scholarly journals Long-Read Genome Sequence of the Sugar Beet Rhizosphere Mycoparasite Pythium oligandrum

2019 ◽  
Vol 10 (2) ◽  
pp. 431-436 ◽  
Author(s):  
Charlène Faure ◽  
Marine Veyssière ◽  
Betty Boëlle ◽  
Hélène San Clemente ◽  
Olivier Bouchez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Dna ◽  
Genetic Determinants ◽  
Pythium Oligandrum ◽  
Free Living ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Rnaseq Data ◽  
Long Read ◽  
Root Tissues

Pythium oligandrum is a soil born free living oomycete able to parasitize fungi and oomycetes prey, including important plant and animals pathogens. Pythium oligandrum can colonize endophytically the root tissues of diverse plants where it induces plant defenses. Here we report the first long-read genome sequencing of a P. oligandrum strain sequenced by PacBio technology. Sequencing of genomic DNA loaded onto six SMRT cells permitted the acquisition of 913,728 total reads resulting in 112X genome coverage. The assembly and polishing of the genome sequence yielded180 contigs (N50 = 1.3 Mb; L50 = 12). The size of the genome assembly is 41.9 Mb with a longest contig of 2.7 Mb and 15,007 predicted protein-coding genes among which 95.25% were supported by RNAseq data, thus constituting a new Pythium genome reference. This data will facilitate genomic comparisons of Pythium species that are commensal, beneficial or pathogenic on plant, or parasitic on fungi and oomycete to identify key genetic determinants underpinning their diverse lifestyles. In addition comparison with plant pathogenic or zoopathogenic species will illuminate genomic adaptations for pathogenesis toward widely diverse hosts.

scholarly journals Draft Genome Sequence of Biocontrol Agent Pythium oligandrum Strain Po37, an Oomycota

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Harald Berger ◽  
Amira Yacoub ◽  
Jonathan Gerbore ◽  
Damien Grizard ◽  
Patrice Rey ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Biocontrol Agent ◽  
Draft Genome ◽  
Plant Diseases ◽  
Draft Genome Sequence ◽  
Pythium Oligandrum ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Total Length

The oomycota Pythium oligandrum Po37 is used as a biocontrol agent of plant diseases. Here, we present the first draft of the P. oligandrum Po37 genome sequence, which comprises 725 scaffolds with a total length of 35.9 Mb and 11,695 predicted protein-coding genes.

scholarly journals Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74

2017 ◽  
Vol 5 (21) ◽  
Author(s):  
Sandeep K. Kushwaha ◽  
Ramesh R. Vetukuri ◽  
Laura J. Grenville-Briggs
Keyword(s):  
Biological Control ◽  
Genome Sequence ◽  
Biological Control Agent ◽  
Draft Genome ◽  
Control Agent ◽  
Draft Genome Sequence ◽  
Pythium Oligandrum ◽  
Protein Coding ◽  
Protein Coding Genes

ABSTRACT The oomycete Pythium oligandrum is a mycoparasite and licenced biological control agent. Here, we report the draft genome sequence of P. oligandrum strain CBS 530.74, which is 36.80 Mb. It contains 341 scaffolds and 11,647 predicted protein-coding genes. As reported for plant-pathogenic Pythium species, RXLR-type effector sequences are absent.

scholarly journals The draft genome sequence of the grove snail Cepaea nemoralis

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Suzanne V Saenko ◽  
Dick S J Groenenberg ◽  
Angus Davison ◽  
Menno Schilthuizen
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Agricultural Pests ◽  
Shell Color ◽  
Protein Coding ◽  
Cepaea Nemoralis ◽  
Edible Species ◽  
Wide Range ◽  
In Captivity ◽  
Long Read

Abstract Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific variation. More recently, Cepaea has been the focus of citizen science projects on shell color evolution in relation to climate change and urbanization. C. nemoralis is particularly useful for studies on the genetics of shell polymorphism and the evolution of “supergenes,” as well as evo-devo studies of shell biomineralization, because it is relatively easily maintained in captivity. However, an absence of genomic resources for C. nemoralis has generally hindered detailed genetic and molecular investigations. We therefore generated ∼23× coverage long-read data for the ∼3.5 Gb genome, and produced a draft assembly composed of 28,537 contigs with the N50 length of 333 kb. Genome completeness, estimated by BUSCO using the metazoa dataset, was 91%. Repetitive regions cover over 77% of the genome. A total of 43,519 protein-coding genes were predicted in the assembled genome, and 97.3% of these were functionally annotated from either sequence homology or protein signature searches. This first assembled and annotated genome sequence for a helicoid snail, a large group that includes edible species, agricultural pests, and parasite hosts, will be a core resource for identifying the loci that determine the shell polymorphism, as well as in a wide range of analyses in evolutionary and developmental biology, and snail biology in general.

