scholarly journals Telomere to telomere genome assembly of Fusarium musae F31, causal agent of crown rot disease of banana.

2021 ◽  
Author(s):  
Luca Degradi ◽  
Valeria Tava ◽  
Andrea Kunova ◽  
Paolo Cortesi ◽  
Marco Saracchi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Species Complex ◽  
Crown Rot ◽  
Fusarium Fujikuroi ◽  
Valuable Resource ◽  
High Quality ◽  
Long Reads ◽  
Fusarium Fujikuroi Species Complex ◽  
Rot Disease ◽  
Chromosome Level

Fusarium musae van Hove causes crown rot of banana and it is also associated to clinical fusariosis. A chromosome-level genome assembly of Fusarium musae F31 obtained combining Nanopore long reads and Illumina paired end reads resulted in 12 chromosomes plus one contig with overall N50 of 4.36 Mb, and is presented together with its mitochondrial genome (58072 bp). F31 genome includes telomeric regions for 11 of the 12 chromosomes representing the most complete genome available in the Fusarium fujikuroi species complex. The high-quality assembly of the F31 genome will be a valuable resource for studying the pathogenic interactions occurring between F. musae and banana. Moreover, it represents an important resource for understanding the genome evolution in the Fusarium fujikuroi species complex.

scholarly journals Fusarium musae from Diseased Bananas and Human Patients: Susceptibility to Fungicides Used in Clinical and Agricultural Settings

2021 ◽  
Vol 7 (9) ◽  
pp. 784
Author(s):  
Valeria Tava ◽  
Anna Prigitano ◽  
Paolo Cortesi ◽  
Maria Carmela Esposto ◽  
Matias Pasquali
Keyword(s):  
Species Complex ◽  
Crown Rot ◽  
Fusarium Fujikuroi ◽  
Clinical Settings ◽  
Skin Infections ◽  
Minimal Inhibitory Concentrations ◽  
Worldwide Population ◽  
Fusarium Fujikuroi Species Complex ◽  
Rot Disease ◽  
Systemic Infections

Fusarium musae belongs to the Fusarium fujikuroi species complex. It causes crown rot disease in banana but also keratitis and skin infections as well as systemic infections in immunocompromised patients. Antifungal treatments in clinical and agricultural settings rely mostly on molecules belonging to the azole class. Given the potential risk of pathogen spread from food to clinical settings, the goal of the work was to define the level of susceptibility to different azoles of a worldwide population of F. musae. Eight fungicides used in agriculture and five antifungals used in clinical settings (4 azoles and amphotericin B) were tested using the CLSI (Clinical and Laboratory Standards Institute) protocol methodology on 19 F. musae strains collected from both infected patients and bananas. The level of susceptibility to the different active molecules was not dependent on the source of isolation with the exception of fenbuconazole and difenoconazole which had a higher efficiency on banana-isolated strains. Minimal inhibitory concentrations (MICs) of the different molecules ranged from 0.12–0.25 mg/L for prochloraz to more than 16 mg/L for tetraconazole and fenbuconazole. Compared to the F. verticillioides, F. musae MICs were higher suggesting the importance of monitoring the potential future spread of this species also in clinical settings.

scholarly journals Chromosome-Level Genome Assembly and Annotation of a Sciaenid Fish, Argyrosomus japonicus

2021 ◽  
Vol 13 (2) ◽  
Author(s):  
Linlin Zhao ◽  
Shengyong Xu ◽  
Zhiqiang Han ◽  
Qi Liu ◽  
Wensi Ke ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Wide Distribution ◽  
High Quality ◽  
Protein Coding ◽  
Repeat Elements ◽  
Long Reads ◽  
The Family ◽  
Solid Foundation ◽  
Genomic Resource ◽  
Chromosome Level

