Draft Genome Assembly of the Poultry Red Mite, Dermanyssus gallinae

The poultry red mite, Dermanyssus gallinae, is a major worldwide concern in the egg-laying industry. Here, we report the first draft genome assembly and gene prediction of Dermanyssus gallinae, based on combined PacBio and MinION long-read de novo sequencing.

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Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

Genome Announcements ◽

10.1128/genomea.00265-18 ◽

2018 ◽

Vol 6 (16) ◽

pp. e00265-18 ◽

Cited By ~ 8

Author(s):

Stewart T. G. Burgess ◽

Kathryn Bartley ◽

Edward J. Marr ◽

Harry W. Wright ◽

Robert J. Weaver ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Gene Prediction ◽

Draft Genome ◽

Psoroptes Ovis ◽

Protein Coding ◽

Content Type ◽

Sheep Scab ◽

Draft Genome Assembly ◽

Intense Pruritus

ABSTRACT Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene prediction of P. ovis based on PacBio de novo sequencing. The ∼63.2-Mb genome encodes 12,041 protein-coding genes.

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Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

Genome Biology and Evolution ◽

10.1093/gbe/evaa016 ◽

2020 ◽

Vol 12 (2) ◽

pp. 3917-3925

Author(s):

Greer A Dolby ◽

Matheo Morales ◽

Timothy H Webster ◽

Dale F DeNardo ◽

Melissa A Wilson ◽

...

Keyword(s):

Genome Assembly ◽

Mojave Desert ◽

De Novo ◽

Stop Codon ◽

Draft Genome ◽

Gene Families ◽

Sea Turtle ◽

Desert Tortoise ◽

Draft Genome Assembly ◽

Gene Expansion

Abstract Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.

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LongStitch: High-quality genome assembly correction and scaffolding using long reads

10.1101/2021.06.17.448848 ◽

2021 ◽

Author(s):

Lauren Coombe ◽

Janet X Li ◽

Theodora Lo ◽

Johnathan Wong ◽

Vladimir Nikolic ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Draft Genome ◽

Model Organisms ◽

High Quality ◽

De Novo Genome Assembly ◽

Long Reads ◽

Long Read ◽

Genomic Regions ◽

Genome Assemblies

Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 2.0-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently runs in under five hours using less than 23GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.

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First draft genome assembly of the Argane tree (Argania spinosa)

F1000Research ◽

10.12688/f1000research.15719.2 ◽

2020 ◽

Vol 7 ◽

pp. 1310

Author(s):

Slimane Khayi ◽

Nour Elhouda Azza ◽

Fatima Gaboun ◽

Stacy Pirro ◽

Oussama Badad ◽

...

Keyword(s):

Genome Assembly ◽

Environmental Changes ◽

De Novo ◽

Arid Zone ◽

Draft Genome ◽

Illumina Hiseq ◽

Argania Spinosa ◽

Draft Genome Assembly ◽

Food And Feed ◽

Tree Genetics

Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.6 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological.

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Extensive genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

10.1101/2020.02.18.945246 ◽

2020 ◽

Cited By ~ 2

Author(s):

Stephen R. Doyle ◽

Alan Tracey ◽

Roz Laing ◽

Nancy Holroyd ◽

David Bartley ◽

...

Keyword(s):

Genome Assembly ◽

Haemonchus Contortus ◽

Vaccine Development ◽

De Novo ◽

Anthelmintic Resistance ◽

Draft Genome ◽

Small Ruminants ◽

High Quality ◽

Long Read ◽

Genome Assemblies

AbstractBackgroundHaemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants, and has become the key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Two draft genome assemblies for H. contortus were reported in 2013, however, both were highly fragmented, incomplete, and differed from one another in important respects. While the introduction of long-read sequencing has significantly increased the rate of production and contiguity of de novo genome assemblies broadly, achieving high quality genome assemblies for small, genetically diverse, outcrossing eukaryotic organisms such as H. contortus remains a significant challenge.ResultsHere, we report using PacBio long read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome. We show a remarkable pattern of almost complete conservation of chromosome content (synteny) with Caenorhabditis elegans, but almost no conservation of gene order. Long-read transcriptome sequence data has allowed us to define coordinated transcriptional regulation throughout the life cycle of the parasite, and refine our understanding of cis- and trans-splicing relative to that observed in C. elegans. Finally, we use this assembly to give a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally.ConclusionsThe H. contortus MHco3(ISE).N1 genome assembly presented here represents the most contiguous and resolved nematode assembly outside of the Caenorhabditis genus to date, together with one of the highest-quality set of predicted gene features. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes, and extends the experimental tractability of this model parasitic nematode in understanding pathogen biology, drug discovery and vaccine development, and important adaptive traits such as drug resistance.

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ONT-based draft genome assembly and annotation of Alternaria atra

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-01-21-0016-a ◽

2021 ◽

Author(s):

Bhawna Bonthala ◽

Corinn Sophia Small ◽

Maximilian Anton Lutz ◽

Alexander Graf ◽

Stefan Krebs ◽

...

Keyword(s):

Genome Assembly ◽

Plant Pathogens ◽

Biocontrol Agent ◽

Reference Genome ◽

Gene Prediction ◽

Draft Genome ◽

Protein Coding ◽

Draft Genome Assembly ◽

Reference Genome Assembly ◽

Wide Range

Species of Alternaria (phylum Ascomycota, family Pleosporaceae) are known as serious plant pathogens, causing major losses on a wide range of crops. Alternaria atra (Preuss) Woudenb. & Crous (previously known as Ulocladium atrum) can grow as a saprophyte on many hosts and causes Ulocladium blight on potato. It has been reported that it can also be used as a biocontrol agent against a.o. Botrytis cinerea Here we present a scaffold-level reference genome assembly for A. atra. The assembly contains 43 scaffolds with a total length of 39.62 Mbp, with scaffold N50 of 3,893,166 bp , L50 of 4 and the longest 10 scaffolds containing 89.9% of the assembled data. RNA Seq-guided, gene prediction using BRAKER resulted in 12,173 protein-coding genes with their functional annotation. This first high-quality reference genome assembly and annotation for A. Atra can be used as a resource for studying evolution in the highly complicated Alternaria genus and might help understand the mechanisms defining its role as pathogen or biocontrol agent.

