scholarly journals A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

2021 ◽  
Author(s):  
Nikolay Alabi ◽  
Yihan Wu ◽  
Oliver Bossdorf ◽  
Loren H. Rieseberg ◽  
Robert I. Colautti
Keyword(s):  
Western Europe ◽  
De Novo ◽  
Genome Mapping ◽  
Draft Genome ◽  
Alliaria Petiolata ◽  
Ecological Knowledge ◽  
Garlic Mustard ◽  
Draft Genome Assembly ◽  
A Genome ◽  
Invasion Genetics

AbstractThe emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ~70× coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121Mb; L50 = 2) with 99.7% of the 1.1Gb genome mapping to contigs of at least 50Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe Almost, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite a genome-wide average of < 2% heterozygosity. The continuity and gene space quality of our draft genome assembly will enable genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation efforts.

scholarly journals Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

2021 ◽  
Author(s):  
Nikolay Alabi ◽  
Yihan Wu ◽  
Oliver Bossdorf ◽  
Loren H Rieseberg ◽  
Robert I Colautti
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Genome Mapping ◽  
Draft Genome ◽  
Alliaria Petiolata ◽  
Conservation Strategies ◽  
Ecological Knowledge ◽  
Garlic Mustard ◽  
A Genome ◽  
Invasion Genetics

Abstract The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite &lt; 2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.

scholarly journals Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

2019 ◽  
Author(s):  
Haley Wight ◽  
Junhui Zhou ◽  
Muzi Li ◽  
Sridhar Hannenhalli ◽  
Stephen M. Mount ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Rubus Idaeus ◽  
Slow Process ◽  
Red Raspberry ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Protein Coding Genes ◽  
A Genome ◽  
Exceptional Value

AbstractThe red raspberry, Rubus idaeus, is widely distributed in all temperate regions of Europe, Asia, and North America and is a major commercial fruit valued for its taste, high antioxidant and vitamin content. However, Rubus breeding is a long and slow process hampered by limited genomic and molecular resources. Genomic resources such as a complete genome sequencing and transcriptome will be of exceptional value to improve research and breeding of this high value crop. Using a hybrid sequence assembly approach including data from both long and short sequence reads, we present the first assembly of the Rubus idaeus genome (Joan J. variety). The de novo assembled genome consists of 2,145 scaffolds with a genome completeness of 95.3% and an N50 score of 638 KB. Leveraging a linkage map, we anchored 80.1% of the genome onto seven chromosomes. Using over 1 billion paired-end RNAseq reads, we annotated 35,566 protein coding genes with a transcriptome completeness score of 97.2%. The Rubus idaeus genome provides an important new resource for researchers and breeders.

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

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.

scholarly journals A high-quality fungal genome assembly resolved from a sample accidentally contaminated by multiple taxa

BioTechniques ◽  
2021 ◽  
Author(s):  
Janneke Aylward ◽  
Michael J Wingfield ◽  
Francois Roets ◽  
Brenda D Wingfield
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Low Complexity ◽  
Fungal Genome ◽  
High Quality ◽  
Sequencing Project ◽  
Draft Genome Assembly ◽  
A Genome ◽  
Genome Features

Contamination in sequenced genomes is a relatively common problem and several methods to remove non-target sequences have been devised. Typically, the target and contaminating organisms reside in different kingdoms, simplifying their separation. The authors present the case of a genome for the ascomycete fungus Teratosphaeria eucalypti, contaminated by another ascomycete fungus and a bacterium. Approaching the problem as a low-complexity metagenomics project, the authors used two available software programs, BlobToolKit and anvi'o, to filter the contaminated genome. Both the de novo and reference-assisted approaches yielded a high-quality draft genome assembly for the target fungus. Incorporating reference sequences increased assembly completeness and visualization elucidated previously unknown genome features. The authors suggest that visualization should be routine in any sequencing project, regardless of suspected contamination.

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

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

AbstractAmong all molluscs, land snails are an economically and scientifically interesting group comprising edible species, alien species and agricultural pests. Yet, despite its high diversity, the number of whole genomes 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, which belongs to Geomitridae family, a group highly diversified in the Western-Palearctic region. We performed a 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 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, and 22,464 protein-coding genes were identified in the genome, where the 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.

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

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.

scholarly journals De Novo Genome Sequence of “ Candidatus Liberibacter solanacearum” from a Single Potato Psyllid in California

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
F. Wu ◽  
X. Deng ◽  
G. Liang ◽  
C. Wallis ◽  
J. T. Trumble ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Open Reading Frames ◽  
Potato Psyllid ◽  
Bactericera Cockerelli ◽  
Solanacearum Strain ◽  
A Genome ◽  
Candidatus Liberibacter ◽  
Rna Genes

The draft genome sequence of “ Candidatus Liberibacter solanacearum” strain RSTM from a potato psyllid ( Bactericera cockerelli ) in California is reported here. The RSTM strain has a genome size of 1,286,787 bp, a G+C content of 35.1%, 1,211 predicted open reading frames (ORFs), and 43 RNA genes.

scholarly journals A draft genome sequence of the elusive giant squid, Architeuthis dux

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Rute R da Fonseca ◽  
Alvarina Couto ◽  
Andre M Machado ◽  
Brona Brejova ◽  
Carolin B Albertin ◽  
...  
Keyword(s):  
Deep Sea ◽  
Draft Genome ◽  
Deep Ocean ◽  
High Arctic ◽  
Dosidicus Gigas ◽  
Final Size ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Giant Squid ◽  
A Genome

ABSTRACT Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

scholarly journals Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

2018 ◽  
Vol 6 (16) ◽  
pp. e00265-18 ◽  
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.

scholarly journals De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aysenur Soyturk ◽  
Fatima Sen ◽  
Ali Tevfik Uncu ◽  
Ibrahim Celik ◽  
Ayse Ozgur Uncu
Keyword(s):  
Ab Initio ◽  
De Novo ◽  
Draft Genome ◽  
Mirna Precursor ◽  
Machine Learning Algorithms ◽  
Genomic Research ◽  
Support Vector ◽  
Cydonia Oblonga ◽  
Protein Coding ◽  
A Genome

AbstractQuince (Cydonia oblonga Mill.) is the sole member of the genus Cydonia in the Rosacea family and closely related to the major pome fruits, apple (Malus domestica Borkh.) and pear (Pyrus communis L.). In the present work, whole genome shotgun paired-end sequencing was employed in order to assemble the first draft genome of quince. A genome assembly that spans 488.4 Mb of sequence corresponding to 71.2% of the estimated genome size (686 Mb) was produced in the study. Gene predictions via ab initio and homology-based sequence annotation strategies resulted in the identification of 25,428 and 30,684 unique putative protein coding genes, respectively. 97.4 and 95.6% of putative homologs of Arabidopsis and rice transcription factors were identified in the ab initio predicted genic sequences. Different machine learning algorithms were tested for classifying pre-miRNA (precursor microRNA) coding sequences, identifying Support Vector Machine (SVM) as the best performing classifier. SVM classification predicted 600 putative pre-miRNA coding loci. Repetitive DNA content of the assembly was also characterized. The first draft assembly of the quince genome produced in this work would constitute a foundation for functional genomic research in quince toward dissecting the genetic basis of important traits and performing genomics-assisted breeding.

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