De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii

Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 – 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.

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Complete Circular Genome Sequences of Brachyspira hyodysenteriae Isolates of the Four Different Sequence Types Causing Swine Dysentery in Switzerland

Microbiology Resource Announcements ◽

10.1128/mra.00847-21 ◽

2021 ◽

Vol 10 (39) ◽

Author(s):

Ana B. García-Martín ◽

Sarah Schmitt ◽

Friederike Zeeh ◽

Vincent Perreten

Keyword(s):

High Throughput Sequencing ◽

De Novo ◽

Hybrid Assembly ◽

Swine Dysentery ◽

Content Type ◽

Brachyspira Hyodysenteriae ◽

Oxford Nanopore ◽

Sequencing Platforms ◽

Sequence Types ◽

Oxford Nanopore Technologies

The complete genomes of four Brachyspira hyodysenteriae isolates of the four different sequence types (STs) (ST6, ST66, ST196, and ST197) causing swine dysentery in Switzerland were generated by whole-genome sequencing and de novo hybrid assembly of reads obtained from second (Illumina) and third (Oxford Nanopore Technologies and Pacific Biosciences) high-throughput sequencing platforms.

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Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American killifish from the Fundulus genus

10.1101/686246 ◽

2019 ◽

Author(s):

Lisa K. Johnson ◽

Ruta Sahasrabudhe ◽

Tony Gill ◽

Jennifer Roach ◽

Lutz Froenicke ◽

...

Keyword(s):

North American ◽

De Novo ◽

Draft Genome ◽

Sequencing Data ◽

Sequence Coverage ◽

Illumina Platform ◽

Oxford Nanopore ◽

Fundulus Olivaceus ◽

Genome Assemblies ◽

Oxford Nanopore Technologies

AbstractDraft de novo reference genome assemblies were obtained from four North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) using sequence reads from Illumina and Oxford Nanopore Technologies’ PromethION platforms. For each species, the PromethION platform was used to generate 30-45x sequence coverage, and the Illumina platform was used to generate 50-160x sequence coverage. Contig N50 values ranged from 0.4 Mb to 2.7 Mb, and BUSCO scores were consistently above 90% complete using the Eukaryota database. Draft assemblies and raw sequencing data are available for public use. We encourage use and re-use of these data for assembly benchmarking and external analyses.

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A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

10.1101/327817 ◽

2018 ◽

Cited By ~ 2

Author(s):

Stáphane Deschamps ◽

Yun Zhang ◽

Victor Llaca ◽

Liang Ye ◽

Gregory May ◽

...

Keyword(s):

Sorghum Bicolor ◽

De Novo ◽

Hybrid Assembly ◽

The Public ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Long Read ◽

Optical Maps ◽

Eukaryotic Genomes ◽

Direct Label

The advent of long-read sequencing technologies has greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer were combined with BioNano Genomics Direct Label and Stain (DLS) optical maps to generate a chromosome-scale de novo assembly of the repeat-rich Sorghum bicolor Tx430 genome. The final hybrid assembly consists of 29 scaffolds, encompassing in most cases entire chromosome arms. It has a scaffold N50 value of 33.28Mbps and covers >90% of Sorghum bicolor expected genome length. A sequence accuracy of 99.67% was obtained in unique regions after aligning contigs against Illumina Tx430 data. Alignments showed that 99.4% of the 34,211 public gene models are present in the assembly, including 94.2% mapping end-to-end. Comparisons of the DLS optical maps against the public Sorghum Bicolor v3.0.1 BTx623 genome assembly suggest the presence of substantial genomic rearrangements whose origin remains to be determined.

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Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

10.21203/rs.3.rs-712747/v1 ◽

2021 ◽

Author(s):

Arang Rhie ◽

Ann Mc Cartney ◽

Kishwar Shafin ◽

Michael Alonge ◽

Andrey Bzikadze ◽

...

