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July 7, 2019

A novel type pathway-specific regulator and dynamic genome environments of solanapyrone biosynthesis gene cluster in the fungus Ascochyta rabiei.

Secondary metabolite genes are often clustered together and situated in particular genomic regions, like the subtelomere, that can facilitate niche adaptation in fungi. Solanapyrones are toxic secondary metabolites produced by fungi occupying different ecological niches. Full-genome sequencing of the ascomycete Ascochyta rabiei revealed a solanapyrone biosynthesis gene cluster embedded in an AT-rich region proximal to a telomere end and surrounded by Tc1/Mariner-type transposable elements. The highly AT-rich environment of the solanapyrone cluster is likely the product of repeat-induced point mutations. Several secondary metabolism-related genes were found in the flanking regions of the solanapyrone cluster. Although the solanapyrone cluster appears to be resistant to repeat-induced point mutations, a P450 monooxygenase gene adjacent to the cluster has been degraded by such mutations. Among the six solanapyrone cluster genes (sol1 to sol6), sol4 encodes a novel type of Zn(II)2Cys6 zinc cluster transcription factor. Deletion of sol4 resulted in the complete loss of solanapyrone production but did not compromise growth, sporulation, or virulence. Gene expression studies with the sol4 deletion and sol4-overexpressing mutants delimited the boundaries of the solanapyrone gene cluster and revealed that sol4 is likely a specific regulator of solanapyrone biosynthesis and appears to be necessary and sufficient for induction of the solanapyrone cluster genes. Despite the dynamic surrounding genomic regions, the solanapyrone gene cluster has maintained its integrity, suggesting important roles of solanapyrones in fungal biology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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July 7, 2019

A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose.

Thermophilic Campylobacter species colonize the intestine of agricultural and domestic animals commensally but cause severe gastroenteritis in humans. In contrast to other enteropathogenic bacteria, Campylobacter has been considered to be non-glycolytic, a metabolic property originally used for their taxonomic classification. Contrary to this dogma, we demonstrate that several Campylobacter coli strains are able to utilize glucose as a growth substrate. Isotopologue profiling experiments with (13) C-labeled glucose suggested that these strains catabolize glucose via the pentose phosphate and Entner-Doudoroff (ED) pathways and use glucose efficiently for de novo synthesis of amino acids and cell surface carbohydrates. Whole genome sequencing of glycolytic C.?coli isolates identified a genomic island located within a ribosomal RNA gene cluster that encodes for all ED pathway enzymes and a glucose permease. We could show in vitro that a non-glycolytic C.?coli strain could acquire glycolytic activity through natural transformation with chromosomal DNA of C.?coli and C.?jejuni subsp. doylei strains possessing the ED pathway encoding plasticity region. These results reveal for the first time the ability of a Campylobacter species to catabolize glucose and provide new insights into how genetic macrodiversity through intra- and interspecies gene transfer expand the metabolic capacity of this food-borne pathogen. © 2015 John Wiley & Sons Ltd.

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July 7, 2019

Advances in DNA sequencing technologies for high resolution HLA typing.

This communication describes our experience in large-scale G group-level high resolution HLA typing using three different DNA sequencing platforms – ABI 3730 xl, Illumina MiSeq and PacBio RS II. Recent advances in DNA sequencing technologies, so-called next generation sequencing (NGS), have brought breakthroughs in deciphering the genetic information in all living species at a large scale and at an affordable level. The NGS DNA indexing system allows sequencing multiple genes for large number of individuals in a single run. Our laboratory has adopted and used these technologies for HLA molecular testing services. We found that each sequencing technology has its own strengths and weaknesses, and their sequencing performances complement each other. HLA genes are highly complex and genotyping them is quite challenging. Using these three sequencing platforms, we were able to meet all requirements for G group-level high resolution and high volume HLA typing. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

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July 7, 2019

Integration of a transfected gene into the genome of Babesia bovis occurs by legitimate homologous recombination mechanisms.

This study examines the patterns of gene integration of gfp-bsd upon stable transfection into the T3Bo strain of Babesia bovis using a plasmid designed to integrate homologous sequences of the parasite’s two identical ef-1a A and B genes. While the transfected BboTf-149-6 cell line displayed two distinct patterns of gene integration, clonal lines derived from this strain by cell sorting contained only single gfp-bsd insertions. Whole genome sequencing of two selected clonal lines, E9 and C6, indicated two distinct patterns of gfp-bsd insertion occurring by legitimate homologous recombination mechanisms: one into the expected ef-1a orf B, and another into the ef-1a B promoter. The data suggest that expression of the ef-1a orf B is not required for development of B. bovis in cultured erythrocyte stages. Use of legitimate homologous recombination mechanisms in transfected B. bovis supports the future use of transfection methods for developing efficient gene function assignment experiments using gene knockout techniques. Published by Elsevier B.V.

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July 7, 2019

An integrated map of structural variation in 2,504 human genomes.

