scholarly journals Draft Genome Sequence and intraspecific diversification of the wild crop relative Brassica cretica Lam. using demographic model selection

2019 ◽  
Author(s):  
Antonis Kioukis ◽  
Vassiliki A. Michalopoulou ◽  
Laura Briers ◽  
Stergios Pirintsos ◽  
David J. Studholme ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Sequence Data ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Crop Wild Relatives ◽  
Demographic Model ◽  
Sequencing Data

AbstractCrop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security.The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves.Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape.Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica.De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins.Furthermore, our demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.

scholarly journals The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus

2019 ◽  
Vol 11 (7) ◽  
pp. 1965-1970 ◽  
Author(s):  
Nikola Palevich ◽  
Paul H Maclean ◽  
Abdul Baten ◽  
Richard W Scott ◽  
David M Leathwick
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Sequence Data ◽  
Animal Health ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Parasitic Nematodes ◽  
Hybrid Assembly ◽  
Genetic Structures

Abstract Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites. A de novo hybrid assembly was generated from PCR-free whole genome sequence data, resulting in a chromosome-level assembly that is 465 Mb in size encoding 22,341 genes. The genome sequence presented here is consistent with the genome architecture of the existing Haemonchus species and is a valuable resource for future studies regarding population genetic structures of parasitic nematodes. Additionally, comparative pan-genomics with other species of economically important parasitic nematodes have revealed highly open genomes and strong collinearities within the phylum Nematoda.

scholarly journals Draft Genome Sequence of a New Zealand Isolate of Mycoplasma ovipneumoniae

2020 ◽  
Vol 9 (10) ◽  
Author(s):  
B. J. Bridgeman ◽  
S. K. Gupta ◽  
A. Murray ◽  
V. S. R. Dukkipati ◽  
E. Altermann ◽  
...  
Keyword(s):  
New Zealand ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Mycoplasma Ovipneumoniae

The genome of New Zealand Mycoplasma ovipneumoniae isolate 90 was sequenced and assembled using an Illumina MiSeq system and combining the built-in Geneious de novo and Velvet de novo assemblers. The 1,031,345-bp-long genome harbored 711 genes with a coding percentage of 86.6.

scholarly journals Draft Genome Sequence of Anoxybacillus sp. Strain UARK-01, a New Thermophilic Lignin-Utilizing Bacterium Isolated from Soil in Arkansas, USA

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Thamir H. Alkahem Albalawi ◽  
Douglas D. Rhoads ◽  
Ravi D. Barabote
Keyword(s):  
United States ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Illumina Miseq ◽  
The United States ◽  
Soil Bacterium ◽  
Lignocellulose Degradation ◽  
Illumina Miseq Platform ◽  
Miseq Platform

ABSTRACT The draft genome of Anoxybacillus sp. strain UARK-01, a novel lignin-utilizing thermophilic soil bacterium, represents the first sequence of an Anoxybacillus isolate from the United States. The genome was sequenced using the Illumina MiSeq platform, de novo assembled using SeqMan NGen, and annotated at NCBI. The genome sequence revealed genes for laccase and lignocellulose degradation enzymes.

scholarly journals Data on the Draft Genome Sequence of Bacillus sp. Strain AN2 Isolated from Agricultural Soil in Brazil

2020 ◽  
pp. 11-13
Author(s):  
Andressa Sbano ◽  
Juliana B. Succar ◽  
João Victor R. Ferreira ◽  
Lidiane C. Berbert ◽  
Vinicius R. Flores ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Dna ◽  
Agricultural Soil ◽  
Genomic Library ◽  
Sequence Data ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Bacillus Sp ◽  
State University ◽  
Study Laboratory

Aims: This research aims to report the genome sequence of the Bacillus sp. strain AN2, isolated from agricultural soil from Rio de Janeiro, Brazil. Place and Duration of Study: Laboratory of Environmental Biotechnology, Western Rio Janeiro State University in Brazil, between January 2019 and December 2019. Methodology: High-quality genomic DNA was extracted using a GenElute Bacterial Genomic DNA kit. The Nextera XT DNA Library Prep Kit was used for genomic library construction. Paired-end sequence reads were generated by an Illumina MiSeq instrument with the 600 cycles MiSeq Reagent Kit v3. Sequence data were assembled with A5-MiSeq pipeline software and the contigs were annotated by Rapid Annotation using Subsystems Technology (RAST). Results: The obtained genome sequence of Bacillus AN2 included 21 contigs with a calculated size of 3,681,081 bp in length. The G + C content for the draft genome is 41.4%. A total of 3824 coding sequences (CDS) were predicted and encoded at least 88 tRNAs.