Abstract Argyrosomus japonicus is an economically and ecologically important fish species in the family Sciaenidae with a wide distribution in the world’s oceans. Here, we report a high-quality, chromosome-level genome assembly of A. japonicus based on PacBio and Hi-C sequencing technology. A 673.7-Mb genome containing 282 contigs with an N50 length of 18.4 Mb was obtained based on PacBio long reads. These contigs were further ordered and clustered into 24 chromosome groups based on Hi-C data. In addition, a total of 217.2 Mb (32.24% of the assembled genome) of sequences were identified as repeat elements, and 23,730 protein-coding genes were predicted based on multiple approaches. More than 97% of BUSCO genes were identified in the A. japonicus genome. The high-quality genome assembled in this work not only provides a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of A. japonicus but also lays a solid foundation for the study of Sciaenidae evolution.

scholarly journals A high‐quality chromosome‐level genome assembly of a generalist herbivore, Trichoplusia ni

2019 ◽  
Vol 19 (2) ◽  
pp. 485-496 ◽  
Author(s):  
Wenbo Chen ◽  
Xiaowei Yang ◽  
Guillaume Tetreau ◽  
Xiaozhao Song ◽  
Cathy Coutu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Trichoplusia Ni ◽  
High Quality ◽  
Generalist Herbivore ◽  
Chromosome Level

scholarly journals Chromosome-level de novo assembly of Coprinopsis cinerea A43mut B43mut pab1-1 #326 and genetic variant identification of mutants using Nanopore MinION sequencing

2020 ◽  
Author(s):  
Yichun Xie ◽  
Yiyi Zhong ◽  
Jinhui Chang ◽  
Hoi Shan Kwan
Keyword(s):  
Genome Assembly ◽  
Dna Isolation ◽  
Variant Calling ◽  
Genomic Analysis ◽  
Single Nucleotide ◽  
Sequencing Platform ◽  
Genomic Dna Isolation ◽  
Long Reads ◽  
Dna Isolation Protocol ◽  
Chromosome Level

AbstractThe homokaryotic Coprinopsis cinerea strain A43mut B43mut pab1-1 #326 is a widely used experimental model for developmental studies in mushroom-forming fungi. It can grow on defined artificial media and complete the whole lifecycle within two weeks. The mutations in mating type factors A and B result in the special feature of clamp formation and fruiting without mating. This feature allows investigations and manipulations with a homokaryotic genetic background. Current genome assembly of strain #326 was based on short-read sequencing data and was highly fragmented, leading to the bias in gene annotation and downstream analyses. Here, we report a chromosome-level genome assembly of strain #326. Oxford Nanopore Technology (ONT) MinION sequencing was used to get long reads. Illumina short reads was used to polish the sequences. A combined assembly yield 13 chromosomes and a mitochondrial genome as individual scaffolds. The assembly has 15,250 annotated genes with a high synteny with the C. cinerea strain Okayama-7 #130. This assembly has great improvement on contiguity and annotations. It is a suitable reference for further genomic studies, especially for the genetic, genomic and transcriptomic analyses in ONT long reads. Single nucleotide variants and structural variants in six mutagenized and cisplatin-screened mutants could be identified and validated. A 66 bp deletion in Ras GTPase-activating protein (RasGAP) was found in all mutants. To make a better use of ONT sequencing platform, we modified a high-molecular-weight genomic DNA isolation protocol based on magnetic beads for filamentous fungi. This study showed the use of MinION to construct a fungal reference genome and to perform downstream studies in an individual laboratory. An experimental workflow was proposed, from DNA isolation and whole genome sequencing, to genome assembly and variant calling. Our results provided solutions and parameters for fungal genomic analysis on MinION sequencing platform.HighlightA chromosome-level genome assembly of C. cinerea #326A fast and efficient high-molecular-weight fungal genomic DNA isolation protocolStructural variant and single nucleotide variant calling using Nanopore readsA series of solutions and reference parameters for fungal genomic analysis on MinION

scholarly journals Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master’s Course

2020 ◽  
Vol 10 (7) ◽  
pp. 2179-2183 ◽  
Author(s):  
Stefan Prost ◽  
Malte Petersen ◽  
Martin Grethlein ◽  
Sarah Joy Hahn ◽  
Nina Kuschik-Maczollek ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Siamese Fighting Fish ◽  
Betta Splendens ◽  
High Quality ◽  
Sequencing Platform ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Chromosome Level

Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master’s course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master’s course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.

