scholarly journals Complete Genome Assembly of Myxococcus xanthus Strain DZ2 Using Long High-Fidelity (HiFi) Reads Generated with PacBio Technology

2021 ◽  
Vol 10 (28) ◽  
Author(s):  
Rikesh Jain ◽  
Bianca H. Habermann ◽  
Tâm Mignot
Keyword(s):  
Genome Assembly ◽  
Complete Genome ◽  
Reference Genome ◽  
Myxococcus Xanthus ◽  
High Fidelity ◽  
High Quality ◽  
Microbial Ecosystem ◽  
Gram Negative ◽  
Content Type

Myxococcus xanthus is a Gram-negative social bacterium belonging to the order Myxococcales of the class Deltaproteobacteria . It is a facultative social predator found in soils across the globe and is thought to be crucial for the microbial ecosystem. Here, we report a complete high-quality reference genome of the M. xanthus strain DZ2.

scholarly journals High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534

2021 ◽  
Vol 10 (21) ◽  
Author(s):  
Jason E. Stajich ◽  
Andrea L. Vu ◽  
Howard S. Judelson ◽  
Gregory M. Vogel ◽  
Michael A. Gore ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Transcriptome Sequencing ◽  
Reference Genome ◽  
Phytophthora Capsici ◽  
Rna Seq ◽  
High Quality ◽  
Content Type ◽  
Wide Range ◽  
Illumina Data

The oomycete Phytophthora capsici is a destructive pathogen of a wide range of vegetable hosts, especially peppers and cucurbits. A 94.17-Mb genome assembly was constructed using PacBio and Illumina data and annotated with support from transcriptome sequencing (RNA-Seq) reads.

scholarly journals Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China

2021 ◽  
Author(s):  
Yuanchao Liu ◽  
Longhua Huang ◽  
Huiping Hu ◽  
Manjun Cai ◽  
Xiaowei Liang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Southwest China ◽  
Reference Genome ◽  
Biological Activities ◽  
Single Copy ◽  
The Tibetan Plateau ◽  
Whole Genome ◽  
High Quality ◽  
Pharmacological Activities ◽  
Genetic Studies

Abstract Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. G. leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with a N50 scaffold size of 3.06 Mb, 78,206 coding sequences and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and G. lucidum. G. leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals Complete Genome Sequence of SMBL-WEM22, a Halotolerant Strain of Kosakonia cowanii Isolated from Hong Kong Seawater

2021 ◽  
Vol 10 (41) ◽  
Author(s):  
W. E. Moore ◽  
G. K. K. Lai ◽  
S. D. J. Griffin ◽  
F. C. C. Leung
Keyword(s):  
Hong Kong ◽  
Dna Sequences ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Hybrid Assembly ◽  
Gram Negative ◽  
Content Type ◽  
Facultative Anaerobic ◽  
Long Read

Kosakonia cowanii is a Gram-negative, motile, facultative anaerobic enterobacterium that is found in soil, water, and sewage. K. cowanii SMBL-WEM22 is a halotolerant strain that was isolated from seawater in Hong Kong. The complete genome of SMBL-WEM22 (5,037,617 bp, with a GC content of 55.02%) was determined by hybrid assembly of short- and long-read DNA sequences.

scholarly journals Complete Genome Sequencing of 10 Brucella abortus Biovar 3 Strains Isolated from Water Buffalo

2018 ◽  
Vol 6 (16) ◽  
pp. e00180-18 ◽  
Author(s):  
Rubina Paradiso ◽  
Massimiliano Orsini ◽  
Daniela Criscuolo ◽  
Rosanna Borrelli ◽  
Ornella Valvini ◽  
...  
Keyword(s):  
Latin America ◽  
Central Asia ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
Brucella Abortus ◽  
Complete Genome ◽  
Water Buffalo ◽  
Mediterranean Area ◽  
Campania Region ◽  
Content Type

ABSTRACT Brucellosis is a zoonotic disease that affects both humans and animals. Its distribution is global, concentrated in the Mediterranean area, India, Central Asia, and Latin America. Here, we present a complete genome assembly of 10 Brucella abortus strains isolated from water buffaloes farmed in the Campania region of Italy.

