scholarly journals Genome Sequence Resource for Erysiphe necator NAFU1, a Grapevine Powdery Mildew Isolate Identified in Shaanxi Province of China

2021 ◽  
Author(s):  
Xingyuan Zhang ◽  
Bo Mu ◽  
Kaicheng Cui ◽  
Min Liu ◽  
Guihua Ke ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Gene Prediction ◽  
Molecular Genetic ◽  
Shaanxi Province ◽  
Erysiphe Necator ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
Grapevine Powdery Mildew

Erysiphe necator is an economically important biotrophic fungal pathogen responsible for powdery mildew disease on grapevine. Currently, genome sequences are available for only a few Erysiphe necator isolates from USA. Based on the combination of Nanopore and Illumina sequencing technologies, we present here the complete genome assembly for an isolate of E. necator NAFU1 identified in China. We acquired a total of 15.93 Gb raw reads. These reads were processed into a 61.12 Mb genome assembly containing 73 contigs with the N50 of 2.06 Mb and a maximum length of 6.05 Mb. Combining the results of three gene-prediction modules, i.e. an evidence-based gene modeler (EVidenceModeler or EVM), an ab initio gene modeler, and a homology-based gene modeler, we predicted 7235 protein-coding genes in the assembled genome of E. necator NAFU1. This information will facilitate studies of genome evolution and pathogenicity mechanisms of E. necator and other powdery mildew species through comparative genome sequence analysis and other molecular genetic tools.

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 The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 258
Author(s):  
Konrad Lohse ◽  
Alexander Mackintosh ◽  
Roger Vila ◽  
◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Protein Coding ◽  
Individual Male ◽  
Protein Coding Genes ◽  
A Genome ◽  
Inachis Io

We present a genome assembly from an individual male Aglais io (also known as Inachis io and Nymphalis io) (the European peacock; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority (99.91%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 11,420 protein coding genes.

scholarly journals Genetic Structure and Aggressiveness of Erysiphe necator Populations during Grapevine Powdery Mildew Epidemics

2008 ◽  
Vol 74 (20) ◽  
pp. 6327-6332 ◽  
Author(s):  
Josselin Montarry ◽  
Philippe Cartolaro ◽  
François Delmotte ◽  
Jérôme Jolivet ◽  
Laetitia Willocquet
Keyword(s):  
Powdery Mildew ◽  
Latency Period ◽  
Growing Season ◽  
Spore Production ◽  
Erysiphe Necator ◽  
Genetic Groups ◽  
Grapevine Powdery Mildew ◽  
Temporal Differentiation ◽  
Group A ◽  
Group B

ABSTRACT Isolates of the causal ascomycete of grapevine powdery mildew, Erysiphe necator, correspond to two genetically differentiated groups (A and B) that coexist on the same host. This coexistence was analyzed by investigating temporal changes in the genetic and phenotypic structures of E. necator populations during three epidemics. Group A was present only at the start of the growing season, whereas group B was present throughout all three epidemics. Group A was less aggressive in terms of germination and infection efficiency but was more aggressive than group B in terms of the latency period, lesion diameter, and spore production. Our results are consistent with a temporal differentiation of niches, preventing recombination, and suggest an association between the disease level and the frequencies of genetic groups.

scholarly journals Complete Genome Sequence of Buffalopox Virus

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Babak Afrough ◽  
Afia Zafar ◽  
Rumina Hasan ◽  
Roger Hewson
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Virus Isolate ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type

ABSTRACT The first complete genome assembly of buffalopox virus isolate Karachi 2005, with a length of 195,630 bp, is presented here. Phylogenetic analysis shows the virus to cluster within Vaccinia species, and the genome contains 177 protein-coding sequences.

scholarly journals Draft Genome Sequence and Assembly ofPhotorhabdus heterorhabditisStrain VMG, a Bacterial Symbiont Associated with the Entomopathogenic NematodeHeterorhabditis zealandica

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Stephanie Naidoo ◽  
Boipelo Mothupi ◽  
Jonathan Featherston ◽  
Phelelani T. Mpangase ◽  
Vincent M. Gray
Keyword(s):  
South Africa ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Entomopathogenic Nematode ◽  
Draft Genome ◽  
Bacterial Symbiont ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Protein Coding Genes

Here, we report the draft genome sequence ofPhotorhabdus heterorhabditisstrain VMG, a symbiont of the entomopathogenic nematodeHeterorhabditis zealandicain South Africa. The draft genome sequence is 4,878,919 bp long and contains 4,023 protein-coding genes. The genome assembly contains 262 contigs with a G+C content of 42.22%.

scholarly journals LRSDAY: Long-read Sequencing Data Analysis for Yeasts

2017 ◽  
Author(s):  
Jia-Xing Yue ◽  
Gianni Liti
Keyword(s):  
Genome Assembly ◽  
Model Organism ◽  
Sequencing Data ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Long Read ◽  
Downstream Analysis ◽  
Eukaryotic Organisms ◽  
Genomic Regions

AbstractLong-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here we present LRSDAY, the first one-stop solution to streamline this process. LRSDAY can produce chromosome-level end-to-end genome assembly and comprehensive annotations for various genomic features (including centromeres, protein-coding genes, tRNAs, transposable elements and telomere-associated elements) that are ready for downstream analysis. Although tailored for S. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable for virtually any eukaryotic organisms. Applying LRSDAY to a S. cerevisiae strain takes ∼43 hrs to generate a complete and well-annotated genome from ∼100X Pacific Biosciences (PacBio) reads using four threads.

scholarly journals The genome sequence of the Glanville fritillary, Melitaea cinxia (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 266
Author(s):  
Roger Vila ◽  
Alex Hayward ◽  
Konrad Lohse ◽  
Charlotte Wright ◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Melitaea Cinxia ◽  
Protein Coding ◽  
Individual Male ◽  
Protein Coding Genes ◽  
A Genome

We present a genome assembly from an individual male Melitaea cinxia (the Glanville fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 499 megabases in span. The complete assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 13,666 protein coding genes.

scholarly journals The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775)

2021 ◽  
Vol 6 ◽  
pp. 304
Author(s):  
Alex Hayward ◽  
Roger Vila ◽  
Dominik R. Laetsch ◽  
Konrad Lohse ◽  
Tobias Baril ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Protein Coding ◽  
Individual Female ◽  
Protein Coding Genes ◽  
A Genome

We present a genome assembly from an individual female Melitaea athalia (also known as Mellicta athalia; the heath fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 610 megabases in span. In total, 99.98% of the assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 12,824 protein coding genes.

scholarly journals Draft Genome Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica

2020 ◽  
Vol 9 (14) ◽  
Author(s):  
Claudia Coleine ◽  
Sawyer Masonjones ◽  
Silvano Onofri ◽  
Laura Selbmann ◽  
Jason E. Stajich
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Basidiomycetous Yeast ◽  
Draft Genome Sequence ◽  
Polar Regions ◽  
Dry Valleys ◽  
Antarctic Soil ◽  
Protein Coding ◽  
Protein Coding Genes

A draft genome sequence was assembled and annotated of the basidiomycetous yeast Rhodotorula sp. strain CCFEE 5036, isolated from Antarctic soil communities. The genome assembly is 19.07 megabases and encodes 6,434 protein-coding genes. The sequence will contribute to understanding the diversity of fungi inhabiting polar regions.

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