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Auto Tag: PacBio library

July 7, 2019  |  

SiLiCO: A simulator of long read sequencing in PacBio and Oxford Nanopore

Long read sequencing platforms, which include the widely used Pacific Biosciences (PacBio) platform and the emerging Oxford Nanopore platform, aim to produce sequence fragments in excess of 15-20 kilobases, and have proved advantageous in the identification of structural variants and easing genome assembly. However, long read sequencing remains relatively expensive and error prone, and failed sequencing runs represent a significant problem for genomics core facilities. To quantitatively assess the underlying mechanics of sequencing failure, it is essential to have highly re-producible and controllable reference data sets to which sequencing results can be compared. Here, we present SiLiCO, the first in silico simulation tool to generate standardized sequencing results from both of the leading long read sequenc-ing platforms.

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July 7, 2019  |  

Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes.

Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence.A high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to the assemblies of the four other isolates. Whole genome analysis showed a high level of genetic diversity between the five isolates (2.85-16.8 SNPs/kb), which grouped into two distinct phylogenetic clusters. Mating type gene analysis revealed the presence of either the MAT1-1-1 or the MAT1-2-1 gene. Moreover, a putative new MAT gene (MAT1-2-8) was detected in the MAT1-2 locus. Comparative genome analysis revealed that Bb8028 contains 163 genes exclusive for this isolate. These unique genes have a tendency to cluster in the genome and to be often located near the telomeres. Among the genes unique to Bb8028 are a Non-Ribosomal Peptide Synthetase (NRPS) secondary metabolite gene cluster, a polyketide synthase (PKS) gene, and five genes with homology to bacterial toxins. A survey of candidate virulence genes for B. bassiana is presented.Our results indicate several genes and molecular processes that may underpin virulence towards mosquitoes. Thus, the genome sequences of five isolates of B. bassiana provide a better understanding of the natural variation in virulence and will offer a major resource for future research on this important biological control agent.

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July 7, 2019  |  

The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance.

The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is among the 100 worst invasive species in the world. As one of the most important crop pests and virus vectors, B. tabaci causes substantial crop losses and poses a serious threat to global food security. We report the 615-Mb high-quality genome sequence of B. tabaci Middle East-Asia Minor 1 (MEAM1), the first genome sequence in the Aleyrodidae family, which contains 15,664 protein-coding genes. The B. tabaci genome is highly divergent from other sequenced hemipteran genomes, sharing no detectable synteny. A number of known detoxification gene families, including cytochrome P450s and UDP-glucuronosyltransferases, are significantly expanded in B. tabaci. Other expanded gene families, including cathepsins, large clusters of tandemly duplicated B. tabaci-specific genes, and phosphatidylethanolamine-binding proteins (PEBPs), were found to be associated with virus acquisition and transmission and/or insecticide resistance, likely contributing to the global invasiveness and efficient virus transmission capacity of B. tabaci. The presence of 142 horizontally transferred genes from bacteria or fungi in the B. tabaci genome, including genes encoding hopanoid/sterol synthesis and xenobiotic detoxification enzymes that are not present in other insects, offers novel insights into the unique biological adaptations of this insect such as polyphagy and insecticide resistance. Interestingly, two adjacent bacterial pantothenate biosynthesis genes, panB and panC, have been co-transferred into B. tabaci and fused into a single gene that has acquired introns during its evolution.The B. tabaci genome contains numerous genetic novelties, including expansions in gene families associated with insecticide resistance, detoxification and virus transmission, as well as numerous horizontally transferred genes from bacteria and fungi. We believe these novelties likely have shaped B. tabaci as a highly invasive polyphagous crop pest and efficient vector of plant viruses. The genome serves as a reference for resolving the B. tabaci cryptic species complex, understanding fundamental biological novelties, and providing valuable genetic information to assist the development of novel strategies for controlling whiteflies and the viruses they transmit.

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July 7, 2019  |  

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D.

Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction. Assembly of the reads derived from all three technologies resulted in complete sequences for all 16 yeast chromosomes, as well as the mitochondrial chromosome, in one step. Further, we identified three types of DNA methylation (5mC, 4mC and 6mA). Comparison between the reference strain S288C and strain CEN.PK113-7D identified chromosomal rearrangements against a background of similar gene content between the two strains. We identified full-length transcripts through ONT direct RNA sequencing technology. This allows for the identification of transcriptional landscapes, including untranslated regions (UTRs) (5′ UTR and 3′ UTR) as well as differential gene expression quantification. About 91% of the predicted transcripts could be consistently detected across biological replicates grown either on glucose or ethanol. Direct RNA sequencing identified many polyadenylated non-coding RNAs, rRNAs, telomere-RNA, long non-coding RNA and antisense RNA. This work demonstrates a strategy to obtain complete genome sequences and transcriptional landscapes that can be applied to other eukaryal organisms.

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July 7, 2019  |  

Complete genome sequence of Pseudomonas sp. strain NC02, isolated from soil.

We report here the complete genome sequence of Pseudomonas sp. strain NC02, isolated from soil in eastern Massachusetts. We assembled PacBio reads into a single closed contig with 132× mean coverage and then polished this contig using Illumina MiSeq reads, yielding a 6,890,566-bp sequence with 61.1% GC content. Copyright © 2018 Cerra et al.

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July 7, 2019  |  

Complete genome sequence of Escherichia coli ML35.

We report here the complete genome sequence of Escherichia coli strain ML35. We assembled PacBio reads into a single closed contig with 169× mean coverage and then polished this contig using Illumina MiSeq reads, yielding a 4,918,774-bp sequence with 50.8% GC content. Copyright © 2018 Casale et al.

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July 7, 2019  |  

Complete genome sequence of a ciprofloxacin-resistant Salmonella enterica subsp. enterica serovar Kentucky sequence type 198 strain, PU131, isolated from a human patient in Washington State.

Strains of the ciprofloxacin-resistant (Cipr) Salmonella enterica subsp. enterica serovar Kentucky sequence type 198 (ST198) have rapidly and extensively disseminated globally to become a major food safety and public health concern. Here, we report the complete genome sequence of a CiprS. Kentucky ST198 strain, PU131, isolated from a human patient in Washington State (USA).

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July 7, 2019  |  

Complete genome sequence of Bacillus licheniformis BL-010.

The biodegradation of Aflatoxin B1 (AFB1) is an industry of increasing importance. Bacillus licheniformis BL-010 was isolated from the aflatoxin contaminated corn feed storage, and was shown to degrade AFB1 efficiently. Here we present the complete genome sequence of BL-010, the genome comprises 4,287,714 bp in a circular chromosome with a GC content of 46.12% and contains genes encoding AFB1 degrading enzymes. The genome sequence displayed that this strain contains genes involved in production of laccase, aromatic ring-opening dioxygenase which could detoxify AFB1. Complete genome sequence of the strain BL-010 can further provide the genomic basis for the biotechnological application of strain BL-010 as an effective way to degrade AFB1. Copyright © 2018 Elsevier Ltd. All rights reserved.

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July 7, 2019  |  

The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes.

Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales. We found that all haloalkaliphilic strains contain the mrpB gene coding for the B subunit of the MRP Na+/H+ antiporter, while this gene is absent in all non-alkaliphilic strains, which indicates its importance for adaptation to high pH. Further analysis showed that alga05 requires organic carbon sources for growth, but it also contains genes encoding the ethylmalonyl-CoA pathway for CO2 fixation. Remarkable is the genetic potential to utilize organophosphorus compounds as a source of phosphorus. In summary, its genetic inventory indicates a large flexibility of the alga05 metabolism, which is advantageous in rapidly changing environmental conditions in soda lakes.

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July 7, 2019  |  

Complete genome sequence of herpes simplex virus 2 strain 333.

Herpes simplex virus 2, or human herpesvirus 2, is a ubiquitous human pathogen that causes genital ulcerations and establishes latency in sacral root ganglia. We fully sequenced and manually curated the viral genome sequence of herpes simplex virus 2, strain 333 using Pacific Biosciences and Illumina sequencing technologies.

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July 7, 2019  |  

Complete genome of the multidrug-resistant Escherichia coli strain KBN10P04869 isolated from a patient with acute myeloid leukemia

Recently, we isolated a multidrug-resistant Escherichia coli strain KBN10P04869 from a patient with acute myeloid leukemia. We report the complete genome of this strain which consists of 5,104,264 bp with 4,457 protein-coding genes, 88 tRNAs, and 22 rRNAs, and the co-occurrence of multidrug- resistant genes including bla CMY-2, bla TEM-1, bla CTX-M-15, bla NDM-5, and blaOXA-18.

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