scholarly journals Genome announcement of Steinernema khuongi and its associated symbiont from Florida

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Anil Baniya ◽  
Peter DiGennaro
Keyword(s):  
Biological Control ◽  
Comparative Genomics ◽  
Genome Sequence ◽  
Bacterial Genome ◽  
Draft Genome ◽  
Control Measures ◽  
Symbiotic Bacteria ◽  
Total Length ◽  
Central Ridge ◽  
Promising Source

Abstract Citrus root weevil (Diaprepes abbreviates) causes significant yield loss in citrus, especially in Florida. A promising source of control for this pest is biological control agents, namely, native entomopathogenic nematodes (EPNs) within the genus Steinernema. Two species of endemic EPN in Florida are S. diaparepesi, abundant within the central ridge, and S. khuongi, dominating the flatwood regions of the state. These citrus-growing regions differ significantly in their soil habitats, which impacts the potential success of biological control measures. Although the genome sequence of S. diaprepesi is currently available, the genome sequence of S. khuongi and identity of the symbiotic bacteria is still unknown. Understanding the genomic differences between these two nematodes and their favored habitats can inform successful biological control practices. Here, MiSeq libraries were used to simultaneously sequence and assemble the draft genome of S. khuongi and its associated symbionts. The final draft genome for S. khuongi has 8,794 contigs with a total length of ∼82 Mb, a largest contig of 428,226 bp, and N50 of 46 kb; its BUSCO scores indicate that it is > 86% complete. An associated bacterial genome was assembled with a total length of ∼3.5 Mb, a largest contig at 116,532 bp, and N50 of 17,487 bp. The bacterial genome encoded 3,721 genes, similar to other Xenorhabdus genomes. Comparative genomics identified the symbiotic bacteria of S. khuongi as Xenorhabdus poinarii. These new draft genomes of a host and symbiont can be used as a valuable tool for comparative genomics with other EPNs and its symbionts to understand host range and habitat suitability.

scholarly journals Draft Genome Sequence of NDM-1-Producing Leclercia adecarboxylata

2017 ◽  
Vol 5 (17) ◽  
Author(s):  
Yannick Hoyos-Mallecot ◽  
María Dolores Rojo-Martín ◽  
Rémy A. Bonnin ◽  
Elodie Creton ◽  
Jose María Navarro Marí ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Opportunistic Pathogen ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Total Length

ABSTRACT Here, we provide the first draft genome sequence of NDM-1-producing Leclercia adecarboxylata, a human-opportunistic pathogen. The draft genome sequence consists of a total length of 5.13 Mbp, with an average G+C content of 55.2%.

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 Draft Genome Sequence of Streptomyces sp. Strain IB2014011-1, Isolated from Trichoptera sp. Larvae of Lake Baikal

2017 ◽  
Vol 5 (17) ◽  
Author(s):  
Denis V. Axenov-Gribanov ◽  
Bogdan T. Tokovenko ◽  
Yuriy V. Rebets ◽  
Irina V. Voytsekhovskaya ◽  
Zhanna M. Shatilina ◽  
...  
Keyword(s):  
Lake Baikal ◽  
Genome Sequence ◽  
Environmental Conditions ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Ancient Lake ◽  
Streptomyces Sp ◽  
Promising Source ◽  
Species Biodiversity

ABSTRACT Unique ecosystems with specific environmental conditions have been proven to be a promising source for isolation of new Actinobacteria strains. Ancient Lake Baikal is one of the greatest examples of an ecosystem with high species biodiversity and endemicity caused by long-lasting isolated evolution and stable environmental conditions. Herein we report the draft genome sequence of Streptomyces sp. strain IB2014011-1, which was isolated from insect Trichoptera sp. larvae collected at the bottom of Lake Baikal.

scholarly journals Draft Genome Sequence of Bacillus licheniformis Strain UASWS1606, a Plant Biostimulant for Agriculture

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Julien Crovadore ◽  
Bastien Cochard ◽  
Damien Grizard ◽  
Romain Chablais ◽  
Marine Baillarguet ◽  
...  
Keyword(s):  
Biological Control ◽  
Genome Sequence ◽  
Bacillus Licheniformis ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Biological Control Agents ◽  
Content Type ◽  
Agricultural Biostimulant

ABSTRACT Bacillus licheniformis is a well-known industrial bacterium. New strains show interesting properties of biostimulants and biological control agents for agriculture. Here, we report the draft genome sequence, obtained with an Illumina MiniSeq system, of strain UASWS1606 of the bacterium Bacillus licheniformis, which is being developed as an agricultural biostimulant.

