scholarly journals High-quality genome assembly and annotation resource of Botryosphaeria dothidea strain BDLA16-7, causing trunk canker disease on Chinese hickory

Plant Disease ◽  
2021 ◽  
Author(s):  
Jiandong Bao ◽  
Q. Q. Wu ◽  
Jianqin Huang ◽  
Chuan-Qing Zhang
Keyword(s):  
Genome Assembly ◽  
Gene Clusters ◽  
Botryosphaeria Dothidea ◽  
Cytochrome P450 Enzymes ◽  
Protein Coding ◽  
Canker Disease ◽  
Host Interaction ◽  
Oxford Nanopore ◽  
Infection Mechanisms ◽  
High Quality Genome

Botryosphaeria dothidea is a latent pathogen with global importance to woody plant health, which causes serious tree trunk cankers on Chinese hickory. To date, only one Illumina short-read-based genome assembly of strain CK16 is available for host Chinese hickory. To address this problem, we reported a near telomere-to-telomere genome assembly of strain BDLA16-7 (46.05 Mb, N50 3.87 Mb) using Oxford Nanopore Sequencing Technology. Our genome assembly was consisted of 15 contigs, of which, 3 were assembled into chromosomal level and the maximum contig length was 6.19 Mb. The assembly contained 7.96% repeats and 12,815 protein-coding genes (10,274 genes were functional annotated). We also identified 3,642 pathogen-host interaction (PHI) genes, 250 carbohydrateactive enzymes (CAZymes), 252 cytochrome P450 enzymes (CYPs), 752 putative secreted proteins and 63 secondary metabolite biosynthesis gene clusters (SMBGCs). The BUSCO completeness of genome assembly and predicted genes was 99.34% and 97.50%, respectively, at fungal level (n=758). The almost chromosomal-level and well-annotated genome assembly will provide a valuable genetic resource for understanding of the infection mechanisms of B. dothidea in future.

scholarly journals Genome Sequence Data of Peronophythora litchii, an Oomycete Pathogen Causing Litchi Downy Blight

2021 ◽  
Author(s):  
Hengyuan Guo ◽  
Jiandong Bao ◽  
Lianyu Lin ◽  
Zhixin Wang ◽  
Mingyue Shi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Sequence Data ◽  
Protein Coding ◽  
Rxlr Effectors ◽  
Oxford Nanopore ◽  
Long Read ◽  
Infection Mechanisms ◽  
Oomycete Pathogen ◽  
High Quality Genome ◽  
Oxford Nanopore Technologies

Peronophythora litchii is an oomycete pathogen that exclusively infects litchi, with infection stages affecting a broad range of tissues. In this study, we obtained a near chromosome-level genome assembly of P. litchii strain ZL2018 from China using Oxford Nanopore Technologies (ONT) long-read sequencing and Illumina short-read sequencing. The genome assembly was 64.15 Mb in size and consisted of 81 contigs with an N50 of 1.43 Mb and a maximum length of 4.74 Mb. Excluding 34.67% of repeat sequences, a total of 14,857 protein-coding genes were identified, among which 14,447 genes were annotated. We also predicted 306 candidate RXLR effectors in the assembly. The high-quality genome assembly and annotation resources reported in this study will provide new insight into the infection mechanisms of P. litchii.

scholarly journals Genome Sequence Resource of Phytophthora colocasiae from China Using Nanopore Sequencing Technology

Plant Disease ◽  
2021 ◽  
Author(s):  
Zhixin Wang ◽  
Jiandong Bao ◽  
Lin Lv ◽  
Lianyu Lin ◽  
Zhiting Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Protein Coding ◽  
Short Read ◽  
Rxlr Effectors ◽  
Phytophthora Colocasiae ◽  
Oxford Nanopore ◽  
Long Read ◽  
Infection Mechanisms ◽  
Oomycete Pathogen ◽  
Taro Leaf Blight

Phytophthora colocasiae is a destructive oomycete pathogen of taro (Colocasia esculenta), which causes taro leaf blight. To date, only one highly fragmented Illumina short-read-based genome assembly is available for this species. To address this problem, we sequenced strain Lyd2019 from China using Oxford Nanopore Technologies (ONT) long-read sequencing and Illumina short-read sequencing. We generated a 92.51-Mb genome assembly consisting of 105 contigs with an N50 of 1.70 Mb and a maximum length of 4.17 Mb. In the genome assembly, we identified 52.78% repeats and 18,322 protein-coding genes, of which 12,782 genes were annotated. We also identified 191 candidate RXLR effectors and 1 candidate CRN effectors. The updated near-chromosome genome assembly and annotation resources will provide a better understanding of the infection mechanisms of P. colocasiae.

scholarly journals Genome Sequence Resource for Colletotrichum viniferum, the cause of grapevine ripe rot in China.