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

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July 7, 2019

Hybrid de novo tandem repeat detection using short and long reads.

As one of the most studied genome rearrangements, tandem repeats have a considerable impact on genetic backgrounds of inherited diseases. Many methods designed for tandem repeat detection on reference sequences obtain high quality results. However, in the case of a de novo context, where no reference sequence is available, tandem repeat detection remains a difficult problem. The short reads obtained with the second-generation sequencing methods are not long enough to span regions that contain long repeats. This length limitation was tackled by the long reads obtained with the third-generation sequencing platforms such as Pacific Biosciences technologies. Nevertheless, the gain on the read length came with a significant increase of the error rate. The main objective of nowadays studies on long reads is to handle the high error rate up to 16%.In this paper we present MixTaR, the first de novo method for tandem repeat detection that combines the high-quality of short reads and the large length of long reads. Our hybrid algorithm uses the set of short reads for tandem repeat pattern detection based on a de Bruijn graph. These patterns are then validated using the long reads, and the tandem repeat sequences are constructed using local greedy assemblies.MixTaR is tested with both simulated and real reads from complex organisms. For a complete analysis of its robustness to errors, we use short and long reads with different error rates. The results are then analysed in terms of number of tandem repeats detected and the length of their patterns.Our method shows high precision and sensitivity. With low false positive rates even for highly erroneous reads, MixTaR is able to detect accurate tandem repeats with pattern lengths varying within a significant interval.

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July 7, 2019

Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33.

Thermoanaerobacter thermohydrosulfuricus BSB-33 is a thermophilic gram positive obligate anaerobe isolated from a hot spring in West Bengal, India. Unlike other T. thermohydrosulfuricus strains, BSB-33 is able to anaerobically reduce Fe(III) and Cr(VI) optimally at 60 °C. BSB-33 is the first Cr(VI) reducing T. thermohydrosulfuricus genome sequenced and of particular interest for bioremediation of environmental chromium contaminations. Here we discuss features of T. thermohydrosulfuricus BSB-33 and the unique genetic elements that may account for the peculiar metal reducing properties of this organism. The T. thermohydrosulfuricus BSB-33 genome comprises 2597606 bp encoding 2581 protein genes, 12 rRNA, 193 pseudogenes and has a G?+?C content of 34.20 %. Putative chromate reductases were identified by comparative analyses with other Thermoanaerobacter and chromate-reducing bacteria.

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July 7, 2019

The genus Brachypodium as a model for perenniality and polyploidy

The genus Brachypodium contains annual and perennial species with both diploid and polyploid genomes. Like the annual species B. distachyon, some of the perennial and polyploid species have traits compatible with use as a model system (e.g. small genomes, rapid generation time, self-fertile and easy to grow). Thus, there is an opportunity to leverage the resources and knowledge developed for B. distachyon to use other Brachypodium species as models for perenniality and the regulation and evolution of polyploid genomes. There are two factors driving an increased interest in perenniality. First, several perennial grasses are being developed as biomass crops for the sustainable production of biofuel and it would be useful to have a perennial model system to rapidly test biotechnological crop improvement strategies for undesirable impacts on perenniality and winter hardiness. In addition, a deeper understanding of the molecular mechanisms underlying perenniality could be used to design strategies for improving energy crops, for example, by changing resource allocation during growth or by altering the onset of dormancy. The second factor driving increased interest in perenniality is the potential environmental benefits of developing perennial grain crops. B. sylvaticum is a perennial with attributes suitable for use as a perennial model system. A high efficiency transformation system has been developed and a genome sequencing project is underway. Since many important crops, including emerging biomass crops, are polyploid, there is a pressing need to understand the rules governing the evolution and regulation of polyploid genomes. Unfortunately, it is difficult to study polyploid crop genomes because of their size and the difficulty of manipulating those plants in the laboratory. By contrast, B. hybridum has a small polyploid genome and is easy to work with in the laboratory. In addition, analysis of the B. hybridum genome, will be greatly aided by the genome sequences of the two extant diploid species (B. distachyon and B. stacei) that apparently gave rise to B. hybridum. Availability of high quality reference genomes for these three species will be a powerful resource for the study of polyploidy.

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July 7, 2019

A synteny-based draft genome sequence of the forage grass Lolium perenne.

Here we report the draft genome sequence of perennial ryegrass (Lolium perenne), an economically important forage and turf grass species that is widely cultivated in temperate regions worldwide. It is classified along with wheat, barley, oats and Brachypodium distachyon in the Pooideae sub-family of the grass family (Poaceae). Transcriptome data was used to identify 28 455 gene models, and we utilized macro-co-linearity between perennial ryegrass and barley, and synteny within the grass family, to establish a synteny-based linear gene order. The gametophytic self-incompatibility mechanism enables the pistil of a plant to reject self-pollen and therefore promote out-crossing. We have used the sequence assembly to characterize transcriptional changes in the stigma during pollination with both compatible and incompatible pollen. Characterization of the pollen transcriptome identified homologs to pollen allergens from a range of species, many of which were expressed to very high levels in mature pollen grains, and are potentially involved in the self-incompatibility mechanism. The genome sequence provides a valuable resource for future breeding efforts based on genomic prediction, and will accelerate the development of new varieties for more productive grasslands.© 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

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July 7, 2019

Complete genome sequence of the probiotic bacterium Bifidobacterium breve KCTC 12201BP isolated from a healthy infant.