Keyword(s):

Genome Assembly ◽

Tandem Repeats ◽

Hydatidiform Mole ◽

Segmental Duplications ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Human Genome Assembly ◽

Long Read ◽

Genome Assemblies ◽

Oxford Nanopore Technologies

Abstract Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Though derived from highly accurate sequencing, evaluation revealed that the initial T2T draft assembly had evidence of small errors and structural misassemblies. To correct these errors, we designed a novel repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly QV to 73.9. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies

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NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly

10.1101/586842 ◽

2019 ◽

Author(s):

Héctor Rodríguez-Pérez ◽

Tamara Hernández-Beeftink ◽

José M. Lorenzo-Salazar ◽

José L. Roda-García ◽

Carlos J. Pérez-González ◽

...

Keyword(s):

Quality Control ◽

Sequence Analysis ◽

Dna Sequence ◽

Dna Sequences ◽

Genome Assembly ◽

Interactive Visualization ◽

Hybrid Assembly ◽

Genomic Technologies ◽

Oxford Nanopore ◽

Oxford Nanopore Technologies

AbstractBackgroundThe Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.ResultsWe present NanoDJ, a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices. It integrates basecalling, read trimming and quality control, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly.ConclusionsWith the use of Jupyter-facilitated access to self-explanatory contents of applications and the interactive visualization of results, as well as by its distribution into a Docker software container, NanoDJ is aimed to simplify and make more reproducible ONT DNA sequence analysis. The NanoDJ package code, documentation and installation instructions are freely available at https://github.com/genomicsITER/NanoDJ.

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De novo genome assembly of the olive fruit fly (Bactrocera oleae) developed through a combination of linked-reads and long-read technologies

10.1101/505040 ◽

2018 ◽

Cited By ~ 1

Author(s):

Haig Djambazian ◽

Anthony Bayega ◽

Konstantina T. Tsoumani ◽

Efthimia Sagri ◽

Maria-Eleni Gregoriou ◽

...

Keyword(s):

Y Chromosome ◽

De Novo ◽

Fruit Fly ◽

Bactrocera Oleae ◽

Olive Fruit Fly ◽

Olive Fruit ◽

Long Reads ◽

Oxford Nanopore ◽

Long Read ◽

Oxford Nanopore Technologies

AbstractLong-read sequencing has greatly contributed to the generation of high quality assemblies, albeit at a high cost. It is also not always clear how to combine sequencing platforms. We sequenced the genome of the olive fruit fly (Bactrocera oleae), the most important pest in the olive fruits agribusiness industry, using Illumina short-reads, mate-pairs, 10x Genomics linked-reads, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT). The 10x linked-reads assembly gave the most contiguous assembly with an N50 of 2.16 Mb. Scaffolding the linked-reads assembly using long-reads from ONT gave a more contiguous assembly with scaffold N50 of 4.59 Mb. We also present the most extensive transcriptome datasets of the olive fly derived from different tissues and stages of development. Finally, we used the Chromosome Quotient method to identify Y-chromosome scaffolds and show that the long-reads based assembly generates very highly contiguous Y-chromosome assembly.JR is a member of the MinION Access Program (MAP) and has received free-of-charge flow cells and sequencing kits from Oxford Nanopore Technologies for other projects. JR has had no other financial support from ONT.AB has received re-imbursement for travel costs associated with attending Nanopore Community meeting 2018, a meeting organized my Oxford Nanopore Technologies.

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Metagenomic data for Halichondria panicea from Illumina and Nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts.

10.1101/2021.10.18.464794 ◽

2021 ◽

Author(s):

Brian W Strehlow ◽

Astrid Schuster ◽

Warren R Francis ◽

Donald E Canfield

Keyword(s):

Additional Data ◽

Illumina Miseq ◽

Metagenomic Data ◽

Single Individual ◽

Halichondria Panicea ◽

Oxford Nanopore ◽

Long Read ◽

Microbial Symbionts ◽

Genome Assemblies ◽

Oxford Nanopore Technologies

Objectives: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses. Data description: These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of H. panicea - one Illumina MiSeq (2x300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the best assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3,084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.