2021 ◽  
Author(s):  
Mengru Dou ◽  
Yu Hao ◽  
Jing Yang ◽  
Xiaojian Yuan ◽  
Xiao Yin ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Clusters ◽  
Cytochrome P450 Enzymes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Yield And Quality ◽  
Genome Analyses ◽  
High Quality Genome ◽  
Important Disease

Grape ripe rot is an important disease that has seriously damaged the yield and quality of grape worldwide. The disease is caused by Colletotrichum viniferum, a hemibiotrophic fungus that belongs to the Glomerellaceae family of Sordariomycetes class. Here, this work presents the genome of C. viniferum stain CvYL2a from grape based on Illumina HiSeq 2500 and PacBio RS II. The high-quality genome consists of 70 contigs with a 73.41 Mb genome size and encodes 14,668 protein-coding genes. These genes were annotated using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, EuKaryotic Orthologous Groups, Non-redundant Protein, and Swiss-Prot database. In addition, we identified a series of genes involved in pathogenicity including 909 carbohydrate-active enzymes, 67 secondary metabolite gene clusters, and 307 Cytochrome P450 enzymes. This genome sequence provides a valuable reference for the research on grape-C. viniferum interactions, the pathogenesis of C. viniferum, and comparative genome analyses. Keywords: Colletotrichum viniferum, grape, genome, pathogenesis

scholarly journals High-quality genome assembly of Pseudopestalotiopsis theae, the pathogenic fungus of tea grey blight

Plant Disease ◽  
2021 ◽  
Author(s):  
Shiqin Zheng ◽  
Ruiqi Chen ◽  
Zhe Wang ◽  
Juan Liu ◽  
Yan Cai ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Pathogenic Fungus ◽  
High Quality ◽  
Tea Tree ◽  
Sequencing Technologies ◽  
Host Interaction ◽  
Long Read ◽  
Infection Mechanisms ◽  
Grey Blight ◽  
High Quality Genome

Tea grey blight is one of the most serious foliar diseases of tea tree caused by the plant pathogenic fungus Pseudopestalotiopsis theae which can affect production and quality of tea worldwide. We generated a highly contiguous, 50.41Mbp genome assembly (N50 1.30 Mbp) of P. theae strain CYF27 by combining PacBio long-read and Illumina short-read sequencing technologies. We identified a total of 15,626 gene models, of which 1,038 genes encode putative secreted proteins. The high-quality genome assembly and annotation resource reported here will be useful for the study of fungal infection mechanisms and pathogen-host interaction.

scholarly journals Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes

Toxins ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 488 ◽  
Author(s):  
Shiyong Zhang ◽  
Jia Li ◽  
Qin Qin ◽  
Wei Liu ◽  
Chao Bian ◽  
...  
Keyword(s):  
High Throughput ◽  
Genome Assembly ◽  
Raw Materials ◽  
Pelteobagrus Fulvidraco ◽  
Yellow Catfish ◽  
High Quality ◽  
Protein Coding ◽  
Toxin Genes ◽  
Sequencing Platforms ◽  
High Quality Genome

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.

scholarly journals A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis

2020 ◽  
Vol 12 (7) ◽  
pp. 1074-1079 ◽  
Author(s):  
Ruihao Shu ◽  
Jihong Zhang ◽  
Qian Meng ◽  
Huan Zhang ◽  
Guiling Zhou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gene Clusters ◽  
Tibet Plateau ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Ophiocordyceps Sinensis ◽  
Homologous Protein ◽  
Genome Features

Abstract Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or “DongChongXiaCao,” is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genome assembly of O. sinensis. The assembly of 23 contigs was ∼110.8 Mb with a N50 length of 18.2 Mb. We used RNA-seq and homologous protein sequences to identify 8,916 protein-coding genes in the IOZ07 assembly. Moreover, 63 secondary metabolite gene clusters were identified in the improved assembly. The improved assembly and genome features described in this study will further inform the evolutionary study and resource utilization of Chinese cordyceps.

