De novo sequencing and assembly of the whole genome of Novosphingobium sp. strain PP1Y.
Ontology highlight
ABSTRACT:
SUBMITTER: D'Argenio V
PROVIDER: S-EPMC3147705 | biostudies-literature | 2011 Aug
REPOSITORIES: biostudies-literature
Publications
De novo sequencing and assembly of the whole genome of Novosphingobium sp. strain PP1Y.
D'Argenio V V Petrillo M M Cantiello P P Naso B B Cozzuto L L Notomista E E Paolella G G Di Donato A A Salvatore F F
Journal of bacteriology 20110617 16
Novosphingobium sp. strain PP1Y is a marine bacterium specifically adapted to use fuels as an energy source. We sequenced and assembled its entire genome using the Roche 454 genome sequencer system, which led to the identification of two plasmids and one megaplasmid, besides a 3.9-Mb circular chromosome. ...[more]
Similar Datasets
Project description:BackgroundThe bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese.MethodsIn this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation.Results10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau.ConclusionWe reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.
| S-EPMC7144584 | biostudies-literature
Project description:Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling.Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers.Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal .
| S-EPMC5699183 | biostudies-literature
Project description:Background: The introduction of the MinION sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. Nanopore sequence data offers great potential for de novo assembly of complex genomes without using other technologies. Furthermore, Nanopore data combined with other sequencing technologies is highly useful for accurate annotation of all genes in the genome. In this manuscript we used nanopore sequencing as a tool to classify yeast strains. Methods: We compared various technical and software developments for the nanopore sequencing protocol, showing that the R9 chemistry is, as predicted, higher in quality than R7.3 chemistry. The R9 chemistry is an essential improvement for assembly of the extremely AT-rich mitochondrial genome. We double corrected assemblies from four different assemblers with PILON and assessed sequence correctness before and after PILON correction with a set of 290 Fungi genes using BUSCO. Results: In this study, we used this new technology to sequence and de novo assemble the genome of a recently isolated ethanologenic yeast strain, and compared the results with those obtained by classical Illumina short read sequencing. This strain was originally named Candida vartiovaarae ( Torulopsis vartiovaarae) based on ribosomal RNA sequencing. We show that the assembly using nanopore data is much more contiguous than the assembly using short read data. We also compared various technical and software developments for the nanopore sequencing protocol, showing that nanopore-derived assemblies provide the highest contiguity. Conclusions: The mitochondrial and chromosomal genome sequences showed that our strain is clearly distinct from other yeast taxons and most closely related to published Cyberlindnera species. In conclusion, MinION-mediated long read sequencing can be used for high quality de novo assembly of new eukaryotic microbial genomes.
| S-EPMC6081980 | biostudies-literature
Project description:We report the first complete genome sequence of Pandoraea sp. strain RB-44, which was found to possess quorum-sensing properties. To the best of our knowledge, this is the first documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea species.
| S-EPMC3974938 | biostudies-literature
Project description:The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.
| S-EPMC5389512 | biostudies-literature
Project description:Single-cell genome sequencing has the potential to allow the in-depth exploration of the vast genetic diversity found in uncultured microbes. We used the marine cyanobacterium Prochlorococcus as a model system for addressing important challenges facing high-throughput whole genome amplification (WGA) and complete genome sequencing of individual cells.We describe a pipeline that enables single-cell WGA on hundreds of cells at a time while virtually eliminating non-target DNA from the reactions. We further developed a post-amplification normalization procedure that mitigates extreme variations in sequencing coverage associated with multiple displacement amplification (MDA), and demonstrated that the procedure increased sequencing efficiency and facilitated genome assembly. We report genome recovery as high as 99.6% with reference-guided assembly, and 95% with de novo assembly starting from a single cell. We also analyzed the impact of chimera formation during MDA on de novo assembly, and discuss strategies to minimize the presence of incorrectly joined regions in contigs.The methods describe in this paper will be useful for sequencing genomes of individual cells from a variety of samples.
| S-EPMC2731171 | biostudies-literature
Project description:Saccharomyces sensu stricto complex consist of yeast species, which are not only important in the fermentation industry but are also model systems for genomic and ecological analysis. Here, we present the complete genome assemblies of Saccharomyces jurei, a newly discovered Saccharomyces sensu stricto species from high altitude oaks. Phylogenetic and phenotypic analysis revealed that S. jurei is more closely related to S. mikatae, than S. cerevisiae, and S. paradoxus The karyotype of S. jurei presents two reciprocal chromosomal translocations between chromosome VI/VII and I/XIII when compared to the S. cerevisiae genome. Interestingly, while the rearrangement I/XIII is unique to S. jurei, the other is in common with S. mikatae strain IFO1815, suggesting shared evolutionary history of this species after the split between S. cerevisiae and S. mikatae The number of Ty elements differed in the new species, with a higher number of Ty elements present in S. jurei than in S. cerevisiae Phenotypically, the S. jurei strain NCYC 3962 has relatively higher fitness than the other strain NCYC 3947T under most of the environmental stress conditions tested and showed remarkably increased fitness in higher concentration of acetic acid compared to the other sensu stricto species. Both strains were found to be better adapted to lower temperatures compared to S. cerevisiae.
| S-EPMC6118302 | biostudies-literature
Project description:Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arrays and generate a de novo assembly of 2.93?Gb (contig N50: 8.3?Mb, scaffold N50: 22.0?Mb, including 39.3?Mb N-bases), together with 206?Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8?Mb of HX1-specific sequences, including 4.1?Mb that are not present in previously reported Asian genomes. Furthermore, long-read sequencing of the transcriptome reveals novel spliced genes that are not annotated in GENCODE and are missed by short-read RNA-Seq. Our results imply that improved characterization of genome functional variation may require the use of a range of genomic technologies on diverse human populations.
| S-EPMC4931320 | biostudies-literature
Project description:BackgroundMassive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior.ResultsThe de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity.ConclusionsPathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships.
| S-EPMC7487993 | biostudies-literature
Project description:BACKGROUND: De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies. FINDINGS: Utilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. We demonstrate that whole genome mapping can be used to identify these mis-assemblies and can guide the selection of the best k-mer size which yields the highest N50 without mis-assemblies. CONCLUSIONS: We demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes.
| S-EPMC4118782 | biostudies-literature