species are vector-borne parasitic bacteria with unusual, highly fragmented genomes that include a linear chromosome and linear as well as circular plasmids that differ numerically between and within ...various species. Strain CA690
, which was cultivated from a questing
nymph in the San Francisco Bay area, CA, was determined to be genetically distinct from all other described species belonging to the
complex. The genome, including plasmids, was assembled using a hybrid assembly of short Illumina reads and long reads obtained via Oxford Nanopore Technology. We found that strain CA690
has a main linear chromosome containing 902176 bp with a blast identity ≤91 % compared with other
species chromosomes and five linear and two circular plasmids. A phylogeny based on 37 single-copy genes of the main linear chromosome and rooted with the relapsing fever species
strain Ly revealed that strain CA690
had a sister-group relationship with, and occupied a basal position to, species occurring in North America. We propose to name this species
sp. nov. The type strain, CA690
, has been deposited in two national culture collections, DSMZ (=107169) and ATCC (=TSD-160).
The assembly of billions of short sequencing reads into a contiguous genome is a daunting task. The foundation knowledge of current DNA assembly models is concentrated among a select group, where the ...solution to the genome assembly challenge lies in proper ordering the genomic data. This contribution’s objective is to provide an overview of the original graph models used in DNA sequencing by hybridization. With the updated analytical approach based on the bidirectional bipartite graph class, the theoretical basic structure of the DNA assembly model has been described in new perspective by incorporating few short hypothetical DNA sequences. On the Galaxy platform, by using Spades assembler and Velvet assembler, the comparative outcomes of an experiment are presented, and we also identify their working schemes. Here, the working principle of de Bruijn graph has been discussed in broader point of view.
While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a ...shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects. To address this limitation, we developed the first de Bruijn graph assembler, dipSPAdes, for HP genomes that significantly improves on the state-of-the-art assemblers for HP diploid genomes.
Sequencing of the
gene of methicillin-resistant Staphylococcus aureus (MRSA) is used for assigning
types to e.g., detect transmission and control outbreaks. Traditionally,
typing is performed by ...Sanger sequencing but has in recent years been replaced by whole-genome sequencing (WGS) in some laboratories.
typing by WGS involves
assembly of millions of short sequencing reads into larger contiguous sequences, from which the
type is then determined. The choice of assembly program therefore potentially impacts the
typing result. In this study, WGS of 1,754 MRSA isolates was followed by
assembly using the assembly programs SPAdes (with two different sets of parameters) and SKESA. The
types were assigned and compared to the
types obtained by Sanger sequencing, regarding the latter as the correct
types. SPAdes with the two different settings resulted in assembly of the correct
type for 84.8% and 97.6% of the isolates, respectively, while SKESA assembled the correct
type in 98.6% of cases. The misassembled
types were generally two
repeats shorter than the correct
type and mainly included
types with repetition of the same repeats. WGS-based
typing is thus very accurate compared to Sanger sequencing, when the best assembly program for this purpose is used.
typing of methicillin-resistant Staphylococcus aureus (MRSA) is widely used by clinicians, infection control workers, and researchers both in local outbreak investigations and as an easy way to communicate and compare MRSA types between laboratories and countries. Traditionally,
types are determined by Sanger sequencing, but in recent years a whole-genome sequencing (WGS)-based approach has become increasingly used. In this study, we compared
typing by WGS using different methods for assembling the genome from short sequencing reads and compared to Sanger sequencing as the gold standard. We find substantial differences in correct assembly of
types between the assembly methods. Our findings are therefore important for the quality of WGS based
typing data being exchanged by clinical microbiology laboratories.
During the recent pandemics of COVID-19, sequencing technics became a powerful tool for gaining information about the SARS-CoV-2 virus and using this knowledge to our advantage. Thanks to this ...advantage, scientists all over the world were able to search for emerging variations, watching the virus evolve in real time. Assembly of the virus genomes is a crucial part of obtaining this kind of useful information. In our study, we sequenced 79 samples from nasopharyngeal swabs of COVID-19 patients. Positivity to disease was evaluated using RT-qPCR. In this work, we described the relationship between RT-qPCR Ct value and genome construction success (plus genome lineage assignment). The specific value of this study is that this relationship was described for data from metatranscriptomic sequencing of human tissue, while there was no step of viral RNA isolation (usual for genome assembly procedure). RT-qPCR Ct value and assembly quality metric NG50 were correlated. We observed that the RT-qPCR Ct value threshold of the certain success of genome assembly (Ct value < 25) and certain failure (Ct value > 30) could be drawn, while results varied for values between (with completed, completed with lower quality, and failed assemblies).
