scholarly journals The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence

2019 ◽  
Author(s):  
Joeri S. Strijk ◽  
Damien D. Hinsinger ◽  
Mareike M. Roeder ◽  
Lars W. Chatrou ◽  
Thomas L. P. Couvreur ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Evolutionary History ◽  
Draft Genome ◽  
Critical Assessment ◽  
Whole Genome ◽  
Annona Muricata ◽  
High Quality ◽  
Basal Angiosperms ◽  
Complete Genomes ◽  
Analytical Approaches

AbstractDeep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used. Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop (Annona muricata, Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history.

scholarly journals Whole-Genome Sequences of Two Closely Related Bacteria, Actinomyces sp. Strain Chiba101 and Actinomyces denticolens DSM 20671T

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Yu Kanesaki ◽  
Taichiro Ishige ◽  
Yuriko Sekigawa ◽  
Tomoko Kobayashi ◽  
Yasushi Torii ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type

ABSTRACT Actinomyces sp. strain Chiba101, isolated from an arthritic leg joint of a pig raised in Japan, is a bacterium closely related to Actinomyces denticolens. Here, we deciphered the complete genome sequence of Actinomyces sp. Chiba101 and the high-quality draft genome sequence of A. denticolens DSM 20671T.

scholarly journals Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250092
Author(s):  
Bruce Parrello ◽  
Rory Butler ◽  
Philippe Chlenski ◽  
Gordon D. Pusch ◽  
Ross Overbeek
Keyword(s):  
Draft Genome ◽  
Single Copy ◽  
Metagenomic Data ◽  
Use Case ◽  
High Quality ◽  
Complete Genomes ◽  
Downstream Analysis ◽  
Low Coverage ◽  
Derived Data ◽  
Reference Genomes

Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples.

scholarly journals Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Yu Xing ◽  
Yang Liu ◽  
Qing Zhang ◽  
Xinghua Nie ◽  
Yamin Sun ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Genetic Improvement ◽  
De Novo ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
High Quality ◽  
Chinese Chestnut ◽  
Castanea Mollissima

AbstractBackgroundThe Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima.FindingsWe produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago.ConclusionsThe high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

scholarly journals A draft genome at chromosome level and metabolomes of leave, root and flowers provide insights into the molecular basis of medicinal ingredients of loquat (Eriobotrya japonica (Thunb.) Lindl)

2021 ◽  
Author(s):  
Yunsheng Wang
Keyword(s):  
Big Five ◽  
Molecular Basis ◽  
Draft Genome ◽  
Eriobotrya Japonica ◽  
Whole Genome ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Pointed Star ◽  
Chromosome Level

Abstract Eriobotrya japonica, commonly called loquat, is a type of fruit and a famous traditional Chinese medicinal material. Here, a high-quality draft genome of the E. japonica cultivar, Big Five-pointed Star, containing 733.32 million bases (Mb) covering approximately 98% of estimated whole genome size (749.25 Mb) is reported. A total of 45,492 protein-coding genes were predicted. Meanwhile, metabolomes of flower, leave and root of this loquat variety were also determined by UPLC-ESI-MS/M system. 577 metabolites were determined in total, including 98 phenolic acids, 95 flavonoids, 33 alkaloids, 28 terpenoids, one steroids. The accumulation difference of these metabolites among leaf, flower and root of loquat were also clarified. Based on KEGG annotation, genes related to the biosynthesis of medicinal ingredients including some flavonoids and terpenoids were identified. Overall, this study provides global fundamental molecular insights into the medical biology of Eriobotrya japonica.

scholarly journals High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and Whole-Genome Maps

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Rebecca L. Lindsey ◽  
Dhwani Batra ◽  
Lori Rowe ◽  
Vladimir N. Loparev ◽  
Phalasy Juieng ◽  
...  
Keyword(s):  
Draft Genome ◽  
Shigella Sonnei ◽  
Whole Genome ◽  
Drug Resistant ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Content Type ◽  
Genome Maps ◽  
Public Health Challenge

ABSTRACT Drug-resistant Shigella sonnei poses a clinical and public health challenge. We report here the high-quality draft whole-genome sequences of four outbreak-associated S. sonnei isolates; three were resistant to two or more antibiotics, and one was resistant to streptomycin only.

