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 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 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 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 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 The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 708 ◽  
Author(s):  
Julien Alban Nguinkal ◽  
Ronald Marco Brunner ◽  
Marieke Verleih ◽  
Alexander Rebl ◽  
Lidia de los Ríos-Pérez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Gene Prediction ◽  
Draft Genome ◽  
Single Copy ◽  
Sander Lucioperca ◽  
Illumina Platform ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
And Performance

The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.

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 Draft Genome Assembly of Rhodobacter sphaeroides 2.4.1 Substrain H2 from Nanopore Data

2020 ◽  
Vol 9 (29) ◽  
Author(s):  
Robert Maximilian Leidenfrost ◽  
Nadine Wappler ◽  
Röbbe Wünschiers
Keyword(s):  
Rhodobacter Sphaeroides ◽  
Genome Assembly ◽  
Draft Genome ◽  
Purple Bacterium ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Content Type ◽  
Draft Genome Assembly ◽  
Genomic Architecture

ABSTRACT Rhodobacter sphaeroides is a purple bacterium with complex genomic architecture. Here, a draft genome is reported for R. sphaeroides strain 2.4.1 substrain H2, which was generated exclusively from Nanopore sequencing data.

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 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 The Draft Genome of a Flat Peach (Prunus persica L. cv. ‘124 Pan’) Provides Insights into Its Good Fruit Flavor Traits

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 538
Author(s):  
Aidi Zhang ◽  
Hui Zhou ◽  
Xiaohan Jiang ◽  
Yuepeng Han ◽  
Xiujun Zhang
Keyword(s):  
Genome Assembly ◽  
Prunus Persica ◽  
Sugar Content ◽  
Draft Genome ◽  
Single Copy ◽  
Terpene Biosynthesis ◽  
Total Size ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Fruit Flavor

The flat peach has become more and more popular worldwide for its fruit quality with relatively low acidity, high sugar content and rich flavor. However, the draft genome assembly of flat peach is still unavailable and the genetic basis for its fruit flavor remains unclear. In this study, the draft genome of a flat peach cultivar ‘124 Pan’ was assembled by using a hybrid assembly algorithm. The final assembly resulted in a total size of 206 Mb with a N50 of 26.3 Mb containing eight chromosomes and seven scaffolds. Genome annotation revealed that a total of 25,233 protein-coding genes were predicted with comparable gene abundance among the sequenced peach species. The phylogenetic tree and divergence times inferred from 572 single copy genes of 13 plant species confirmed that Prunus ferganensis was the ancestor of the domesticated peach. By comparing with the genomes of Prunus persica (Lovell) and Prunus ferganensis, the expansion of genes encoding enzymes involved in terpene biosynthesis was found, which might contribute to the good fruit flavor traits of ‘124 Pan’. The flat peach draft genome assembly obtained in this study will provide a valuable genomic resource for peach improvement and molecular breeding.

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