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November 1, 2018

Correcting palindromes in long reads after whole-genome amplification.

Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long sequencing reads.Here, we present Pacasus, a tool for correcting such errors. Two datasets show that it markedly improves read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA.With Pacasus long-read technologies become available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.

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August 1, 2018

Novel energy conservation strategies and behavior of Pelotomaculum schinkii driving syntrophic propionate catabolism.

Under methanogenic conditions, short-chain fatty acids are common byproducts from degradation of organic compounds and conversion of these acids is an important component of the global carbon cycle. Due to the thermodynamic difficulty of propionate degradation, this process requires syntrophic interaction between a bacterium and partner methanogen; however, the metabolic strategies and behavior involved are not fully understood. In this study, the first genome analysis of obligately syntrophic propionate degraders (Pelotomaculum schinkii HH and P. propionicicum MGP) and comparison with other syntrophic propionate degrader genomes elucidated novel components of energy metabolism behind Pelotomaculum propionate oxidation. Combined with transcriptomic examination of…

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July 1, 2018

Investigating the central metabolism of Clostridium thermosuccinogenes.

Clostridium thermosuccinogenes is a thermophilic anaerobic bacterium able to convert various carbohydrates to succinate and acetate as main fermentation products. Genomes of the four publicly available strains have been sequenced, and the genome of the type strain has been closed. The annotated genomes were used to reconstruct the central metabolism, and enzyme assays were used to validate annotations and to determine cofactor specificity. The genes were identified for the pathways to all fermentation products, as well as for the Embden-Meyerhof-Parnas pathway and the pentose phosphate pathway. Notably, a candidate transaldolase was lacking, and transcriptomics during growth on glucose versus that…

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March 7, 2018

Dynamic virulence-related regions of the fungal plant pathogen Verticillium dahliae display remarkably enhanced sequence conservation

Selection pressure impacts genomes unevenly, as different genes adapt with differential speed to establish an organisms optimal fitness. Plant pathogens co-evolve with their hosts, which implies continuously adaption to evade host immunity. Effectors are secreted proteins that mediate immunity evasion, but may also typically become recognized by host immune receptors. To facilitate effector repertoire alterations, in many pathogens, effector genes reside in dynamic genomic regions that are thought to display accelerated evolution, a phenomenon that is captured by the two-speed genome hypothesis. The genome of the vascular wilt pathogen Verticillium dahliae has been proposed to obey to a similar two-speed…

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March 1, 2018

Genotype assembly, biological activity and adaptation of spatially separated isolates of Spodoptera litura nucleopolyhedrovirus.

The cotton leafworm Spodoptera litura is a polyphagous insect. It has recently made a comeback as a primary insect pest of cotton in Pakistan due to reductions in pesticide use on the advent of genetically modified cotton, resistant to Helicoverpa armigera. Spodoptera litura nucleopolyhedrovirus (SpltNPV) infects S. litura and is recognized as a potential candidate to control this insect. Twenty-two NPV isolates were collected from S. litura from different agro-ecological zones (with collection sites up to 600?km apart) and cropping systems in Pakistan to see whether there is spatial dispersal and adaptation of the virus and/or adaptation to crops. Therefore,…

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October 26, 2017

Complete genome sequence of Eubacterium hallii strain L2-7.

The complete genome sequence of Eubacterium hallii strain L2-7 is reported here. This intestinal strain produces butyrate from glucose as well as lactate when acetate is provided in the growth medium. In addition, strain L2-7 has been shown to improve insulin sensitivity in db/db mice, indicating its application potential. Copyright © 2017 Shetty et al.

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September 25, 2017

PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi: Insights, challenges andopportunities.

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored…

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April 6, 2017

Genome sequences of Cyberlindnera fabianii 65, Pichia kudriavzevii 129, and Saccharomyces cerevisiae 131 isolated from fermented masau fruits in Zimbabwe.