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Complete Closed Genome Sequence of the Inulin-Utilizing Lactiplantibacillus plantarum Strain Lp900, Obtained Using a Hybrid Nanopore and Illumina Assembly

Microbiology Resource Announcements ◽

10.1128/mra.00185-21 ◽

2021 ◽

Vol 10 (17) ◽

Author(s):

Jori Fuhren ◽

Reindert Nijland ◽

Michiel Wels ◽

Jos Boekhorst ◽

Michiel Kleerebezem

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Dna Sequence ◽

Genome Sequence ◽

De Novo ◽

Circular Chromosome ◽

Content Type ◽

Diverse Species ◽

Oxford Nanopore ◽

Oxford Nanopore Technologies

Lactiplantibacillus plantarum is a genetically and phenotypically diverse species of lactic acid bacteria. We announce the hybrid de novo assembly of Oxford Nanopore Technologies and Illumina DNA sequence reads, producing a closed circular chromosome of 3,206,992 bp and six plasmids of the inulin-utilizing L. plantarum strain Lp900.

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Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish

GigaScience ◽

10.1093/gigascience/giaa067 ◽

2020 ◽

Vol 9 (6) ◽

Cited By ~ 3

Author(s):

Lisa K Johnson ◽

Ruta Sahasrabudhe ◽

James Anthony Gill ◽

Jennifer L Roach ◽

Lutz Froenicke ◽

...

Keyword(s):

North American ◽

De Novo ◽

Draft Genome ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Sequence Coverage ◽

Short Read ◽

Oxford Nanopore ◽

Long Read ◽

Genome Assemblies

Abstract Background Whole-genome sequencing data from wild-caught individuals of closely related North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) were obtained using long-read Oxford Nanopore Technology (ONT) PromethION and short-read Illumina platforms. Findings Draft de novo reference genome assemblies were generated using a combination of long and short sequencing reads. For each species, the PromethION platform was used to generate 30–45× sequence coverage, and the Illumina platform was used to generate 50–160× sequence coverage. Illumina-only assemblies were fragmented with high numbers of contigs, while ONT-only assemblies were error prone with low BUSCO scores. The highest N50 values, ranging from 0.4 to 2.7 Mb, were from assemblies generated using a combination of short- and long-read data. BUSCO scores were consistently >90% complete using the Eukaryota database. Conclusions High-quality genomes can be obtained from a combination of using short-read Illumina data to polish assemblies generated with long-read ONT data. Draft assemblies and raw sequencing data are available for public use. We encourage use and reuse of these data for assembly benchmarking and other analyses.

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Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacbio Sequel II system and ultralong reads of Oxford Nanopore

10.1101/2020.02.13.948489 ◽

2020 ◽

Author(s):

Dandan Lang ◽

Shilai Zhang ◽

Pingping Ren ◽

Fan Liang ◽

Zongyi Sun ◽

...

Keyword(s):

Gene Families ◽

Single Chromosome ◽

Small Indels ◽

Base Level ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Long Read ◽

Single Rice ◽

Genome Assemblies ◽

Oxford Nanopore Technologies

AbstractThe availability of reference genomes has revolutionized the study of biology. Multiple competing technologies have been developed to improve the quality and robustness of genome assemblies during the last decade. The two widely-used long read sequencing providers – Pacbio (PB) and Oxford Nanopore Technologies (ONT) – have recently updated their platforms: PB enable high throughput HiFi reads with base-level resolution with >99% and ONT generated reads as long as 2 Mb. We applied the two up-to-date platforms to one single rice individual, and then compared the two assemblies to investigate the advantages and limitations of each. The results showed that ONT ultralong reads delivered higher contiguity producing a total of 18 contigs of which 10 were assembled into a single chromosome compared to that of 394 contigs and three chromosome-level contigs for the PB assembly. The ONT ultralong reads also prevented assembly errors caused by long repetitive regions for which we observed a total 44 genes of false redundancies and 10 genes of false losses in the PB assembly leading to over/under-estimations of the gene families in those long repetitive regions. We also noted that the PB HiFi reads generated assemblies with considerably less errors at the level of single nucleotide and small InDels than that of the ONT assembly which generated an average 1.06 errors per Kb assembly and finally engendered 1,475 incorrect gene annotations via altered or truncated protein predictions.

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