scholarly journals High quality genome resource of mango bacterial black spot pathogen Xanthomonas citri pv. mangiferaeindicae GXG07 isolated from Guangxi, China

Plant Disease ◽  
2021 ◽  
Author(s):  
Fengzhi Bie ◽  
Yiming Li ◽  
Zhibin Liu ◽  
Meijing Qin ◽  
Shuping Li ◽  
...  
Keyword(s):  
Black Spot ◽  
Economic Losses ◽  
High Fidelity ◽  
Whole Genome ◽  
Sequencing Technology ◽  
Xanthomonas Citri ◽  
High Quality ◽  
Genomic Resources ◽  
High Quality Genome ◽  
Growing Region

Xanthomonas citri pv. mangiferaeindicae (Xcm) is the causal agent of mango bacterial black spot which is present in many mango growing regions and leads to great economic losses to mango industry. Due to the limitation of high-quality genomic resources, little is known about the molecular pathogenesis of Xcm. Here, we used PacBio High Fidelity reads (HiFi) sequencing technology to sequence and analyze the whole genome of an Xcm strain GXG07 isolated from Guangxi, the largest mango growing region in China. PacBio HiFi reads with a mean coverage of 450× had been assembled into three contigs of 5,166,537, 79,634 and 30,169 bp, revealing that the genome of Xcm GXG07 contains one chromosome and two plasmids. This genome provides a resource to better understand the biology and pathogenicity of mango bacterial black spot.

scholarly journals Genomic Variability of Phytophthora palmivora Isolates from Different Oil Palm Cultivation Regions in Colombia

2020 ◽  
Vol 110 (9) ◽  
pp. 1553-1564
Author(s):  
Juanita Gil ◽  
Mariana Herrera ◽  
Jorge Duitama ◽  
Greicy Sarria ◽  
Silvia Restrepo ◽  
...  
Keyword(s):  
Palm Oil ◽  
Oil Palm ◽  
Plant Pathogens ◽  
Host Cells ◽  
Phytophthora Palmivora ◽  
Economic Losses ◽  
Sequencing Data ◽  
High Quality ◽  
Genomic Resources ◽  
High Quality Genome

Palm oil is the most consumed vegetable oil globally, and Colombia is the largest palm oil producer in South America and fourth worldwide. However, oil palm plantations in Colombia are affected by bud rot disease caused by the oomycete Phytophthora palmivora, leading to significant economic losses. Infection processes by plant pathogens involve the secretion of effector molecules, which alter the functioning or structure of host cells. Current long-read sequencing technologies provide the information needed to produce high-quality genome assemblies, enabling a comprehensive annotation of effectors. Here, we describe the development of genomic resources for P. palmivora, including a high-quality genome assembly based on long and short-read sequencing data, intraspecies variability for 12 isolates from different oil palm cultivation regions in Colombia, and a catalog of over 1,000 candidate effector proteins. A total of 45,416 genes were annotated from the new genome assembled in 2,322 contigs adding to 165.5 Mbp, which represents an improvement of two times more gene models, 33 times better contiguity, and 11 times less fragmentation compared with currently available genomic resources for the species. Analysis of nucleotide evolution in paralogs suggests a recent whole-genome duplication event. Genetic differences were identified among isolates showing variable virulence levels. We expect that these novel genomic resources contribute to the characterization of the species and the understanding of the interaction of P. palmivora with oil palm and could be further exploited as tools for the development of effective strategies for disease control.

scholarly journals Whole-genome sequencing and de novo assembly of a 2019 novel coronavirus (SARS-CoV-2) strain isolated in Vietnam

2020 ◽  
Vol 18 (2) ◽  
pp. 197-208
Author(s):  
Le Tung Lam ◽  
Nguyen Trung Hieu ◽  
Nguyen Hong Trang ◽  
Ho Thi Thuong ◽  
Tran Huyen Linh ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sanger Sequencing ◽  
De Novo ◽  
Whole Genome ◽  
Smrt Sequencing ◽  
Sequencing Technology ◽  
High Quality ◽  
Long Read ◽  
Novel Coronavirus

The pandemic COVID-19 caused by the virus SARS-CoV-2 has devastated countries worldwide, infecting more than 4.5 million people and leading to more than 300,000 deaths as of May 16th, 2020. Whole-genome sequencing (WGS) is an effective tool to monitor emerging strains and provide information for intervention, thus help to inform outbreak control decisions. Here, we reported the first effort to sequence and de novo assemble the whole genome of SARS-CoV-2 using PacBio’s SMRT sequencing technology in Vietnam. We also presented the annotation results and a brief analysis of the variants found in our SARS-CoV-2 strain, which was isolated from a Vietnamese patient. The sequencing was successfully completed and de novo assembled in less than 30 hours, resulting in one contig with no gap and a length of 29,766 bp. All detected variants as compared to the NCBI reference were highly accurate, as confirmed by Sanger sequencing. The results have shown the potential of long read sequencing to provide high quality WGS data to support public health responses and advance understanding of this and future pandemics.

scholarly journals A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology

2020 ◽  
Author(s):  
Aundrea K. Westfall ◽  
Rory S. Telemeco ◽  
Mariana B. Grizante ◽  
Damien S. Waits ◽  
Amanda D. Clark ◽  
...  
Keyword(s):  
Behavioral Ecology ◽  
Genome Assembly ◽  
Evolutionary Ecology ◽  
Whole Genome ◽  
Sceloporus Undulatus ◽  
High Quality ◽  
Whole Genome Analysis ◽  
Genomic Resources ◽  
Eastern Fence Lizard ◽  
Chromosome Level