We present the completely sequenced genome of Bifidobacterium breve CBT BR3, which was isolated from the feces of a healthy infant. The 2.43-Mb genome contains several kinds of genetic factors associated with health promotion of the human host such as oligosaccharide-degrading genes and vitamin-biosynthetic genes. Copyright © 2015. Published by Elsevier B.V.

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July 7, 2019

PAFFT: A new homology search algorithm for third-generation sequencers.

DNA sequencers that can conduct real-time sequencing from a single polymerase molecule are known as third-generation sequencers. Third-generation sequencers enable sequencing of reads that are several kilobases long. However, the raw data generated from third-generation sequencers are known to be error-prone. Because of sequencing errors, it is difficult to identify which genes are homologous to the reads obtained using third-generation sequencers. In this study, a new method for homology search algorithm, PAFFT, is developed. This method is the extension of the MAFFT algorithm which was used for multiple alignments. PAFFT detects global homology rather than local homology so that homologous regions can be detected even when the error rate of sequencing is high. PAFFT will boost application of third-generation sequencers. Copyright © 2015 Elsevier Inc. All rights reserved.

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July 7, 2019

First detection of Klebsiella variicola producing OXA-181 carbapenemase in fresh vegetable imported from Asia to Switzerland.

The emergence and worldwide spread of carbapenemase-producing Enterobacteriaceae is of great concern to public health services. The aim of this study was to investigate the occurrence of carbapenemase-producing Enterobacteriaceae in fresh vegetables and spices imported from Asia to Switzerland.Twenty-two different fresh vegetable samples were purchased in March 2015 from different retail shops specializing in Asian food. The vegetables included basil leaves, bergamont leaves, coriander, curry leaves, eggplant and okra (marrow). Samples had been imported from Thailand, the Socialist Republic of Vietnam and India. After an initial enrichment-step, carbapenemase-producing Enterobacteriaceae were isolated from two carbapenem-containing selective media (SUPERCARBA II and Brilliance CRE Agar). Isolates were screened by PCR for the presence of bla KPC, bla NDM, bla OXA-48-like and bla VIM. An OXA-181-producing Klebsiella variicola was isolated in a coriander sample with origin Thailand/Vietnam. The bla OXA-181 gene was encoded in a 14’027 bp region flanked by two IS26-like elements on a 51-kb IncX3-type plasmid.The results of this study suggest that the international production and trade of fresh vegetables constitute a possible route for the spread of carbapenemase-producing Enterobacteriaceae. The presence of carbapenemase-producing organisms in the food supply is alarming and an important food safety issue.

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July 7, 2019

Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani.

Dickeya solani is an emerging pathogen that causes soft rot and blackleg diseases in several crops including Solanum tuberosum, but little is known about its genomic diversity and evolution.We combined Illumina and PacBio technologies to complete the genome sequence of D. solani strain 3337 that was used as a reference to compare with 19 other genomes (including that of the type strain IPO2222(T)) which were generated by Illumina technology. This population genomic analysis highlighted an unexpected variability among D. solani isolates since it led to the characterization of two distinct sub-groups within the D. solani species. This approach also revealed different types of variations such as scattered SNP/InDel variations as well as replacing and additive horizontal gene transfers (HGT). Infra-species (between the two D. solani sub-groups) and inter-species (between D. solani and D. dianthicola) replacing HGTs were observed. Finally, this work pointed that genetic and functional variation in the motility trait could contribute to aggressiveness variability in D. solani.This work revealed that D. solani genomic variability may be caused by SNPs/InDels as well as replacing and additive HGT events, including plasmid acquisition; hence the D. solani genomes are more dynamic than that were previously proposed. This work alerts on precautions in molecular diagnosis of this emerging pathogen.

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July 7, 2019

Completing the human genome: the progress and challenge of satellite DNA assembly.

Genomic studies rely on accurate chromosome assemblies to explore sequence-based models of cell biology, evolution and biomedical disease. However, even the extensively studied human genome has not yet reached a complete, ‘telomere-to-telomere’, chromosome assembly. The largest assembly gaps remain in centromeric regions and acrocentric short arms, sites known to contain megabase-sized arrays of tandem repeats, or satellite DNAs. This review aims to briefly address the progress and challenges of generating correct assemblies of satellite DNA arrays. Although the focus is placed on the human genome, many concepts presented here are applicable to other genomes.

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