scholarly journals High-Quality Draft Genome Sequences for Five Non-O157 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing and Optical Maps: TABLE 1

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Rebecca L. Lindsey ◽  
Lori Rowe ◽  
Lisley Garcia-Toledo ◽  
Vladimir Loparev ◽  
Kristen Knipe ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Draft Genome ◽  
Foodborne Pathogen ◽  
The United States ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Optical Maps

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen. We report here the high-quality draft whole-genome sequences of five STEC strains isolated from clinical cases in the United States. This report is for STEC of serotypes O55:H7, O79:H7, O91:H14, O153:H2, and O156:H25.

scholarly journals Whole-Genome Sequencing of Two Latin American–Mediterranean Extensively Drug-Resistant  Mycobacterium tuberculosis  Clinical Isolates from Medellín, Colombia

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
N. Alvarez ◽  
D. Haft ◽  
U. A. Hurtado ◽  
J. Robledo ◽  
F. Rouzaud
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequencing ◽  
Latin American ◽  
Draft Genome ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Drug Resistant ◽  
Genome Sequences ◽  
High Quality ◽  
Extensively Drug Resistant

Colombia, with a tuberculosis incidence of 33 cases per 100,000 population, is one of the countries that have reported extensively drug-resistant  Mycobacterium tuberculosis  (XDR-TB). We report the high-quality draft genome sequences of two Latin American–Mediterranean XDR-TB clinical isolates (TBR-152 and TBR-175), comprising 4,303,775 bp and 4,330,115 bp, respectively.

scholarly journals Draft Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains OK3, VB11, and NOB1, Isolated from Bunch and Muscadine Grapes Grown in Southern Mississippi

2020 ◽  
Vol 9 (25) ◽  
Author(s):  
Olga V. Mavrodi ◽  
Dmitri V. Mavrodi ◽  
Eric T. Stafne ◽  
John J. Adamczyk ◽  
Ebrahiem M. Babiker
Keyword(s):  
Xylella Fastidiosa ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
Muscadine Grape ◽  
Genome Assemblies ◽  
Muscadine Grapes

ABSTRACT We report here high-quality draft whole-genome assemblies of Xylella fastidiosa subsp. fastidiosa strains OK3, VB11, and NOB1, which were isolated from symptomatic bunch and muscadine grape plants grown in southern Mississippi.

scholarly journals High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping

2018 ◽  
Vol 6 (1) ◽  
Author(s):  
Max R. Schroeder ◽  
Phalasy Juieng ◽  
Dhwani Batra ◽  
Kristen Knipe ◽  
Lori A. Rowe ◽  
...  
Keyword(s):  
Draft Genome ◽  
Shigella Dysenteriae ◽  
Reference Level ◽  
Whole Genome ◽  
Foodborne Disease ◽  
Genome Sequences ◽  
High Quality ◽  
E Coli ◽  
Shigella Spp ◽  
Causative Agents

ABSTRACT Escherichia spp., including E. albertii and E. coli, Shigella dysenteriae, and S. flexneri are causative agents of foodborne disease. We report here reference-level whole-genome sequences of E. albertii (2014C-4356), E. coli (2011C-4315 and 2012C-4431), S. dysenteriae (BU53M1), and S. flexneri (94-3007 and 71-2783).

scholarly journals High-Quality Draft Genome Sequence of a Rickettsiales Bacterium Found in Acropora tenuis Coral from Okinawa, Japan

2020 ◽  
Vol 9 (48) ◽  
Author(s):  
Keigo Ide ◽  
Yohei Nishikawa ◽  
Masato Kogawa ◽  
Eisuke Iwamoto ◽  
Ashok Zachariah Samuel ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequence ◽  
Bacterial Strain ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
High Quality ◽  
Complete Genomes ◽  
Acropora Tenuis ◽  
Cell Genome ◽  
Single Cell Genome

ABSTRACT Rickettsiales-like organisms are important for the survival and functioning of corals, prompting an investigation of their complete genomes. Earlier reports of the genomes of these organisms remain incomplete. Here, we report a novel draft genome of Rickettsiales bacterial strain SESOKO1, found in Acropora tenuis coral, using single-cell genome technology.

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