scholarly journals Draft genome sequence data of the facultative, thermophilic, xylanolytic bacterium Paenibacillus sp. strain DA-C8

Data in Brief ◽  
2021 ◽  
Vol 35 ◽  
pp. 106784
Author(s):  
Chinda Chhe ◽  
Ayaka Uke ◽  
Sirilak Baramee ◽  
Umbhorn Ungkulpasvich ◽  
Chakrit Tachaapaikoon ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Genome Sequence Data ◽  
Paenibacillus Sp

scholarly journals Draft genome sequence data of a chromium reducing bacterium, Bacillus licheniformis strain KNP

Data in Brief ◽  
2021 ◽  
Vol 34 ◽  
pp. 106640
Author(s):  
Pankaj Kumar Arora ◽  
Rupali Mishra ◽  
Rishabh Anand Omar ◽  
Raj Shekhar Saroj ◽  
Alok Srivastava ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Bacillus Licheniformis ◽  
Sequence Data ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Genome Sequence Data ◽  
Bacterium Bacillus

scholarly journals Draft Genome Sequence of Leifsonia xyli subsp. xyli Strain gdw1

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Jihua Wang ◽  
Li Wang ◽  
Gan Cao ◽  
Muqing Zhang ◽  
Ying Guo
Keyword(s):  
Genome Sequence ◽  
Genetic Improvement ◽  
De Novo ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Coding Sequences ◽  
Ratoon Stunting Disease

Here, we report the draft genome sequence of Leifsonia xyli subsp. xyli strain gdw1, isolated from the stem of Badila sugarcane located at the Guangdong Key Laboratory for Crops Genetic Improvement (Guanzhou, China), that causes ratoon stunting disease of sugarcane. The de novo genome of Leifsonia xyli subsp. xyli was assembled with 48 scaffolds and a G+C content of 67.68%, and contained 2.6 Mb bp and 2,838 coding sequences.

scholarly journals Draft Genome Sequence of Probiotic Lactobacillus brevis TUCO-5E, Isolated from Porcine Milk

2018 ◽  
Vol 7 (19) ◽  
Author(s):  
Sandra Rayen Quilodran-Vega ◽  
Leonardo Albarracin ◽  
Elvira Maria Hebert ◽  
Lucila Saavedra ◽  
Alexis Fonseca ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Probiotic Strain ◽  
Lactobacillus Brevis ◽  
Illumina Miseq ◽  
Draft Genome Sequence ◽  
Maternal Milk ◽  
Content Type ◽  
Probiotic Lactobacillus ◽  
Porcine Milk

This report describes the draft genome sequence of Lactobacillus brevis TUCO-5E, a probiotic strain isolated from porcine maternal milk. The reads were generated by a whole-genome sequencing (WGS) strategy on an Illumina MiSeq sequencer and were assembled into contigs with a total estimated size of 2,461,089 bp.

scholarly journals Draft Genome Sequence of the Community-Associated Staphylococcus aureus Sequence Type 88 Strain LVP-7, Isolated from an Ocular Infection

2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Savitha Nadig ◽  
Sneha Murthy ◽  
Muralidharan Vandanashree ◽  
Hosahalli S. Subramanya ◽  
Balasubramanian Gopal ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Sequence Type ◽  
Draft Genome Sequence ◽  
Ocular Infection ◽  
Content Type ◽  
Type V ◽  
Panton Valentine Leukocidin

ABSTRACT We report a de novo-assembled draft genome sequence of the Indian Staphylococcus aureus sequence type 88 (ST88) strain LVP-7, isolated from an ocular infection. The genome harbors a Panton-Valentine leukocidin phage, a type V staphylococcal cassette chromosome mec element, the delta-hemolysin-converting Newman phage ΦNM3, and the pathogenicity island SaPI3, encoding the superantigen enterotoxin B.

scholarly journals De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

2019 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akifumi Azuma ◽  
Fumiya Taniguchi ◽  
Toshiya Yamamoto ◽  
Akihiko Sato ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Genome Structure ◽  
Table Grape ◽  
Sequencing Analysis ◽  
Entire Genome ◽  
Table Grapes ◽  
Eukaryotic Genes

AbstractThis study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.

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