scholarly journals Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms

Pathogens ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 834
Author(s):  
Xinxin Wang ◽  
Jingyu Peng ◽  
Lei Sun ◽  
Gregory Bonito ◽  
Yuxiu Guo ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Gene Clusters ◽  
Single Copy ◽  
Dual Culture ◽  
Edible Fungi ◽  
Fungal Cell ◽  
Sequencing Platform ◽  
Phylogenetic Placement

Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.

scholarly journals A Complete Genome Sequence of the Wood Stem Endophyte Bacillus velezensis BY6 Strain Possessing Plant Growth-Promoting and Antifungal Activities

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Ping Zhang ◽  
Jian Diao ◽  
Guangqiang Xie ◽  
Ling Ma ◽  
Lihai Wang
Keyword(s):  
Secondary Metabolite ◽  
Single Molecule ◽  
Complete Genome ◽  
Pathogenic Fungus ◽  
Gc Content ◽  
Endophytic Bacterium ◽  
Gene Clusters ◽  
Bacillus Velezensis ◽  
Sequencing Platform ◽  
Plant Growth Promoting

An endophytic bacterium Bacillus velezensis BY6 was isolated from the wood stems of healthy Populus davidiana × P. alba var. pyramidalis (PdPap). The BY6 strain can inhibit pathogenic fungus Alternaria alternate in PdPap and promote growth of PdPap seedlings. In the present study, we used the Pacific Biosciences long-read sequencing platform, a single-molecule real-time (SMRT) technology for strain BY6, to perform complete genome sequencing. The genome size was 3,898,273 bp, the number of genes was 4,045, and the average GC content was 47.33%. A complete genome of strain BY6 contained 110 secondary metabolite gene clusters. Nine of the secondary metabolite gene clusters exhibited antifungal activity and promoted growth functions primarily involved in the synthesis of surfactin, bacteriocins, accumulated iron ions, and related antibiotics. Gene clusters provide genetic resources for biotechnology and genetic engineering, and enhance understanding of the relationship between microorganisms and plants.

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 De Novo Whole-Genome Sequencing of the Wood Rot Fungus Polyporus brumalis, Which Exhibits Potential Terpenoid Metabolism

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Su-Yeon Lee ◽  
Ji-eun An ◽  
Sun-Hwa Ryu ◽  
Myungkil Kim
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Gene Annotation ◽  
Draft Genome ◽  
Fungal Growth ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Protein Coding Genes ◽  
Polyporus Brumalis ◽  
Terpenoid Metabolism

ABSTRACT Polyporus brumalis is able to synthesize several sesquiterpenes during fungal growth. Using a single-molecule real-time sequencing platform, we present the 53-Mb draft genome of P. brumalis, which contains 6,231 protein-coding genes. Gene annotation and isolation support genetic information, which can increase the understanding of sesquiterpene metabolism in P. brumalis.

scholarly journals Full-length Transcriptome Analysis of Pecan (Carya illinoinensis) Kernels

2021 ◽  
Author(s):  
Chengcai Zhang ◽  
Huadong Ren ◽  
Xiaohua Yao ◽  
Kailiang Wang ◽  
Jun Chang
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Alternative Polyadenylation ◽  
Full Length ◽  
Functional Annotations ◽  
Predominant Type ◽  
Long Read ◽  
Non Coding Rnas ◽  
Novel Isoforms

Abstract Pecan is rich in bioactive components such as fatty acids and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37 504 isoforms of 16 702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26 080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30 751, 81.99%) had functional annotations. A total of 15 465 alternative splicing (AS) events and 65 761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long non-coding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with fatty acid (FA) and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. The present study provides a full-length transcriptome dataset of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.

scholarly journals High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Andreas J Stroehlein ◽  
Pasi K Korhonen ◽  
Teik Min Chong ◽  
Yan Lue Lim ◽  
Kok Gan Chan ◽  
...  
Keyword(s):  
Long Range ◽  
Single Molecule ◽  
Schistosoma Haematobium ◽  
Gene Annotation ◽  
Draft Genome ◽  
Single Copy ◽  
Phylogenetic Position ◽  
Urogenital Schistosomiasis ◽  
Gene Models ◽  
Genomic Resource

AbstractBackgroundSchistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation.FindingsHere, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available.ConclusionsWe report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions.

scholarly journals The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes)

2020 ◽  
Vol 12 (6) ◽  
pp. 860-866 ◽  
Author(s):  
Qing-Song Zhou ◽  
Arong Luo ◽  
Feng Zhang ◽  
Ze-Qing Niu ◽  
Qing-Tao Wu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Draft Genome ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Single Copy ◽  
Gene Family Evolution ◽  
Nesting Biology ◽  
Protein Coding ◽  
Final Assembly ◽  
Long Reads

Abstract Despite intense interest in bees, no genomes are available for the bee family Colletidae. Colletes gigas, one of the largest species of the genus Colletes in the world, is an ideal candidate to fill this gap. Endemic to China, C. gigas has been the focus of studies on its nesting biology and pollination of the economically important oil tree Camellia oleifera, which is chemically defended. To enable deeper study of its biology, we sequenced the whole genome of C. gigas using single-molecule real-time sequencing on the Pacific Bioscience Sequel platform. In total, 40.58 G (150×) of long reads were generated and the final assembly of 326 scaffolds was 273.06 Mb with a N50 length of 8.11 Mb, which captured 94.4% complete Benchmarking Universal Single-Copy Orthologs. We predicted 11,016 protein-coding genes, of which 98.50% and 84.75% were supported by protein- and transcriptome-based evidence, respectively. In addition, we identified 26.27% of repeats and 870 noncoding RNAs. The bee phylogeny with this newly sequenced colletid genome is consistent with available results, supporting Colletidae as sister to Halictidae when Stenotritidae is not included. Gene family evolution analyses identified 9,069 gene families, of which 70 experienced significant expansions (33 families) or contractions (37 families), and it appears that olfactory receptors and carboxylesterase may be involved in specializing on and detoxifying Ca. oleifera pollen. Our high-quality draft genome for C. gigas lays the foundation for insights on the biology and behavior of this species, including its evolutionary history, nesting biology, and interactions with the plant Ca. oleifera.

scholarly journals A Genome Resource for the Apple Powdery Mildew Pathogen Podosphaera leucotricha

2020 ◽  
Vol 110 (11) ◽  
pp. 1756-1758
Author(s):  
Lederson Gañán ◽  
Richard Allen White ◽  
Maren L. Friesen ◽  
Tobin L. Peever ◽  
Achour Amiri
Keyword(s):  
Powdery Mildew ◽  
Population Biology ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Single Copy ◽  
Sequencing Data ◽  
Pome Fruit ◽  
Podosphaera Leucotricha ◽  
A Genome ◽  
Powdery Mildew Pathogen

Powdery mildew, caused by Podosphaera leucotricha, is an economically important disease of apple and pear trees. A single monoconidial strain (PuE-3) of this biotrophic fungus was used to extract DNA for Illumina sequencing. Data were assembled to form a draft genome of 43.8 Mb consisting of 8,921 contigs, 9,372 predicted genes, and 96.1% of complete benchmarking universal single copy orthologs (BUSCOs). This is the first reported genome sequence of P. leucotricha that will enable studies of the population biology, epidemiology, and fungicide resistance of this pathogen. Furthermore, this resource will be fundamental to uncover the genetic and molecular mechanisms of the apple−powdery mildew interaction, and support future pome fruit breeding efforts.

scholarly journals Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 124 ◽  
Author(s):  
Frederick Sossah ◽  
Zhenghui Liu ◽  
Chentao Yang ◽  
Benjamin Okorley ◽  
Lei Sun ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Divergence Time ◽  
Edible Mushrooms ◽  
Economic Losses ◽  
Phylogenomic Analysis ◽  
Evolutionary Divergence ◽  
Cytochrome P450 Enzymes ◽  
Sequencing Platform ◽  
Cobweb Disease

