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

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.

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

GigaScience ◽

10.1093/gigascience/giz122 ◽

2019 ◽

Vol 8 (10) ◽

Cited By ~ 12

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.

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High-quality genome assemblies of male and female Populus x sibirica plants

Systems Biology and Bioinformatics (SBB-2020) : The Twelfth International Young Scientists School ◽

10.18699/sbb-2020-32 ◽

2020 ◽

Keyword(s):

High Quality ◽

Male And Female ◽

Genome Assemblies ◽

High Quality Genome

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Highly contiguous assemblies of 101 drosophilid genomes

10.1101/2020.12.14.422775 ◽

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.

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

10.1101/158659 ◽

2017 ◽

Cited By ~ 2

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.

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

Phytopathology ◽

10.1094/phyto-05-20-0162-a ◽

2020 ◽

Vol 110 (11) ◽

pp. 1751-1755 ◽

Cited By ~ 1

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.

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Highly contiguous assemblies of 101 drosophilid genomes

eLife ◽

10.7554/elife.66405 ◽

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.

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

Immunogenetics ◽

10.1007/s00251-017-0973-y ◽

2017 ◽

Vol 69 (4) ◽

pp. 255-269 ◽

Cited By ~ 11

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

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

10.1101/267393 ◽

2018 ◽

Cited By ~ 6

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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High-quality genome assemblies uncover caste-specific long non-coding RNAs in ants

10.1101/155119 ◽

2017 ◽

Author(s):

Emily J. Shields ◽

Roberto Bonasio

Keyword(s):

Single Molecule ◽

Behavioral Plasticity ◽

De Novo ◽

High Quality ◽

Camponotus Floridanus ◽

Protein Coding ◽

Long Reads ◽

Non Coding Rnas ◽

And Behavior ◽

Genome Assemblies

ABSTRACTAnts are an emerging model system for neuroepigenetics, as embryos with virtually identical genomes develop into different adult castes that display strikingly different physiology, morphology, and behavior. Although a number of ant genomes have been sequenced to date, their draft quality is an obstacle to sophisticated analyses of epigenetic gene regulation. Using long reads generated with Pacific Biosystem single molecule real time sequencing, we have reassembled de novo high-quality genomes for two ant species: Camponotus floridanus and Harpegnathos saltator. The long reads allowed us to span large repetitive regions and join sequences previously found in separate scaffolds, leading to comprehensive and accurate protein-coding annotations that facilitated the identification of a Gp-9-like gene as differentially expressed in Harpegnathos castes. The new assemblies also enabled us to annotate long non-coding RNAs for the first time in ants, revealing several that were specifically expressed during Harpegnathos development and in the brains of different castes. These upgraded genomes, along with the new coding and non-coding annotations, will aid future efforts to identify epigenetic mechanisms of phenotypic and behavioral plasticity in ants.

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