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 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.

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 Draft Genome Sequence of Fusarium oxysporum f. sp. cubense Strain 160527, a Causal Agent of Panama Disease

2019 ◽  
Vol 8 (29) ◽  
Author(s):  
Shuta Asai ◽  
Yu Ayukawa ◽  
Pamela Gan ◽  
Sachiko Masuda ◽  
Ken Komatsu ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Fusarium Wilt ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Causal Agent ◽  
High Quality ◽  
Panama Disease ◽  
Content Type ◽  
High Quality Genome

Fusarium oxysporum f. sp. cubense is the causal agent of banana Fusarium wilt, also known as Panama disease. Here, we present a high-quality genome sequence of F. oxysporum f. sp. cubense strain 160527. The genome assembly is composed of 12 contigs with a total assembly length of 51,139,495 bp (N 50 contig length, 4,884,632 bp).

scholarly journals Complete Reference Genome Assembly for Commensalibacter sp. Strain AMU001, an Acetic Acid Bacterium Isolated from the Gut of Honey Bees

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Stefanos Siozios ◽  
Josephine Moran ◽  
Mary Chege ◽  
Gregory D. D. Hurst ◽  
Juan C. Paredes
Keyword(s):  
Acetic Acid ◽  
Apis Mellifera ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Honey Bees ◽  
Reference Genome ◽  
Acetic Acid Bacterium ◽  
Content Type ◽  
Reference Genome Assembly

We report here the genome sequence of a Commensalibacter sp. strain (AMU001) isolated from honey bees (Apis mellifera) from Seychelles.

scholarly journals A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Fei Chen ◽  
Liyao Su ◽  
Shuaiya Hu ◽  
Jia-Yu Xue ◽  
Hui Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Floral Development ◽  
Peptide Transporter ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Rosa Rugosa ◽  
High Quality ◽  
Wide Range ◽  
High Quality Genome

AbstractRosa rugosa, commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with a mild fragrance and colorful seed pods. Unlike many other cultivated roses, R. rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity, alkaline, shade, drought, high humidity, and frigid temperatures. Here, we produced and analyzed a high-quality genome sequence for R. rugosa to understand its ecology, floral characteristics and evolution. PacBio HiFi reads were initially used to construct the draft genome of R. rugosa, and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes. We obtained a 382.6 Mb genome encoding 39,704 protein-coding genes. The genome of R. rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication (WGT), which occurred ~100 million years ago in the ancestor of core eudicots. Based on a comparative analysis of the high-quality genome assembly of R. rugosa and other high-quality Rosaceae genomes, we found a unique large inverted segment in the Chinese rose R. chinensis and a retroposition in strawberry caused by post-WGT events. We also found that floral development- and stress response signaling-related gene modules were retained after the WGT. Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2 (DRIP2) and PEPTIDE TRANSPORTER 3 (PTR3) were found to be positively selected in evolution, which may have contributed to the unique ability of this plant to adapt to harsh environments. In summary, the high-quality genome sequence of R. rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.

scholarly journals Genome Sequence of Torulaspora microellipsoides CLIB 830T

2018 ◽  
Vol 6 (26) ◽  
Author(s):  
Virginie Galeote ◽  
Frédéric Bigey ◽  
Hugo Devillers ◽  
Raúl A. Ortiz-Merino ◽  
Sylvie Dequin ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Sequence ◽  
Horizontal Transfer ◽  
Reference Genome ◽  
Genetic Material ◽  
Ascomycetous Yeast ◽  
Content Type ◽  
Transfer Mechanisms

We report here the genome sequence of the ascomycetous yeast Torulaspora microellipsoides CLIB 830T. A reference genome for this species, which has been found as a donor of genetic material in wine strains of Saccharomyces cerevisiae, will undoubtedly give clues to our understanding of horizontal transfer mechanisms between species in the wine environment.

scholarly journals An Adaptive Bitrate Switching Algorithm for Speech Applications in Context of WebRTC

2021 ◽  
Vol 17 (4) ◽  
pp. 1-21
Author(s):  
Mohannad Alahmadi ◽  
Peter Pocta ◽  
Hugh Melvin
Keyword(s):  
Real Time ◽  
Data Exchange ◽  
Quality Of Experience ◽  
End User ◽  
High Quality ◽  
Content Type ◽  
Switching Algorithm ◽  
Wide Range ◽  
The Impact

Web Real-Time Communication (WebRTC) combines a set of standards and technologies to enable high-quality audio, video, and auxiliary data exchange in web browsers and mobile applications. It enables peer-to-peer multimedia sessions over IP networks without the need for additional plugins. The Opus codec, which is deployed as the default audio codec for speech and music streaming in WebRTC, supports a wide range of bitrates. This range of bitrates covers narrowband, wideband, and super-wideband up to fullband bandwidths. Users of IP-based telephony always demand high-quality audio. In addition to users’ expectation, their emotional state, content type, and many other psychological factors; network quality of service; and distortions introduced at the end terminals could determine their quality of experience. To measure the quality experienced by the end user for voice transmission service, the E-model standardized in the ITU-T Rec. G.107 (a narrowband version), ITU-T Rec. G.107.1 (a wideband version), and the most recent ITU-T Rec. G.107.2 extension for the super-wideband E-model can be used. In this work, we present a quality of experience model built on the E-model to measure the impact of coding and packet loss to assess the quality perceived by the end user in WebRTC speech applications. Based on the computed Mean Opinion Score, a real-time adaptive codec parameter switching mechanism is used to switch to the most optimum codec bitrate under the present network conditions. We present the evaluation results to show the effectiveness of the proposed approach when compared with the default codec configuration in WebRTC.

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 De Novo Genome Assembly of a Foxtail Millet Cultivar Huagu11 Uncovered the Genetic Difference to the Cultivar Yugu1, and the Genetic Mechanism of Imazethapyr Tolerance

2021 ◽  
Author(s):  
Jie Wang ◽  
Shiming Li ◽  
Lei Lan ◽  
Mushan Xie ◽  
Shu Cheng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Reference Genome ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Genome Comparison ◽  
Sequencing Technology ◽  
High Quality ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Abstract Background: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97% and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was found that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

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.

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