the horizontal mobility of this toxin gene family appeared to be limited to the genusClostridiumWe report here the closed genome sequence ofChryseobacterium piperi, a Gram-negative bacterium containing coding sequences with homology to clostridial neurotoxin family proteins. Copyright © 2017 Wentz et al.
Bacillus velezensis L-1 is an effective biocontrol agent against pear diseases. Here, we report the complete genome sequence of B. velezensis L-1 in which clusters related to the biosynthesis of secondary metabolites were predicted. This genome provides insights into the possible biocontrol mechanisms and furthers application of this specific bacterium. Copyright © 2017 Sun et al.
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