Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes

2016 ◽  
Vol 223 ◽  
pp. 24-25 ◽  
Author(s):  
Donghwan Shim ◽  
Sin-Gi Park ◽  
Kangmin Kim ◽  
Wonsil Bae ◽  
Gir Won Lee ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Lentinula Edodes ◽  
De Novo ◽  
Edible Mushroom ◽  
De Novo Sequencing ◽  
Whole Genome ◽  
The World

scholarly journals De novo whole-genome assembly of Chrysanthemum makinoi, a key wild chrysanthemum

2021 ◽  
Author(s):  
Natascha van Lieshout ◽  
Martijn van Kaauwen ◽  
Linda Kodde ◽  
Paul Arens ◽  
Marinus J M Smulders ◽  
...  
Keyword(s):  
Ab Initio ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Its Sequence ◽  
Whole Genome ◽  
Annotation Pipeline ◽  
Long Reads ◽  
Oxford Nanopore ◽  
The World

Abstract Chrysanthemum is among the top ten cut, potted and perennial garden flowers in the world. Despite this, to date, only the genomes of two wild diploid chrysanthemums have been sequenced and assembled. Here we present the most complete and contiguous chrysanthemum de novo assembly published so far, as well as a corresponding ab initio annotation. The cultivated hexaploid varieties are thought to originate from a hybrid of wild chrysanthemums, among which the diploid Chrysanthemum makinoi has been mentioned. Using a combination of Oxford Nanopore long reads, Pacific Biosciences long reads, Illumina short reads, Dovetail sequences and a genetic map, we assembled 3.1 Gb of its sequence into 9 pseudochromosomes, with an N50 of 330 Mb and BUSCO complete score of 92.1%. Our ab initio annotation pipeline predicted 95 074 genes and marked 80.0% of the genome as repetitive. This genome assembly of C. makinoi provides an important step forward in understanding the chrysanthemum genome, evolution and history.

scholarly journals Whole genome sequencing and genome annotation of the wild edible mushroom, Russula griseocarnosa

Genomics ◽  
2020 ◽  
Vol 112 (1) ◽  
pp. 603-614 ◽  
Author(s):  
Fei Yu ◽  
Jie Song ◽  
Junfeng Liang ◽  
Shengkun Wang ◽  
Junkun Lu
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Annotation ◽  
Edible Mushroom ◽  
Whole Genome ◽  
Wild Edible Mushroom

scholarly journals Functional Analysis of a Novel ABL (Abnormal Browning Related to Light) Gene in Mycelial Brown Film Formation of Lentinula edodes

2020 ◽  
Vol 6 (4) ◽  
pp. 272
Author(s):  
Chang Pyo Hong ◽  
Suyun Moon ◽  
Seung-il Yoo ◽  
Jong-Hyun Noh ◽  
Han-Gyu Ko ◽  
...  
Keyword(s):  
Lentinula Edodes ◽  
Developmental Process ◽  
Film Formation ◽  
Edible Mushroom ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Mushroom Species ◽  
Commercial Cultivation ◽  
Mushroom Yield

Lentinula edodes is a globally important edible mushroom species that is appreciated for its medicinal properties as well as its nutritional value. During commercial cultivation, a mycelial brown film forms on the surface of the sawdust growth medium at the late vegetative stage. Mycelial film formation is a critical developmental process that contributes to the quantity and quality of the mushroom yield. However, little is known regarding the genetic underpinnings of brown film formation on the surface of mycelial tissue. A novel causal gene associated with the formation of the mycelial brown film, named ABL (Abnormal browning related to light), was identified in this study. The comparative genetic analysis by dihybrid crosses between normal and abnormal browning film cultivars demonstrated that a single dominant allele was responsible for the abnormal mycelium browning phenotype. Whole-genome sequencing analysis of hybrid isolates revealed five missense single-nucleotide polymorphisms (SNPs) in the ABL locus of individuals forming abnormal partial brown films. Additional whole-genome resequencing of a further 16 cultivars showed that three of the five missense SNPs were strongly associated with the abnormal browning phenotype. Overexpression of the dominant abl-D allele in a wild-type background conferred the abnormal mycelial browning phenotype upon transformants, with slender hyphae observed as a general defective mycelial growth phenotype. Our methodology will aid the future discovery of candidate genes associated with favorable traits in edible mushrooms. The discovery of a novel gene, ABL, associated with mycelial film formation will facilitate marker-associated breeding in L. edodes.

