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 Lactobacillus plantarum Strain JDARSH, Isolated from Sheep Milk

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Abhinandan Patil ◽  
Anamika Dubey ◽  
Muneer Ahmad Malla ◽  
John Disouza ◽  
Shivaji Pawar ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Genome Sequence ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Sheep Milk ◽  
Wide Range ◽  
Range Of Functions

Lactobacillus plantarum strain JDARSH, a potential probiotic with a wide range of functions, was isolated from sheep milk. Here, we report the whole-genome sequence of this bacterium. The draft genome yielded a 3.20-Mb genome and 2,980 protein-coding sequences.

scholarly journals The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

2021 ◽  
Author(s):  
Thomas W Woehner ◽  
Ofere Francis Emeriewen ◽  
Alexander Wittenberg ◽  
Harrie Schneiders ◽  
Ilse Vrijenhoek ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Sour Cherry ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Repeat Content ◽  
Long Read ◽  
Chromosome Level

Background: Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall. is one ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type. Finding: The final assemblies obtained from 117.3 Gb cleaned reads representing 97x coverage of expected 1.2 Gb tetraploid (2n=4x=32) and 0.3 Gb haploid (1n=8) genome sequence of P. fruticosa were calculated. The N50 contig length ranged between 0.3 and 0.5 Mb with the longest contig being ~6 Mb. BUSCO estimated a completeness between 98.7 % for the 4n and 96.1 % for the 1n datasets. Using a homology and reference based scaffolding method, we generated a final consensus genome sequence of 366 Mb comprising eight chromosomes. The N50 scaffold was ~44 Mb with the longest chromosome being 66.5 Mb. The repeat content was estimated to ~190 Mb (52 %) and 58,880 protein-coding genes were annotated. The chloroplast and mitochondrial genomes were 158,217 bp and 383,281 bp long, which is in accordance with previously published plastid sequences. Conclusion: This is the first report of the genome of ground cherry (P. fruticosa) sequenced by long read technology only. The datasets obtained from this study provide a foundation for future breeding, molecular and evolutionary analysis in Prunus studies.

scholarly journals Draft Genome Sequence of Urease-Producing Pseudorhodobacter sp. Strain E13, Isolated from the Yellow Sea in Gunsan, South Korea

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Si Chul Kim ◽  
Hyo Jung Lee
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
The Yellow Sea ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gram Negative ◽  
Content Type

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

scholarly journals Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Catarina Leal ◽  
Florence Fontaine ◽  
Aziz Aziz ◽  
Conceiçao Egas ◽  
Christophe Clément ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Vitis Vinifera ◽  
Genome Sequence ◽  
Draft Genome ◽  
Rhizospheric Soil ◽  
Bioactive Substances ◽  
Protein Coding ◽  
Genes Encoding ◽  
Stimulate Plant Growth ◽  
Biocontrol Potential

Abstract Background Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against many pathogens and as influencers to adaptations in a changing environment. This study reports the draft genome sequence of the beneficial Bacillus subtilis PTA-271, isolated from the rhizospheric soil of healthy Vitis vinifera cv. Chardonnay at Champagne Region in France, attempting to draw outlines of its full biocontrol capacity. Results The PTA-271 genome has a size of 4,001,755 bp, with 43.78% of G + C content and 3945 protein coding genes. The draft genome of PTA-271 putatively highlights a functional swarming motility system hypothesizing a colonizing capacity and a strong interacting capacity, strong survival capacities and a set of genes encoding for bioactive substances. Predicted bioactive compounds are known to: stimulate plant growth or defenses such as hormones and elicitors, influence beneficial microbiota, and counteract pathogen aggressiveness such as effectors and many kinds of detoxifying enzymes. Conclusions Plurality of the putatively encoded biomolecules by Bacillus subtilis PTA-271 genome suggests environmentally robust biocontrol potential of PTA-271, protecting plants against a broad spectrum of pathogens.

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 Algoriphagus sp. Strain NH1, a Multidrug-Resistant Bacterium Isolated from Coastal Sediments of the Northern Yellow Sea in China

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Dashuai Mu ◽  
Jinxin Zhao ◽  
Zongjie Wang ◽  
Guanjun Chen ◽  
Zongjun Du
Keyword(s):  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
Multidrug Resistant ◽  
Resistant Bacterium ◽  
Coastal Sediments ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Multidrug Resistant Bacterium ◽  
Northern Yellow Sea

Algoriphagus sp. NH1 is a multidrug-resistant bacterium isolated from coastal sediments of the northern Yellow Sea in China. Here, we report the draft genome sequence of NH1, with a size of 6,131,579 bp, average G+C content of 42.68%, and 5,746 predicted protein-coding sequences.

scholarly journals Genome Sequence of Rheinheimera salexigens sp. nov. Isolated from a Fishing Hook off O‘ahu, Hawai‘i

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Xuehua Wan ◽  
Shaobin Hou ◽  
Kazukuni Hayashi ◽  
James Anderson ◽  
Stuart P. Donachie
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Roche 454

Rheinheimera salexigens KH87 T is an obligately halophilic gammaproteobacterium. The strain’s draft genome sequence, generated by the Roche 454 GS FLX+ platform, comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding sequences and 58 tRNA coding regions. The G+C content is 42 mol%.

scholarly journals Draft Genome Sequence of Lawsonia intracellularis Strain E40504, Isolated from a Horse Diagnosed with Equine Proliferative Enteropathy

2017 ◽  
Vol 5 (19) ◽  
Author(s):  
Nandita S. Mirajkar ◽  
Molly R. Kelley ◽  
Connie J. Gebhart
Keyword(s):  
Genome Sequence ◽  
Genomic Island ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Lawsonia Intracellularis ◽  
Protein Coding ◽  
Content Type ◽  
Obligate Intracellular ◽  
Proliferative Enteropathy ◽  
Rna Genes

ABSTRACT Reported herein is the draft genome sequence of equine-origin Lawsonia intracellularis strain E40504, an obligate intracellular bacterium and the etiological agent of equine proliferative enteropathy. The 1.69-Mb draft genome sequence includes 1,380 protein-coding genes and 49 RNA genes, and it lacks a genomic island reported in swine-origin L. intracellularis strain PHE/MN1-00.

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.

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