Cyberlindnera fabianii 65, Pichia kudriavzevii 129, and Saccharomyces cerevisiae 131 have been isolated from the microbiota of fermented masau fruits. C. fabianii and P. kudriavzevii especially harbor promising features for biotechnology and food applications. Here, we present the draft annotated genome sequences of these isolates. Copyright © 2017 van Rijswijck et al.

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March 8, 2017

Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome.

Using second-generation sequencing (SGS) RNA-Seq strategies, extensive alterative splicing prediction is impractical and high variability of isoforms expression quantification is inevitable in organisms without true reference dataset. we report the development of a novel analysis method, termed hybrid sequencing and map finding (HySeMaFi) which combines the specific strengths of third-generation sequencing (TGS) (PacBio SMRT sequencing) and SGS (Illumina Hi-Seq/MiSeq sequencing) to effectively decipher gene splicing and to reliably estimate the isoforms abundance. Error-corrected long reads from TGS are capable of capturing full length transcripts or as large partial transcript fragments. Both true and false isoforms, from a particular gene, as…

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January 5, 2017

Complete genome sequence of Akkermansia glycaniphila strain PytT, a mucin-degrading specialist of the reticulated python gut.

Akkermansia glycaniphila is a novel Akkermansia species that was isolated from the intestine of the reticulated python and shares the capacity to degrade mucin with the human strain Akkermansia muciniphila Muc(T) Here, we report the complete genome sequence of strain Pyt(T) of 3,074,121 bp. The genomic analysis reveals genes for mucin degradation and aerobic respiration. Copyright © 2017 Ouwerkerk et al.

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August 1, 2016

A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus.

The button mushroom (Agaricus bisporus) is one of the world's most cultivated mushroom species, but in spite of its economic importance generation of new cultivars by outbreeding is exceptional. Previous genetic analyses of the white bisporus variety, including all cultivars and most wild isolates revealed that crossing over frequencies are low, which might explain the lack of introducing novel traits into existing cultivars. By generating two high quality whole genome sequence assemblies (one de novo and the other by improving the existing reference genome) of the first commercial white hybrid Horst U1, a detailed study of the crossover (CO) landscape…

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April 6, 2016

Campylobacter fetus subspecies contain conserved type IV secretion systems on multiple genomic islands and plasmids.

The features contributing to differences in pathogenicity of the Campylobacter fetus subspecies are unknown. Putative factors involved in pathogenesis are located in genomic islands that encode a type IV secretion system (T4SS) and fic domain (filamentation induced by cyclic AMP) proteins, which may disrupt host cell processes. In the genomes of 27 C. fetus strains, three phylogenetically-different T4SS-encoding regions (T4SSs) were identified: one was located in both the chromosome and in extra-chromosomal plasmids; one was located exclusively in the chromosome; and one exclusively in extra-chromosomal plasmids. We observed that C. fetus strains can contain multiple T4SSs and that homologous T4SSs…

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March 17, 2016

Complete genome sequence of Enterococcus faecium commensal isolate E1002.

The emergence of vancomycin-resistant enterococci (VRE) has been associated with an increase in multidrug-resistant nosocomial infections. Here, we report the 2.614-Mb genome sequence of the Enterococcus faecium commensal isolate E1002, which will be instrumental in further understanding the determinants of the commensal and pathogenic lifestyle of E. faecium. Copyright © 2016 Tytgat et al.

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February 4, 2016

Complete genome sequence of Streptococcus salivarius HSISS4, a human commensal bacterium highly prevalent in the digestive tract.

The human commensal bacterium Streptococcus salivarius plays a major role in the equilibrium of microbial communities of the digestive tract. Here, we report the first complete genome sequence of a Streptococcus salivarius strain isolated from the small intestine, namely, HSISS4. Its circular chromosome comprises 1,903 coding sequences and 2,100,988 nucleotides. Copyright © 2016 Mignolet et al.

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