scholarly journals Complete Genome Sequence of Cupriavidus necator H16 (DSM 428)

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Gareth T. Little ◽  
Muhammad Ehsaan ◽  
Christian Arenas-López ◽  
Kamran Jawed ◽  
Klaus Winzer ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cupriavidus Necator ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Cupriavidus Necator H16

The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing. Annotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.

scholarly journals Draft Genome Sequence of Photorhabdus luminescens Strain DSPV002N Isolated from Santa Fe, Argentina

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Leopoldo Palma ◽  
Eleodoro E. Del Valle ◽  
Laureano Frizzo ◽  
Colin Berry ◽  
Primitivo Caballero
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Photorhabdus Luminescens ◽  
Santa Fe ◽  
Significant Similarity ◽  
Insecticidal Toxin ◽  
Protein Coding ◽  
Protein Coding Genes

Here, we report the draft genome sequence of Photorhabdus luminescens strain DSPV002N, which consists of 177 contig sequences accounting for 5,518,143 bp, with a G+C content of 42.3% and 4,701 predicted protein-coding genes (CDSs). From these, 27 CDSs exhibited significant similarity with insecticidal toxin proteins from Photorhabdus luminescens subsp. laumondii TT01.

scholarly journals Draft Genome Sequence of Phosphate-Solubilizing Bacterium Paraburkholderia tropica Strain P-31 Isolated from Pomegranate ( Punica granatum ) Rhizosphere

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Chandandeep Kaur ◽  
Govindan Selvakumar ◽  
Arakalgud Nanjundiah Ganeshamurthy
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Punica Granatum ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phosphate Solubilizing

We report the 8.9 Mb draft genome sequence of phosphate-solubilizing bacterium Paraburkholderia tropica strain P-31, isolated from pomegranate ( Punica granatum ) rhizosphere. The draft genome sequence of Paraburkholderia tropica strain P-31 consists of 8,881,246 bp with a G+C content of 64.7%, 8,039 protein-coding genes, and 49 RNAs.

scholarly journals Comparative Genomics Analysis of Two Different Virulent Bovine Pasteurella multocida Isolates

2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Huihui Du ◽  
Rendong Fang ◽  
Tingting Pan ◽  
Tian Li ◽  
Nengzhang Li ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Pasteurella Multocida ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Insertion Sequences ◽  
Capsular Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Comparative Genomics Analysis

The Pasteurella multocida capsular type A isolates can cause pneumonia and bovine respiratory disease (BRD). In this study, comparative genomics analysis was carried out to identify the virulence genes in two different virulent P. multocida capsular type A isolates (high virulent PmCQ2 and low virulent PmCQ6). The draft genome sequence of PmCQ2 is 2.32 Mbp and contains 2,002 protein-coding genes, 9 insertion sequence (IS) elements, and 1 prophage region. The draft genome sequence of PmCQ6 is 2.29 Mbp and contains 1,970 protein-coding genes, 2 IS elements, and 3 prophage regions. The genome alignment analysis revealed that the genome similarity between PmCQ2 and PmCQ6 is 99% with high colinearity. To identify the candidate genes responsible for virulence, the PmCQ2 and PmCQ6 were compared together with that of the published genomes of high virulent Pm36950 and PmHN06 and avirulent Pm3480 and Pm70 (capsular type F). Five genes and two insertion sequences are identified in high virulent strains but not in low virulent or avirulent strains. These results indicated that these genes or insertion sequences might be responsible for the virulence of P. multocida, providing prospective candidates for further studies on the pathogenesis and the host-pathogen interactions of P. multocida.

scholarly journals Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

2019 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

ABSTRACTThe Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

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 Genome Sequence of Bacteriophage Adumb2043, Isolated from Arthrobacter globiformis in Southern Colorado

2021 ◽  
Vol 10 (41) ◽  
Author(s):  
Darien Brown ◽  
Shannon Isenhart ◽  
Auremie Kleven ◽  
Adam Gillison ◽  
Lee Anne Martínez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Trna Genes ◽  
Arthrobacter Globiformis ◽  
Protein Coding ◽  
Content Type ◽  
Colorado Springs ◽  
Protein Coding Genes

We report the discovery and genome sequence of phage Adumb2043, a siphovirus infecting Arthrobacter globiformis , B2979-SEA. Adumb2043 was isolated from soil collected in Colorado Springs, Colorado. The genome has a length of 43,100 bp and contains 68 predicted protein-coding genes and no tRNA genes. Adumb2043 is related to actinobacteriophages Elezi and London.

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