scholarly journals Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
David Longbottom ◽  
Morag Livingstone ◽  
Paolo Ribeca ◽  
Delphine Sylvie Anne Beeckman ◽  
Arie van der Ende ◽  
...  
Keyword(s):  
De Novo ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Housekeeping Genes ◽  
De Novo Sequencing ◽  
Chlamydia Psittaci ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Chlamydia Abortus ◽  
Generation Vaccine

Abstract Background Chlamydia abortus and Chlamydia psittaci are important pathogens of livestock and avian species, respectively. While C. abortus is recognized as descended from C. psittaci species, there is emerging evidence of strains that are intermediary between the two species, suggesting they are recent evolutionary ancestors of C. abortus. Such strains include C. psittaci strain 84/2334 that was isolated from a parrot. Our aim was to classify this strain by sequencing its genome and explore its evolutionary relationship to both C. abortus and C. psittaci. Results In this study, methods based on multi-locus sequence typing (MLST) of seven housekeeping genes and on typing of five species discriminant proteins showed that strain 84/2334 clustered with C. abortus species. Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to C. abortus in terms of GC content, while 16S rRNA and whole genome phylogenetic analysis, as well as network and recombination analysis showed that the strain clusters more closely with C. abortus strains. The analysis also suggested a closer evolutionary relationship between this strain and the major C. abortus clade, than to two other intermediary avian C. abortus strains or C. psittaci strains. Molecular analyses of genes (polymorphic membrane protein and transmembrane head protein genes) and loci (plasticity zone), found in key virulence-associated regions that exhibit greatest diversity within and between chlamydial species, reveal greater diversity than present in sequenced C. abortus genomes as well as similar features to both C. abortus and C. psittaci species. The strain also possesses an extrachromosomal plasmid, as found in most C. psittaci species but absent from all sequenced classical C. abortus strains. Conclusion Overall, the results show that C. psittaci strain 84/2334 clusters very closely with C. abortus strains, and are consistent with the strain being a recent C. abortus ancestral species. This suggests that the strain should be reclassified as C. abortus. Furthermore, the identification of a C. abortus strain bearing an extra-chromosomal plasmid has implications for plasmid-based transformation studies to investigate gene function as well as providing a potential route for the development of a next generation vaccine to protect livestock from C. abortus infection.

scholarly journals De Novo Sequencing and Assembly of the Whole Genome of Novosphingobium sp. Strain PP1Y

2011 ◽  
Vol 193 (16) ◽  
pp. 4296-4296 ◽  
Author(s):  
V. D'Argenio ◽  
M. Petrillo ◽  
P. Cantiello ◽  
B. Naso ◽  
L. Cozzuto ◽  
...  
Keyword(s):  
De Novo ◽  
De Novo Sequencing ◽  
Whole Genome

scholarly journals De Novo Whole-Genome Sequencing and Annotation of Pathogenic Bovine Pasteurella multocida Type A:3 Strains

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
Morag Livingstone ◽  
Kevin Aitchison ◽  
Mark Dagleish ◽  
David Longbottom
Keyword(s):  
Genome Sequencing ◽  
Pasteurella Multocida ◽  
De Novo ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Pneumonic Pasteurellosis ◽  
The United Kingdom ◽  
The World ◽  
Welfare Implications

ABSTRACT Pneumonic pasteurellosis, caused by Pasteurella multocida, is a common respiratory infection of ruminants that has major economic and welfare implications throughout the world. Here, we report the annotated genome sequences of seven pathogenic strains of P. multocida that were isolated from cattle in the United Kingdom.

scholarly journals De Novo Whole-Genome Sequence and Genome Annotation of Lichtheimia ramosa

2014 ◽  
Vol 2 (5) ◽  
Author(s):  
J. Linde ◽  
V. Schwartze ◽  
U. Binder ◽  
C. Lass-Florl ◽  
K. Voigt ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Annotation ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Lichtheimia Ramosa
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