scholarly journals Improved De Novo Draft Genome Sequence of the Nocavionin-Producing Type Strain Nocardia terpenica IFM 0706 and Comparative Genomics with the Closely Related Strain Nocardia terpenica IFM 0406

2020 ◽  
Vol 9 (34) ◽  
Author(s):  
Anina Buchmann ◽  
Harald Gross
Keyword(s):  
Comparative Genomics ◽  
Genome Size ◽  
Genome Sequence ◽  
Type Strain ◽  
De Novo ◽  
Draft Genome ◽  
Pathogenic Strain ◽  
Draft Genome Sequence ◽  
Related Strain ◽  
Content Type

ABSTRACT We report an improved de novo draft genome sequence of the human-pathogenic strain Nocardia terpenica IFM 0706T. The resequencing unveiled that the genome size is larger than anticipated, reducing significantly the number of contigs and building a basis for comparison with the closely related strain N. terpenica IFM 0406.

scholarly journals Draft Genome Sequence of Plasmodium gonderi, a Malaria Parasite of African Old World Monkeys

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Hajime Honma ◽  
Satoru Kawai ◽  
Daisuke Motooka ◽  
Shota Nakamura ◽  
Takahiro Tougan ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Malaria Parasite ◽  
Draft Genome ◽  
Natural Host ◽  
Draft Genome Sequence ◽  
Old World Monkeys ◽  
Malaria Parasites ◽  
Old World

ABSTRACT Plasmodium gonderi is a primate parasite whose natural host is the African Old World monkeys. Here, we report the draft genome sequence for P. gonderi. The data are useful not only for understanding the evolution of malaria but also for allowing the comparative genomics of malaria parasites.

scholarly journals Draft Genome Sequence of 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading Arthrobacter sp. Strain ATCC 49987

2020 ◽  
Vol 9 (34) ◽  
Author(s):  
Nidhi Gupta ◽  
Kelly A. Skinner ◽  
Zarath M. Summers ◽  
Janaka N. Edirisinghe ◽  
José P. Faria ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Strain Atcc ◽  
Total Length

ABSTRACT Here, we report the draft genome sequence of Arthrobacter sp. strain ATCC 49987, consisting of three contigs with a total length of 4.4 Mbp. Based on the genome sequence, we suggest reclassification of Arthrobacter sp. strain ATCC 49987 as Pseudarthrobacter sp. strain ATCC 49987.

scholarly journals High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
John M. Urban ◽  
Michael S. Foulk ◽  
Jacob E. Bliss ◽  
C. Michelle Coleman ◽  
Nanyan Lu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
De Novo ◽  
Bacterial Genome ◽  
Draft Genome ◽  
Dna Amplification ◽  
Chromosome Elimination ◽  
Paternal Chromosome ◽  
De Novo Genome Assembly ◽  
Long Read

Abstract Background The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. Results We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. Conclusions We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.

scholarly journals Draft Genome Sequence of the Wood-Staining Ascomycete Chlorociboria aeruginascens DSM 107184

2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Enrico Büttner ◽  
Christiane Liers ◽  
Anna Maria Gebauer ◽  
Jérôme Collemare ◽  
Jorge Carlos Navarro-Muñoz ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Total Length ◽  
Bluish Green ◽  
Ascomycetous Fungus

Chlorociboria aeruginascens DSM 107184 is a wood-decomposing ascomycetous fungus known to produce the bluish-green dimeric naphthoquinone derivate xylindein. Here, we present the first draft genome sequence, which contains 588 contigs with a total length of 33.1 Mb.

scholarly journals Draft Genome Sequence of Flavobacterium sp. Strain TAB 87, Able To Inhibit the Growth of Cystic Fibrosis Bacterial Pathogens Belonging to the Burkholderia cepacia Complex

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Luana Presta ◽  
Ilaria Inzucchi ◽  
Emanuele Bosi ◽  
Marco Fondi ◽  
Elena Perrin ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Antibiotic Resistance ◽  
Comparative Genomics ◽  
Bioactive Compounds ◽  
Genome Sequence ◽  
Burkholderia Cepacia ◽  
Draft Genome ◽  
Burkholderia Cepacia Complex ◽  
Draft Genome Sequence ◽  
Antarctic Seawater

We report here the draft genome sequence of the Flavobacterium sp. TAB 87 strain, isolated from Antarctic seawater during a summer campaign near the French Antarctic station Dumont d’Urville (60°40′S, 40°01′E). It will allow for comparative genomics and the fulfillment of both fundamental and application-oriented investigations. It allowed the recognition of genes associated with the production of bioactive compounds and antibiotic resistance.

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