scholarly journals A new and improved genome sequence of Cannabis sativa

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Shivraj Braich ◽  
Rebecca C. Baillie ◽  
German C. Spangenberg ◽  
Noel O. I. Cogan
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Cannabis Sativa ◽  
Draft Genome ◽  
Diploid Species ◽  
Sequence Assembly ◽  
Draft Genome Sequence ◽  
Genome Sequence Assembly ◽  
Long Read ◽  
Genome Assemblies

Cannabis is a diploid species (2n = 20), the estimated haploid genome sizes of the female and male plants using flow cytometry are 818 and 843 Mb respectively. Although the genome of Cannabis has been sequenced (from hemp, wild and high-THC strains), all assemblies have significant gaps. In addition, there are inconsistencies in the chromosome numbering which limits their use. A new comprehensive draft genome sequence assembly (∼900 Mb) has been generated from the medicinal cannabis strain Cannbio-2, that produces a balanced ratio of cannabidiol and delta-9-tetrahydrocannabinol using long-read sequencing. The assembly was subsequently analysed for completeness by ordering the contigs into chromosome-scale pseudomolecules using a reference genome assembly approach, annotated and compared to other existing reference genome assemblies. The Cannbio-2 genome sequence assembly was found to be the most complete genome sequence available based on nucleotides assembled and BUSCO evaluation in Cannabis sativa with a comprehensive genome annotation. The new draft genome sequence is an advancement in Cannabis genomics permitting pan-genome analysis, genomic selection as well as genome editing.

scholarly journals A New and Improved Genome Sequence of Cannabis sativa

2020 ◽  
Author(s):  
Shivraj Braich ◽  
Rebecca C. Baillie ◽  
German Spangenberg ◽  
Noel O.I. Cogan
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Cannabis Sativa ◽  
Draft Genome ◽  
Diploid Species ◽  
Sequence Assembly ◽  
Draft Genome Sequence ◽  
Genome Sequence Assembly ◽  
Long Read ◽  
Genome Assemblies

Cannabis is a diploid species (2n = 20), the estimated haploid genome sizes of the female and male plants using flow cytometry are 818 and 843 Mb respectively. Although the genome of Cannabis has been sequenced (from hemp, wild and high-THC strains), all assemblies have significant gaps. In addition, there are inconsistencies in the chromosome numbering which limits their use. A new comprehensive draft genome sequence assembly (~900 Mb) has been generated from the medicinal cannabis strain Cannbio-2, that produces a balanced ratio of cannabidiol and delta-9-tetrahydrocannabinol using long-read sequencing. The assembly was subsequently analysed for completeness by ordering the contigs into chromosome-scale pseudomolecules using a reference genome assembly approach, annotated and compared to other existing reference genome assemblies. The Cannbio-2 genome sequence assembly was found to be the most complete genome sequence available based on nucleotides assembled and BUSCO evaluation in Cannabis sativa with a comprehensive genome annotation. The new draft genome sequence is an advancement in Cannabis genomics permitting pan-genome analysis, genomic selection as well as genome editing.

scholarly journals Draft Genome Sequence and Annotation of the Apicomplexan Parasite Besnoitia besnoiti

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Gereon Schares ◽  
Pratap Venepally ◽  
Hernán A. Lorenzi
Keyword(s):  
Genome Sequence ◽  
Causative Agent ◽  
Definitive Host ◽  
Draft Genome ◽  
Sequence Assembly ◽  
Apicomplexan Parasite ◽  
Draft Genome Sequence ◽  
Besnoitia Besnoiti ◽  
Genome Sequence Assembly ◽  
Bovine Besnoitiosis

ABSTRACT The apicomplexan parasite Besnoitia besnoiti is the causative agent of bovine besnoitiosis that affects livestock, particularly cattle. The definitive host of B. besnoiti is unknown and its transmission only partially understood. Here, we report the first draft genome sequence, assembly, and annotation of this parasite.

scholarly journals A draft genome sequence for the Ixodes scapularis cell line, ISE6

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 297 ◽  
Author(s):  
Jason R. Miller ◽  
Sergey Koren ◽  
Kari A. Dilley ◽  
Derek M. Harkins ◽  
Timothy B. Stockwell ◽  
...  
Keyword(s):  
Cell Line ◽  
Genome Sequence ◽  
Single Molecule ◽  
Reference Genome ◽  
Sequence Data ◽  
Ixodes Scapularis ◽  
Draft Genome ◽  
Clinical Samples ◽  
Draft Assembly ◽  
Long Read

Background:The tick cell line ISE6, derived fromIxodes scapularis, is commonly used for amplification and detection of arboviruses in environmental or clinical samples.Methods:To assist with sequence-based assays, we sequenced the ISE6 genome with single-molecule, long-read technology.Results:The draft assembly appears near complete based on gene content analysis, though it appears to lack some instances of repeats in this highly repetitive genome. The assembly appears to have separated the haplotypes at many loci. DNA short read pairs, used for validation only, mapped to the cell line assembly at a higher rate than they mapped to theIxodes scapularisreference genome sequence.Conclusions:The assembly could be useful for filtering host genome sequence from sequence data obtained from cells infected with pathogens.

scholarly journals Draft Genome Sequence of Blood-Origin Streptococcus canis Strain FU149, Isolated from a Dog with Necrotizing Soft Tissue Infection

