scholarly journals A High-quality Draft Genome Assembly ofSinella curviseta: A Soil Model Organism (Collembola)

2019 ◽  
Vol 11 (2) ◽  
pp. 521-530 ◽  
Author(s):  
Feng Zhang ◽  
Yinhuan Ding ◽  
Qing-Song Zhou ◽  
Jun Wu ◽  
Arong Luo ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Model Organism ◽  
High Quality ◽  
Draft Genome Assembly ◽  
Soil Model

scholarly journals Draft Genome Sequence ofBacillus subtilisIa1a, a New Strain for Poly-γ-Glutamic Acid and Exopolysaccharide Production

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Mohammad H. A. Ibrahim ◽  
Brady F. Cress ◽  
Robert J. Linhardt ◽  
Mattheos A. G. Koffas ◽  
Richard A. Gross
Keyword(s):  
Bacillus Subtilis ◽  
Glutamic Acid ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Carbon Sources ◽  
Draft Genome Sequence ◽  
High Quality ◽  
Exopolysaccharide Production ◽  
Draft Genome Assembly

We report here the 4.092-Mb high-quality draft genome assembly of a newly isolated poly-γ-glutamic acid–producing strain,Bacillus subtilisIa1a. The genome sequence is considered a critical tool to facilitate the engineering of improved production strains. Exopolysaccharides and many industrially important enzymes can be produced by this new strain utilizing different carbon sources.

scholarly journals Draft Genome Assembly of a Filamentous Euendolithic (True Boring) Cyanobacterium, Mastigocoleus testarum Strain BC008

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Brandon S. Guida ◽  
Ferran Garcia-Pichel
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Model Organism ◽  
Carbonate Dissolution ◽  
Draft Genome Assembly

Mastigocoleus testarum strain BC008 is a model organism used to study marine photoautotrophic carbonate dissolution. It is a multicellular, filamentous, diazotrophic, euendolithic cyanobacterium ubiquitously found in marine benthic environments. We present an accurate draft genome assembly of 172 contigs spanning 12,700,239 bp with 9,131 annotated genes with an average G+C% of 37.3.

scholarly journals The Draft Reference Genome for Hirudo verbana, the Medicinal Leech

2020 ◽  
Author(s):  
Riley T. Paulsen ◽  
Diing D.M. Agany ◽  
Jason Petersen ◽  
Christel M. Davis ◽  
Erik A. Ehli ◽  
...  
Keyword(s):  
Nervous System ◽  
Genome Assembly ◽  
Draft Genome ◽  
Model Organism ◽  
Medicinal Leech ◽  
Comparative Approach ◽  
Neural Pathways ◽  
Sequencing Platform ◽  
Draft Genome Assembly ◽  
Hirudo Verbana

The medicinal leech, Hirudo verbana, is a powerful model organism for investigating fundamental neurobehavioral processes. The well-documented arrangement and properties of H. verbana’s nervous system allows changes at the level of specific neurons or synapses to be linked to physiological and behavioral phenomena. Juxtaposed to the extensive knowledge of H. verbana’s nervous system is a limited, but recently expanding, portfolio of molecular and multi-omics tools. Together, the advancement of genetic databases for H. verbana will complement existing pharmacological and electrophysiological data by affording targeted manipulation and analysis of gene expression in neural pathways of interest. Here, we present the first draft genome assembly for H. verbana, which is approximately 250 Mbp in size and consists of 61,282 contigs. Whole genome sequencing was conducted using an Illumina sequencing platform followed by genome assembly with CLC-Bio Genomics Workbench and subsequent functional annotation. Ultimately, the diversity of organisms for which we have genomic information should parallel the availability of next generation sequencing technologies to widen the comparative approach to understand the involvement and discovery of genes in evolutionarily conserved processes. Results of this work hope to facilitate comparative studies with H. verbana and provide the foundation for future, more complete, genome assemblies of the leech.

scholarly journals High-Quality Draft Genome Sequence of the Causal Agent of the Current Panama Disease Epidemic

2019 ◽  
Vol 8 (36) ◽  
Author(s):  
Rachel J. Warmington ◽  
William Kay ◽  
Aaron Jeffries ◽  
Paul O’Neill ◽  
Audrey Farbos ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Genome Assembly ◽  
Draft Genome ◽  
Vegetative Compatibility Group ◽  
High Quality ◽  
Panama Disease ◽  
Content Type ◽  
Draft Genome Assembly ◽  
Compatibility Group ◽  
Race 4

We present a high-quality draft genome assembly for Fusarium oxysporum f. sp. cubense tropical race 4 (Fusarium odoratissimum), assembled from PacBio reads and consisting of 15 contigs with a total assembly size of 48.59 Mb. This strain appears to belong to vegetative compatibility group complex 01213/16.

scholarly journals Genome Sequence of a California Isolate of Fusarium oxysporum f. sp. lycopersici Race 3, a Fungus Causing Wilt Disease on Tomato

2019 ◽  
Vol 8 (15) ◽  
Author(s):  
Peter M. Henry ◽  
Michelle Stueven ◽  
Sampson Li ◽  
Eugene M. Miyao ◽  
Thomas R. Gordon ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gc Content ◽  
Wilt Disease ◽  
Read Coverage ◽  
High Quality ◽  
Content Type ◽  
Draft Genome Assembly ◽  
Important Disease

Fusarium wilt of tomato, caused by the soilborne fungus Fusarium oxysporum f. sp. lycopersici, is an increasingly important disease of tomato. This paper reports the high-quality draft genome assembly of F. oxysporum f. sp. lycopersici isolate D11 (race 3), which consists of 39 scaffolds with 57,281,978 bp (GC content, 47.5%), an N 50 of 4,408,267 bp, a mean read coverage of 99.8×, and 17,682 predicted genes.