scholarly journals Complete Genome Sequence of Bacillus velezensis Strain DKU_NT_04, Isolated from a Traditional Korean Food Made from Soybeans (Cheonggukjang)

2020 ◽  
Vol 9 (24) ◽  
Author(s):  
Man-Seok Bang ◽  
Hee-Won Jeong ◽  
Yea-Jin Lee ◽  
Sang-Cheol Lee ◽  
Gi Soo Lee ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacillus Velezensis ◽  
Coding Sequences ◽  
Content Type ◽  
Fermented Soybean ◽  
Soybean Paste ◽  
Korean Food

ABSTRACT In the present work, we report the complete genome sequence of Bacillus velezensis DKU_NT_04, isolated from cheonggukjang, which is a traditional Korean fermented soybean paste. The final genome assembly consists of a 4.328-Mbp chromosome with 4,134 coding sequences and a G+C content of 45.21%.

scholarly journals A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

2020 ◽  
Vol 33 (7) ◽  
pp. 880-883
Author(s):  
Stefan Kusch ◽  
Heba M. M. Ibrahim ◽  
Catherine Zanchetta ◽  
Celine Lopez-Roques ◽  
Cecile Donnadieu ◽  
...  
Keyword(s):  
Host Range ◽  
Sclerotinia Sclerotiorum ◽  
Genome Assembly ◽  
Plant Pathogens ◽  
Reference Genome ◽  
Close Relative ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Reference Genome Assembly

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.

scholarly journals Complete High-Quality Genome Sequence of Clostridium limosum (Hathewaya limosa) Isolate 14S0207, Recovered from a Cow with Suspected Blackleg in Germany

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Prasad Thomas ◽  
Mostafa Y. Abdel-Glil ◽  
Anne Busch ◽  
Lothar H. Wieler ◽  
Inga Eichhorn ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Intestinal Tract ◽  
High Quality ◽  
Circular Chromosome ◽  
Content Type ◽  
High Quality Genome

Clostridium limosum can be found in soil and the intestinal tract of animals. In 2014, C. limosum was isolated from a suspected blackleg outbreak in cattle in Schleswig-Holstein, Germany. We present a complete genome sequence of a C. limosum strain represented by a circular chromosome and three plasmids.

scholarly journals Highly Contiguous Nanopore Genome Assembly of Chlamydomonas reinhardtii CC-1690

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Samuel O’Donnell ◽  
Frederic Chaux ◽  
Gilles Fischer
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Genome Size ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Content Type ◽  
Oxford Nanopore ◽  
A Genome ◽  
Reference Quality

ABSTRACT The current Chlamydomonas reinhardtii reference genome remains fragmented due to gaps stemming from large repetitive regions. To overcome the vast majority of these gaps, publicly available Oxford Nanopore Technology data were used to create a new reference-quality de novo genome assembly containing only 21 contigs, 30/34 telomeric ends, and a genome size of 111 Mb.

scholarly journals Genome Assembly and Annotation of Botryosphaeria dothidea sdau11-99, a Latent Pathogen of Apple Fruit Ring Rot in China

Plant Disease ◽  
2020 ◽  
Author(s):  
Chengming Yu ◽  
Yufei Diao ◽  
Quan Lu ◽  
Jiaping Zhao ◽  
Shengnan Cui ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Fungal Pathogen ◽  
Woody Plants ◽  
Reference Genome ◽  
Apple Fruit ◽  
Botryosphaeria Dothidea ◽  
High Quality ◽  
Ring Rot ◽  
Wide Range

Botryosphaeria dothidea is a latent and important fungal pathogen on a wide range of woody plants. Fruit ring rot caused by B. dothidea is a major disease in China on apple. This study establishes a high quality, nearly complete and well annotated genome sequence of B. dothidea strain sdau11-99. The findings of this research provide a reference genome resource for further research on the apple fruit ring rot pathogen on apple and other hosts.

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