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The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

10.1101/2021.06.01.446499 ◽

2021 ◽

Author(s):

Thomas W Woehner ◽

Ofere Francis Emeriewen ◽

Alexander Wittenberg ◽

Harrie Schneiders ◽

Ilse Vrijenhoek ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Draft Genome ◽

Sour Cherry ◽

Evolutionary Analysis ◽

Protein Coding ◽

Draft Genome Assembly ◽

Repeat Content ◽

Long Read ◽

Chromosome Level

Background: Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall. is one ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type. Finding: The final assemblies obtained from 117.3 Gb cleaned reads representing 97x coverage of expected 1.2 Gb tetraploid (2n=4x=32) and 0.3 Gb haploid (1n=8) genome sequence of P. fruticosa were calculated. The N50 contig length ranged between 0.3 and 0.5 Mb with the longest contig being ~6 Mb. BUSCO estimated a completeness between 98.7 % for the 4n and 96.1 % for the 1n datasets. Using a homology and reference based scaffolding method, we generated a final consensus genome sequence of 366 Mb comprising eight chromosomes. The N50 scaffold was ~44 Mb with the longest chromosome being 66.5 Mb. The repeat content was estimated to ~190 Mb (52 %) and 58,880 protein-coding genes were annotated. The chloroplast and mitochondrial genomes were 158,217 bp and 383,281 bp long, which is in accordance with previously published plastid sequences. Conclusion: This is the first report of the genome of ground cherry (P. fruticosa) sequenced by long read technology only. The datasets obtained from this study provide a foundation for future breeding, molecular and evolutionary analysis in Prunus studies.

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De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab180 ◽

2021 ◽

Author(s):

Luis J Chueca ◽

Tilman Schell ◽

Markus Pfenninger

Keyword(s):

Genome Assembly ◽

De Novo ◽

Draft Genome ◽

Land Snail ◽

Land Snails ◽

Agricultural Pests ◽

De Novo Genome Assembly ◽

Draft Genome Assembly ◽

Western Palearctic ◽

A Genome

Abstract Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.

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Genome Report: De novo genome assembly and annotation for the Taita white-eye (Zosterops silvanus)

10.1101/2020.03.06.980599 ◽

2020 ◽

Author(s):

Jan O. Engler ◽

Yvonne Lawrie ◽

Yannick Gansemans ◽

Filip Van Nieuwerburgh ◽

Alexander Suh ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Draft Genome ◽

Wild Female ◽

De Novo Genome Assembly ◽

Small Areas ◽

Fragmented Forest ◽

Draft Genome Assembly ◽

Taita Hills ◽

Genomic Resource

AbstractThe Taita White-eye (Zosterops silvanus) is an endangered songbird endemic to the Taita Hills of Southern Kenya, where it is confined to small areas of fragmented forest. With diversification rates exceeding those reported in most other vertebrates, White-eyes are a prime example of a ‘great speciator’. Nevertheless, we still know surprisingly little about the genomic underpinnings leading to this extraordinary fast radiation. Here, we present a draft genome assembly (ZSil_MB_1.0) for the Taita White-eye generated from a blood sample of a wild, female bird captured in the Taita Hills, Kenya. By performing a de novo assembly with linked-reads and annotation of the assembly with the MAKER pipeline, we generated a 1.069 Gb assembly with a scaffold N50 of 1.105 Mb and an L50 of 244. After quality evaluation of the assembly, we identified 92.1% of BUSCOs complete or fragmented, indicating that our de novo assembly is of high quality. This new assembly provides a genomic resource for future studies into the evolutionary and comparative genomics of this rapidly diversifying group of birds.

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The First Draft Genome Assembly of Snow Sheep (Ovis nivicola)

Genome Biology and Evolution ◽

10.1093/gbe/evaa124 ◽

2020 ◽

Vol 12 (8) ◽

pp. 1330-1336 ◽

Cited By ~ 2

Author(s):

Maulik Upadhyay ◽

Andreas Hauser ◽

Elisabeth Kunz ◽

Stefan Krebs ◽

Helmut Blum ◽

...

Keyword(s):

De Novo ◽

Gene Annotation ◽

Gene Prediction ◽

Repetitive Sequences ◽

Draft Genome ◽

Single Copy ◽

Climatic Conditions ◽

Draft Genome Assembly ◽

Sheep Genome ◽

Long Reads

Abstract The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was ∼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised of 41% of the total genome. BUSCO analysis revealed that the snow sheep assembly contained full-length or partial fragments of 97% of mammalian universal single-copy orthologs (n = 4,104), illustrating the completeness of the assembly. In addition, a total of 20,045 protein-coding sequences were identified using comprehensive gene prediction pipeline. Of which 19,240 (∼96%) sequences were annotated using protein databases. Moreover, homology-based searches and de novo identification detected 1,484 tRNAs; 243 rRNAs; 1,931 snRNAs; and 782 miRNAs in the snow sheep genome. To conclude, we generated the first de novo genome of the snow sheep using long reads; these data are expected to contribute significantly to our understanding related to evolution and adaptation within the Ovis genus.

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