Cladobotryum protrusum is one of the mycoparasites that cause cobweb disease on cultivated edible mushrooms. However, the molecular mechanisms of evolution and pathogenesis of C. protrusum on mushrooms are largely unknown. Here, we report a high-quality genome sequence of C. protrusum using the single-molecule, real-time sequencing platform of PacBio and perform a comparative analysis with closely related fungi in the family Hypocreaceae. The C. protrusum genome, the first complete genome to be sequenced in the genus Cladobotryum, is 39.09 Mb long, with an N50 of 4.97 Mb, encoding 11,003 proteins. The phylogenomic analysis confirmed its inclusion in Hypocreaceae, with its evolutionary divergence time estimated to be ~170.1 million years ago. The genome encodes a large and diverse set of genes involved in secreted peptidases, carbohydrate-active enzymes, cytochrome P450 enzymes, pathogen–host interactions, mycotoxins, and pigments. Moreover, C. protrusum harbors arrays of genes with the potential to produce bioactive secondary metabolites and stress response-related proteins that are significant for adaptation to hostile environments. Knowledge of the genome will foster a better understanding of the biology of C. protrusum and mycoparasitism in general, as well as help with the development of effective disease control strategies to minimize economic losses from cobweb disease in cultivated edible mushrooms.

scholarly journals The Genome Assembly and Annotation of the Southern Elephant Seal Mirounga leonina

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 160
Author(s):  
Bo-Mi Kim ◽  
Yoon Jin Lee ◽  
Jeong-Hoon Kim ◽  
Jin-Hyoung Kim ◽  
Seunghyun Kang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Single Copy ◽  
Elephant Seal ◽  
Iucn Red List ◽  
Genome Project ◽  
Southern Elephant Seal ◽  
Breath Hold ◽  
Mirounga Leonina ◽  
Sequencing Platform

The southern elephant seal Mirounga leonina is the largest phocid seal and one of the two species of elephant seals. They are listed as ‘least concern’ by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species 2015. Here, we have assembled the reference genome for M. leonina using the 10× chromium sequencing platform. The final genome assembly of M. leonina was 2.42 Gb long, with a contig N50 length of 54 Mb and a maximum length of 111.6 Mb. The M. leonina genome contained 20,457 predicted protein-coding genes and possessed 41.51% repeated sequences. The completeness of the M. leonina genome was evaluated using benchmarking universal single-copy orthologous genes (BUSCOs): the assembly was highly complete, containing 95.6% of the core set of mammalian genes. The high-quality genomic information on M. leonina will be essential for further understanding of adaptive metabolism upon repeated breath-hold dives and the exploration of molecular mechanisms contributing to its unique biochemical and physiological characteristics. The southern elephant seal genome project was deposited at NCBI (National Center for Biotechnology Information) under BioProject number PRJNA587380.

scholarly journals First report of reference guided genome assembly of Black Bengal goat (Capra hircus)

2019 ◽  
Author(s):  
Amam Z. Siddiki ◽  
A. Baten ◽  
M. Billah ◽  
MAU. Alam ◽  
KSM. Shawrob ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Capra Hircus ◽  
Sequencing Platform ◽  
Gene Annotations ◽  
Skin Quality ◽  
Genome Information ◽  
Black Bengal Goat ◽  
Illumina Sequencing Platform

AbstractObjectivesBlack Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh. Furthermore, the aptitude of adaptation and disease resistance capacity of it is highly notable which makes its whole genome information an area of research interest.Data descriptionThe genomic DNA of local (Chittagong, Bangladesh) healthy Black Bengal goat (Capra hircus) was extracted and then sequenced. The de novo assembly and structural annotations are being presented here. Sequencing was done using Illumina sequencing platform and the draft genome assembled is about 3.04 Gb. 26458 Genes were annotated using Maker gene annotations tool which predicted BUSCO Gene models. Universal Single Copy Orthologs refer 82.5% completeness of the assembled genome.

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