Conservation approaches that efficiently protect multiple values, such as the umbrella species concept, have been widely promoted with expected dramatic ecosystem changes. Due to its social and ...cultural importance, and recent declining trends, boreal populations of woodland caribou have been suggested as potential umbrella species for other declining taxa, such as boreal landbirds. We propose a generic pixel‐based umbrella index that focuses on fine‐grained habitat overlaps. In light of ongoing conservation efforts worldwide implementing area‐based targets (e.g., 30% by 2030), we used a random neutral model as baseline, as opposed to a no‐conservation scenario, which has been used elsewhere. We found that the conservation efficiency of caribou as an umbrella for 71 co‐occurring landbirds—three of which are priority species—in the Northwest Territories, Canada, is generally lower than our random model, as 53% of the species presented negative umbrella index medians with the interquartile range not overlapping zero. We conclude that in cases where area‐based targets drive decision‐making and the issue at stake involves identifying which areas to conserve—not whether to conserve—woodland caribou may be a leaky umbrella for most co‐occurring landbird species and these might need complementary conservation actions to be brought in from the rain.
Since our chapter on genome sequencing using the GS-FLX pyrosequencer in the First Edition of this book, significant advances have been made in next-generation DNA sequencing (NGS) technology. Not ...only has the GS-FLX become extinct, but the more recent introduction and establishment of the so-called third-generation DNA sequencers by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) has revolutionized genomics yet again by generating ultra-long (>100,000 basepair) sequence reads concomitant with an incredible reduction in cost per sequenced basepair. Unfortunately, the ultra-high sequence yields of third-generation sequencers are compromised by their inherent sequencing error rates, prompting an alternative sequencing strategy, i.e., a hybrid sequencing strategy, which combines PacBio/ONT primary datasets with complementary datasets generated by mainstream short-read NGS platforms, e.g., Illumina or Ion Torrent. Although the concept of a hybrid sequencing strategy is not new, existing yields and accuracy of ultra-long and short-read sequencing technologies makes such a strategy achievable, resulting in complete genome sequences in one hit. In this chapter, we describe our updated laboratory and bioinformatic protocols that will allow the average research group to obtain complete oral microbial genome sequences assembled from a combination of DNA sequence data generated by NGS and third-generation platforms.
The availability of RNA-Seq method allows researchers to capture the spatial or temporal profile of transcriptomes from various types of biological samples. The transcriptome data from a species can ...be analyzed in the context of its sequenced genomes or closely related genome to score biological sample-specific transcript isoforms, novel transcribed regions and to refine gene models including identification of new genes, in addition to the differential gene expression analysis. However, many plant species of importance currently lack a sequenced genome or a closely related reference genome and thus, rely on the de novo methods for generating transcript models and transcriptome assemblies. Here we describe various tools used for de novo transcriptome assembly and discuss the data management practices and standards.
The article analyzes two Petersburg texts by A.S. Pushkin: The Bronze Horseman: A Petersburg Tale and Queen of Spades. The author states that The Bronze Horseman is based on the dichotomy of the ...original spontaneous water principle as opposed to the city’s static fundamentals. The horizontal water element lacks a privileged and superior, authoritative position. On the contrary, the city is dominated by the privileged position of the creator, who controls the city’s hierarchy. This situation is also reflected in the text of the Queen of Spades, in which the author, Pushkin, loses the superior position and leaves the semantic initiative to free formation of meanings, which could be perceived as an ironic opposition to the author’s intention. The theme of the cards, the principle of the play, the narrative of “pereskaz”, the dualism of the Petersburg scene and the constant position of the hero “ashore” bring spontaneity to the text structure and become a source of the free formation of meanings.
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