AbstractHigh-quality genomic resources facilitate population-level and species-level comparisons to answer questions about behavioral ecology, morphological and physiological adaptations, as well as the evolution of genomic architecture. Squamate reptiles (lizards and snakes) are particularly diverse in characteristics that have intrigued evolutionary biologists, but high-quality genomic resources for squamates are relatively sparse. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. We present a high-quality chromosome-level reference genome assembly, SceUnd1.0, (utilizing 10X Genomics Chromium, HiC, and PacBio data) and tissue/developmental stage transcriptomes for the Eastern Fence Lizard, Sceloporus undulatus. We performed synteny analysis with other available squamate chromosome-level assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes in S. undulatus. Using this new S. undulatus genome assembly we conducted reference-based assemblies for 34 other Sceloporus species to improve draft nuclear genomes assemblies from 1% coverage to 43% coverage on average. Across these species, typically >90% of reads mapped for species within 20 million years divergence from S. undulatus, this dropped to 75% reads mapped for species at 35 million years divergence. Finally we use RNAseq and whole genome resequencing data to compare the three assemblies as references, each representing an increased level of sequencing, cost and assembly efforts: Supernova Assembly with data from10X Genomics Chromium library; HiRise Assembly that added data from HiC library; and PBJelly Assembly that added data from PacBio sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq, but the chromosome-level scaffolds provided by the addition of the HiC data allowed the reference to be used for other whole genome analysis, including synteny and whole genome association mapping analyses. The addition of PacBio data provided negligible gains. Overall, these new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

scholarly journals Genome resource for Elsinoë batatas, the causal agent of stem and foliage scab disease of sweet potato

2021 ◽  
Author(s):  
Xinxin Zhang ◽  
Hongda Zou ◽  
Yiling Yang ◽  
Boping Fang ◽  
Lifei Huang
Keyword(s):  
Sweet Potato ◽  
Single Molecule ◽  
Reference Genome ◽  
Gc Content ◽  
Basic Research ◽  
Phytopathogenic Fungus ◽  
Sequencing Technology ◽  
High Quality ◽  
Single Molecule Sequencing ◽  
High Quality Genome

Elsinoë batatas is a phytopathogenic fungus causing stem and foliage scab disease of sweet potato. At present, there is no reference genome available for E. batatas, limiting basic research for the pathogen. The present study applied the nanopore single molecule sequencing technology to sequence the E. batatas genome. This study thus reports the first high-quality genome sequence of E. batatas, with a total contig size of 26.49 Mb, 50.8% GC content and an N50 of 2,546,814bp. The sequences obtained serve as a reference for analysis of E. batatas isolates and provide a resource to better understand the biology of stem and foliage scab disease of sweet potato.

scholarly journals High-quality genome assembly of Metaphire vulgaris

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10313
Author(s):  
Feng Jin ◽  
Zhaoli Zhou ◽  
Qi Guo ◽  
Zhenwen Liang ◽  
Ruoyu Yang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Hox Genes ◽  
Genomic Sequence ◽  
Whole Genome ◽  
High Quality ◽  
Chromosome Fusion ◽  
Chromosome Conformation ◽  
Medicinal Value ◽  
Hormone Secretions ◽  
High Quality Genome

Earthworms enrich the soil and protect the health of their ecological environment. Previous studies on these invertebrates determined their protein content, hormone secretions, medicinal value, and ecological habits, but their whole genomic sequence remains incomplete. We performed whole genome sequencing of Metaphire vulgaris (Chen, 1930), which belongs to the genus Metaphire of the family Megascolecidae. The genome assembly was 729 Mb, with a N50 contig size of 4.2 Mb. In total, 559 contigs were anchored to 41 chromosomes according to the results of Hi-C (High-throughput Chromosome Conformation Capture) technology, which was confirmed by karyological analysis. A comparison of the genomic sequences and genes indicated that there was a whole-genome duplication in M. vulgaris followed by several chromosome fusion events. Hox genes and lumbrokinase genes were identified as partial clusters surrounding the genome. Our high-quality genome assembly of M. vulgaris will provide valuable information for gene function and evolutionary studies in earthworms.

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.

High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan

2021 ◽  
Author(s):  
Hui Zhang ◽  
Yuexing Wang ◽  
Ce Deng ◽  
Sheng Zhao ◽  
Peng Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Quality ◽  
Rice Hybrid ◽  
High Quality Genome

scholarly journals Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Jacqueline King ◽  
Anne Pohlmann ◽  
Kamila Dziadek ◽  
Martin Beer ◽  
Kerstin Wernike
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Economic Losses ◽  
Clinical Samples ◽  
Bovine Viral Diarrhea ◽  
Sequence Information ◽  
Whole Genome ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Viral Loads

Abstract Background As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genetically differentiated into 21 BVDV-1 and four BVDV-2 subtypes. Commonly, the 5’ untranslated region and the Npro protein are utilized for subtyping. However, the genetic variability of BVDV leads to limitations in former studies analyzing genome fragments in comparison to a full-genome evaluation. Results To enable rapid and accessible whole-genome sequencing of both BVDV-1 and BVDV-2 strains, nanopore sequencing of twelve representative BVDV samples was performed on amplicons derived through a tiling PCR procedure. Covering a multitude of subtypes (1b, 1d, 1f, 2a, 2c), sample matrices (plasma, EDTA blood and ear notch), viral loads (Cq-values 19–32) and species (cattle and sheep), ten of the twelve samples produced whole genomes, with two low titre samples presenting 96 % genome coverage. Conclusions Further phylogenetic analysis of the novel sequences emphasizes the necessity of whole-genome sequencing to identify novel strains and supplement lacking sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive and accessible obtainment of complete BVDV genomes.

Sign in / Sign up

Export Citation Format

Share Document