scholarly journals Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica

2021 ◽  
Vol 12 ◽  
Author(s):  
Nataliya V. Melnikova ◽  
Elena N. Pushkova ◽  
Ekaterina M. Dvorianinova ◽  
Artemy D. Beniaminov ◽  
Roman O. Novakovskiy ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Single Copy ◽  
Dioecious Species ◽  
Male And Female ◽  
Male Genome ◽  
Oxford Nanopore ◽  
Genome Assemblies ◽  
First Time ◽  
High Quality Genome ◽  
Y Haplotype

The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.

scholarly journals High-Quality Genome Assembly and Annotation of the California Harvester Ant Pogonomyrmex californicus (Buckley, 1867)

2020 ◽  
Author(s):  
Jonas Bohn ◽  
Reza Halabian ◽  
Lukas Schrader ◽  
Victoria Shabardina ◽  
Raphael Steffen ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Quality ◽  
Protein Coding ◽  
Primary Polygyny ◽  
Pogonomyrmex Californicus ◽  
The North ◽  
Harvester Ant ◽  
Mating Flights ◽  
North And South America ◽  
High Quality Genome

ABSTRACTThe harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America and California harvester ant Pogonomyrmex californicus is the most widely distributed Pogonomyrmex species in the North America. P. californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present high quality genome assembly and annotation of P. californicus. The size of the assembly is 241 Mb, which is in good agreement with previously estimated genome size and we were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO completeness at the 95% level. This high quality genome will pave the way for investigations of the genomic underpinnings of social polymorphism in queen number, regulation of aggression, and the evolution of adaptations to dry habitats in P. californicus.

scholarly journals High-quality genome assembly and high-density genetic map of asparagus bean

2019 ◽  
Author(s):  
Qiuju Xia ◽  
Ru Zhang ◽  
Xuemei Ni ◽  
Lei Pan ◽  
Yangzi Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Agronomic Traits ◽  
High Density ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Economically Valuable Traits ◽  
Sequencing Strategy ◽  
Asparagus Bean ◽  
High Quality Genome

AbstractAsparagus bean (Vigna. unguiculata ssp. sesquipedialis), known for its very long and tender green pods, is an important vegetable crop broadly grown in the developing countries. Despite its agricultural and economic values, asparagus bean does not have a high-quality genome assembly for breeding novel agronomic traits. In this study, we reported a high-quality 632.8 Mb assembly of asparagus bean based on the whole genome shotgun sequencing strategy. We also generated a high-density linkage map for asparagus bean, which helped anchor 94.42% of the scaffolds into 11 pseudo-chromosomes. A total of 42,609 protein-coding genes and 3,579 non-protein-coding genes were predicted from the assembly. Taken together, these genomic resources of asparagus bean will facilitate the investigation of economically valuable traits in a variety of legume species, so that the cultivation of these plants would help combat the protein and energy malnutrition in the developing world.

scholarly journals A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

GigaScience ◽  
2019 ◽  
Vol 8 (8) ◽  
Author(s):  
Lu Wang ◽  
Jinwei Wu ◽  
Xiaomei Liu ◽  
Dandan Di ◽  
Yuhong Liang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Gene Families ◽  
Rhinopithecus Roxellana ◽  
High Quality ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
A Genome ◽  
Close Relationship ◽  
High Quality Genome

Abstract Background The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered colobine species endemic to China, which has several distinct traits including a unique social structure. Although a genome assembly for R. roxellana is available, it is incomplete and fragmented because it was constructed using short-read sequencing technology. Thus, important information such as genome structural variation and repeat sequences may be absent. Findings To obtain a high-quality chromosomal assembly for R. roxellana qinlingensis, we used 5 methods: Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, BioNano optical maps, 10X Genomics link-reads, and high-throughput chromosome conformation capture. The assembled genome was ∼3.04 Gb, with a contig N50 of 5.72 Mb and a scaffold N50 of 144.56 Mb. This represented a 100-fold improvement over the previously published genome. In the new genome, 22,497 protein-coding genes were predicted, of which 22,053 were functionally annotated. Gene family analysis showed that 993 and 2,745 gene families were expanded and contracted, respectively. The reconstructed phylogeny recovered a close relationship between R. rollexana and Macaca mulatta, and these 2 species diverged ∼13.4 million years ago. Conclusion We constructed a high-quality genome assembly of the Qinling golden snub-nosed monkey; it had superior continuity and accuracy, which might be useful for future genetic studies in this species and as a new standard reference genome for colobine primates. In addition, the updated genome assembly might improve our understanding of this species and could assist conservation efforts.

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