scholarly journals High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

2020 ◽  
Vol 33 (5) ◽  
pp. 718-720
Author(s):  
Karthi Natesan ◽  
Ji Yeon Park ◽  
Cheol-Woo Kim ◽  
Dong Suk Park ◽  
Young-Seok Kwon ◽  
...  
Keyword(s):  
Downy Mildew ◽  
De Novo ◽  
Gc Content ◽  
Comparative Genomic ◽  
High Quality ◽  
Sequencing Platform ◽  
Peronospora Destructor ◽  
Genomic Studies ◽  
Genome Assemblies ◽  
High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

scholarly journals A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

GigaScience ◽  
2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Sarah B Kingan ◽  
Julie Urban ◽  
Christine C Lambert ◽  
Primo Baybayan ◽  
Anna K Childers ◽  
...  
Keyword(s):  
Invasive Species ◽  
Genome Assembly ◽  
De Novo ◽  
Fragment Size ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Lycorma Delicatula ◽  
Long Read ◽  
Genome Assemblies ◽  
High Quality Genome

ABSTRACT Background A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. Results The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. Conclusions We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.

scholarly journals Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica

2021 ◽  
Vol 12 ◽  
Author(s):  
Nataliya V. Melnikova ◽  
Elena N. Pushkova ◽  
Ekaterina M. Dvorianinova ◽  
Artemy D. Beniaminov ◽  
Roman O. Novakovskiy ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Single Copy ◽  
Dioecious Species ◽  
Male And Female ◽  
Male Genome ◽  
Oxford Nanopore ◽  
Genome Assemblies ◽  
First Time ◽  
High Quality Genome ◽  
Y Haplotype

The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.

scholarly journals Highly contiguous assemblies of 101 drosophilid genomes

2020 ◽  
Author(s):  
Bernard Y Kim ◽  
Jeremy Wang ◽  
Danny E. Miller ◽  
Olga Barmina ◽  
Emily K. Delaney ◽  
...  
Keyword(s):  
Community Resource ◽  
High Quality ◽  
Public Resource ◽  
Oxford Nanopore ◽  
Starting Point ◽  
Long Read ◽  
Wet Lab ◽  
Species Groups ◽  
Genome Assemblies ◽  
High Quality Genome

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long read sequencing allow high quality genome assemblies for tens or even hundreds of species to be generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution within this key group.

scholarly journals Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

2017 ◽  
Author(s):  
David Thybert ◽  
Maša Roller ◽  
Fábio C.P. Navarro ◽  
Ian Fiddes ◽  
Ian Streeter ◽  
...  
Keyword(s):  
Mus Musculus ◽  
Evolutionary Dynamics ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
High Quality ◽  
Phylogenetic Structure ◽  
Mus Caroli ◽  
Nucleotide Mutation ◽  
Genome Assemblies ◽  
High Quality Genome

ABSTRACTUnderstanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four-and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

scholarly journals High-Quality Draft Genome Sequence Resources of Eight Xylella fastidiosa Strains Isolated from Citrus, Coffee, Plum, and Hibiscus in South America

2020 ◽  
Vol 110 (11) ◽  
pp. 1751-1755 ◽  
Author(s):  
Paulo Marques Pierry ◽  
Wesley Oliveira de Santana ◽  
João Paulo Kitajima ◽  
Joaquim Martins-Junior ◽  
Paulo Adriano Zaini ◽  
...  
Keyword(s):  
South America ◽  
Xylella Fastidiosa ◽  
Draft Genome ◽  
Genomic Diversity ◽  
High Quality ◽  
Brazil Strain ◽  
Coffee Plants ◽  
Genome Assemblies ◽  
High Quality Genome ◽  
Roche 454

Xylella fastidiosa subsp. pauca, once confined to South America and infecting mainly citrus and coffee plants, has been found to be associated with other hosts and in other geographic regions. We present high-quality draft genome sequences of X. fastidiosa subsp. pauca strains J1a12, B111, U24D, and XRB isolated from citrus plants in Brazil, strain Fb7 isolated from a citrus plant in Argentina and strains 3124, Pr8x, and Hib4 isolated, respectively, from coffee, plum, and hibiscus plants in Brazil. Sequencing was performed using Roche 454-GS FLX, MiSeq-Illumina or Pacific Biosciences platforms. These high-quality genome assemblies will be useful for further studies about the genomic diversity, evolution, and biology of X. fastidiosa.

scholarly journals High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains

Cell Reports ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 3078-3090 ◽  
Author(s):  
Emily J. Shields ◽  
Lihong Sheng ◽  
Amber K. Weiner ◽  
Benjamin A. Garcia ◽  
Roberto Bonasio
Keyword(s):  
High Quality ◽  
Non Coding Rnas ◽  
Genome Assemblies ◽  
High Quality Genome

scholarly journals Highly contiguous assemblies of 101 drosophilid genomes

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Bernard Y Kim ◽  
Jeremy Wang ◽  
Danny E Miller ◽  
Olga Barmina ◽  
Emily Kay Delaney ◽  
...  
Keyword(s):  
High Quality ◽  
Coding Regions ◽  
Public Resource ◽  
Oxford Nanopore ◽  
Starting Point ◽  
Long Read ◽  
Species Groups ◽  
Genome Assemblies ◽  
High Quality Genome ◽  
Laboratory Protocol

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

scholarly journals The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation

2017 ◽  
Vol 69 (4) ◽  
pp. 255-269 ◽  
Author(s):  
John C. Schwartz ◽  
Mark S. Gibson ◽  
Dorothea Heimeier ◽  
Sergey Koren ◽  
Adam M. Phillippy ◽  
...  
Keyword(s):  
Natural Killer ◽  
High Quality ◽  
Genome Assemblies ◽  
High Quality Genome

scholarly journals GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing

2018 ◽  
Author(s):  
Danny E. Miller ◽  
Cynthia Staber ◽  
Julia Zeitlinger ◽  
R. Scott Hawley
Keyword(s):  
Single Molecule ◽  
Drosophila Species ◽  
High Quality ◽  
Additional Species ◽  
Oxford Nanopore ◽  
Wide Range ◽  
Long Read ◽  
Genome Assemblies ◽  
High Quality Genome ◽  
Reference Genomes

ABSTRACTThe Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present high-quality genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba), four additional species that had previously reported assemblies (biarmipes, bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close over 60% of the gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately $1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes.

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