scholarly journals Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Feng Shao ◽  
Arne Ludwig ◽  
Yang Mao ◽  
Ni Liu ◽  
Zuogang Peng
Keyword(s):  
Dna Sequences ◽  
Genome Assembly ◽  
Gambusia Affinis ◽  
Comparative Genomic ◽  
Suitable Model ◽  
High Quality ◽  
Western Mosquitofish ◽  
Poeciliid Fish ◽  
Oxford Nanopore ◽  
Chromosome Level

Abstract Background The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it. Results The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated. Conclusions The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.

scholarly journals Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shell

2021 ◽  
Author(s):  
Teng Weiming ◽  
Xie Xi ◽  
Hongtao Nie ◽  
Yamin Sun ◽  
Liu Xiangfeng ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Basis ◽  
Molecular Mechanisms ◽  
Heme Biosynthesis ◽  
High Quality ◽  
Protein Coding ◽  
Conserved Genes ◽  
Long Time ◽  
Muddy Sediments ◽  
Chromosome Level

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we reported a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50=2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the hemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

scholarly journals Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Sven Winter ◽  
Stefan Prost ◽  
Jordi de Raad ◽  
Raphael T. F. Coimbra ◽  
Magnus Wolf ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Morphological Differentiation ◽  
Chromosome Length ◽  
Morphological Transformation ◽  
High Quality ◽  
The North ◽  
Repeat Content ◽  
The Common ◽  
Species Specific ◽  
Chromosome Level

Background The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the ‘benthic associated clade’ of the order Syngnathiformes. The ‘benthic associated clade’ so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in ‘long-snouted’ syngnatiformes such as seahorses and pipefishes. Findings Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies’ long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp and a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.7%. Conclusions The chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.

scholarly journals Fusarium fujikuroi species complex in Brazilian rice: unveiling increased phylogenetic diversity and toxigenic potential

2020 ◽  
Author(s):  
Camila Primieri Nicolli ◽  
Miriam Haidukowskic ◽  
Antonia Susca ◽  
Larissa Bitencourt Gomes ◽  
Antonio Logrieco ◽  
...  
Keyword(s):  
Geographical Distribution ◽  
Species Complex ◽  
Phylogenetic Diversity ◽  
The Other ◽  
Fusarium Fujikuroi ◽  
Phylogenetic Species ◽  
Frequent Species ◽  
New Knowledge ◽  
Fusarium Sp ◽  
Fusarium Fujikuroi Species Complex

Fusarium fujikuroi species complex (FFSC) species are commonly encountered infecting rice, but knowledge of the diversity and toxigenic potential of the species is lacking in Brazil, the largest rice-producing country outside Asia. One hundred FFSC isolates obtained from national rice were identified using morphology and phylogeny of TEF, CAL and TUB genes. Eight previously known and one new phylogenetic species were identified. Three species accounted for around 60% of the strains: F. fujikuroi (n = 23), F. proliferatum (n = 22) and F. verticillioides (n = 16). The less frequent species were F. volatile (n = 8), F. anthophilum (n = 6), F. pseudocircinatum (n = 4), F. sterilihyphosum (n = 2) and F. begoniae (n = 1). The new Fusarium sp. was represented by 18 isolates. All species produced at least one of the analyzed mycotoxins [beauvericin (BEA), fumonisins (FBs), moniliformin (MON) and enniatins (ENNs)]. BEA was produced by all species but F. verticillioides. The FBs (mainly FB1) were produced mostly by F. fujikuroi, F. proliferatum and F. verticillioides. F. begoniae and F. verticillioides did not produce ENNs and F. sterilihyphosum and F. begoniae did no produce MON, while the other species produced MON and ENNs. Our results contribute new knowledge of the diversity, geographical distribution and hosts of FFSC species.

scholarly journals Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

2021 ◽  
Vol 12 ◽  
Author(s):  
Jielong Zhou ◽  
Peifu Wu ◽  
Zhongping Xiong ◽  
Naiyong Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Thaumetopoea Pityocampa ◽  
High Quality ◽  
Protein Coding ◽  
Peptidoglycan Recognition Protein ◽  
Recognition Protein ◽  
Chromosome Level

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

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