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 A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource

2021 ◽  
Author(s):  
Andre Machado ◽  
Andre Gomes-dos-Santos ◽  
Miguel Fonseca ◽  
Rute da Fonseca ◽  
Ana Verissimo ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Single Copy ◽  
Medium Size ◽  
Chub Mackerel ◽  
High Quality ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Scomber Colias ◽  
A Genome

The Atlantic chub mackerel, Scomber colias Gmelin, 1789, is a medium-size pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of S. colias, produced with Pacbio HiFi long reads and Illumina Paired-End short reads. The estimated genome size is 814 Mb distributed into 2,028 scaffolds and 2,093 contigs with an N50 length of 4,19 and 3,34 Mb, respectively. We annotated 27,675 protein-coding genes and the BUSCO analyses indicated high completeness, with 97.3 % of the single-copy orthologs in the Actinopterygii library profile. The present genome assembly represents a valuable resource to address the biology and management of this relevant fishery. Finally, this is the fourth high-quality genome assembly within the Order Scombriformes and the first in the genus Scomber.

scholarly journals New High-Quality Draft Genome of the Brown Rot Fungal Pathogen Monilinia fructicola

2019 ◽  
Vol 11 (10) ◽  
pp. 2850-2855 ◽  
Author(s):  
Rita Milvia De Miccolis Angelini ◽  
Gianfranco Romanazzi ◽  
Stefania Pollastro ◽  
Caterina Rotolo ◽  
Francesco Faretra ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Fungal Pathogen ◽  
Reference Genome ◽  
Draft Genome ◽  
Brown Rot ◽  
Monilinia Fructicola ◽  
Pome Fruit ◽  
High Quality ◽  
Draft Genome Assembly ◽  
Sequencing Technologies

Abstract Brown rot is a worldwide fungal disease of stone and pome fruit that is caused by several Monilinia species. Among these, Monilinia fructicola can cause severe preharvest and postharvest losses, especially for stone fruit. Here, we present a high-quality draft genome assembly of M. fructicola Mfrc123 strain obtained using both Illumina and PacBio sequencing technologies. The genome assembly comprised 20 scaffolds, including 29 telomere sequences at both ends of 10 scaffolds, and at a single end of 9 scaffolds. The total length was 44.05 Mb, with a scaffold N50 of 2,592 kb. Annotation of the M. fructicola assembly identified a total of 12,118 genes and 13,749 proteins that were functionally annotated. This newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within Monilinia species.

scholarly journals A High-quality Draft Genome Assembly of the Black-necked Crane (Grus nigricollis) Based on Nanopore Sequencing

2019 ◽  
Author(s):  
Chuang Zhou ◽  
Haoran Yu ◽  
Yang Geng ◽  
Wei Liu ◽  
Shuai Zheng ◽  
...  
Keyword(s):  
High Altitude ◽  
Genome Assembly ◽  
Draft Genome ◽  
Single Copy ◽  
Nanopore Sequencing ◽  
Orthologous Genes ◽  
High Quality ◽  
Draft Genome Assembly ◽  
Grus Nigricollis ◽  
Demographic Trajectories

Abstract The black-necked crane (Grus nigricollis) which inhabits high-altitude areas has the largest body size of the world’s 15 crane species, and is classified as threatened by the IUCN. To support further studies on population genetics and genomics, we present a high-quality genome assembly based on both Illumina and nanopore sequencing. In total, 54.59 Gb Illumina short reads and 116.5 Gb nanopore long reads were generated. The 1.23 Gb assembled genome has a high contig N50 of 17.89 Mb, and has a longest contig of 87.83 Mb. The completeness (97.7%) of the draft genome was evaluated with single-copy orthologous genes using BUSCO. We identified 17,789 genes and found that 8.11% of the genome is composed of repetitive elements. In total, 84 of the 2,272 one-to-one orthologous genes were under positive selection in the black-necked crane lineage. SNP-based inference indicated two bottlenecks in the recent demographic trajectories of the black-necked crane. The genome information will contribute to future study of crane evolutionary history and provide new insights into the potential adaptation mechanisms of the black-necked crane to its high-altitude habitat.

scholarly journals Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Bhavani Manivannan ◽  
Niranjana Mahalingam ◽  
Sudhir Jadhao ◽  
Amrita Mishra ◽  
Pravin Nilawe ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Genome Assembly ◽  
Biofilm Formation ◽  
Draft Genome ◽  
Drug Resistant ◽  
Draft Genome Assembly ◽  
Extensively Drug Resistant ◽  
History Of ◽  
Urinary Tuberculosis

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.

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