2020 ◽  
Vol 9 (35) ◽  
Author(s):  
Yasuto Fukushima ◽  
Yoshiteru Murata ◽  
Yukie Katayama ◽  
Yuzo Tsuyuki ◽  
Haruno Yoshida ◽  
...  
Keyword(s):  
Soft Tissue ◽  
Genome Sequence ◽  
Soft Tissue Infection ◽  
Reference Genome ◽  
Draft Genome ◽  
Tissue Infection ◽  
Draft Genome Sequence ◽  
Necrotizing Soft Tissue Infection ◽  
Content Type ◽  
Streptococcus Canis

ABSTRACT The draft genome sequence of the blood-origin Streptococcus canis strain FU149, isolated from a dog with a necrotizing soft tissue infection in Japan, is reported. The genome size was 2.108 Mbp, with a G+C content of 39.5%. Sequences unmapped to the reference genome sequence of NCTC 12191T (GenBank accession number LR134293) were characterized.

scholarly journals Draft Genome Sequence of Bacillus coagulans ZB29, a Commercial Probiotic Strain

2019 ◽  
Vol 8 (3) ◽  
Author(s):  
Darshana Chauhan ◽  
Yama Patel ◽  
Jayraj A. Doshi ◽  
Rashesh D. Doshi ◽  
Anjali Bose
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Bacillus Coagulans ◽  
Probiotic Strain ◽  
Sequence Assembly ◽  
Draft Genome Sequence ◽  
Its Sequence ◽  
Content Type ◽  
Beneficial Effects

Bacillus coagulans ZB29, isolated from milk, is a safe strain already available on market shelves and characterized by certified beneficial effects. Here, we report the 3,646,473-bp genome sequence of this bacterium, its sequence assembly, and its annotations.

scholarly journals Draft Reference Genome Sequence of Corynebacterium mastitidis 16-1433, Isolated from a Mouse

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Christopher Cheleuitte-Nieves ◽  
Christopher A. Gulvik ◽  
Ben W. Humrighouse ◽  
Melissa E. Bell ◽  
Aaron Villarma ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Reference Genome ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Read Coverage ◽  
Reference Genome Sequence

ABSTRACT We report here a nearly complete draft genome sequence for a Corynebacterium mastitidis isolate from a mouse. The total read coverage is 198×, and the genome size is 2,264,319 bp with a 69.04% GC content. This genome complements the only other genome available for C. mastitidis , which was obtained from a sheep.

scholarly journals Draft Genome Sequence of Klebsiella pneumoniae Strain AS Isolated from Zhejiang Provincial Hospital of TCM, China

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Xue-Jing Yang ◽  
Sai Wang ◽  
Jun-Min Cao ◽  
Jia-Hui Hou
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Genomic Information ◽  
Gram Negative ◽  
Provincial Hospital ◽  
Facultative Anaerobic ◽  
Zhejiang Provincial ◽  
Genome Assemblies

Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. Here we present draft genome assemblies of Klebsiella pneumoniae AS, which was isolated in China. The genomic information will provide a better understanding of the physiology, adaptation, and evolution of K. pneumoniae.

scholarly journals A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia x Vitis cinerea) and its Exploitation for Marker Development and Targeted Mapping

2019 ◽  
Author(s):  
Daniela Holtgräwe ◽  
Thomas Rosleff Sörensen ◽  
Ludger Hausmann ◽  
Boas Pucker ◽  
Prisca Viehöver ◽  
...  
Keyword(s):  
Genetic Marker ◽  
Genome Sequence ◽  
Plant Protection ◽  
Draft Genome ◽  
Plasmopara Viticola ◽  
Sequence Assembly ◽  
Resistance Locus ◽  
Sources Of Resistance ◽  
Vitis Riparia ◽  
Genome Sequence Assembly

AbstractGrapevine breeding becomes highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. Therefore, in modern breeding programs genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x V. cinerea Arnold, available as the rootstock cultivar ‘Börner’, carries several relevant resistance loci. We applied next generation sequencing to enable the reliable identification of simple sequence repeats (SSR) and also generated a draft genome sequence assembly of ‘Börner’ to access genome wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the ‘Börner’ genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

scholarly journals Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Matthew Hobbs ◽  
Andrew King ◽  
Ryan Salinas ◽  
Zhiliang Chen ◽  
Kyriakos Tsangaras ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Assembly ◽  
Genome Sequence Assembly ◽  
Long Read ◽  
Insight Into

scholarly journals Draft genome sequence resource for the orange rust pathogen of sugarcane Puccinia kuehnii

2021 ◽  
Author(s):  
Daniela E Cardenas ◽  
Jitender Cheema ◽  
Theodora S Oppelaar ◽  
Martha Hincapie ◽  
Sushma Sood ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Fungal Pathogen ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Puccinia Kuehnii ◽  
Rust Pathogen ◽  
The Usa ◽  
Genomic Studies ◽  
Genome Assemblies ◽  
Sugarcane Industry

Puccinia kuehnii is an obligate biotrophic fungal pathogen that causes orange rust of sugarcane, which is prevalent in many countries around the globe. In the USA, orange rust was first detected in sugarcane in Florida in 2007 and poses a persistent and economically damaging threat to the sugarcane industry in this region. Here, we generated the first genome assemblies for two isolates of P. kuehnii (1040 and 2143) collected in Florida in 2017 from two sugarcane cultivars, CL85-1040 and CP89-2143, respectively. These two rust genome resources will be of immense value for future genomic studies, particularly further exploration of the predicted secretomes that may help define key pathogenicity determinants for this economically important pathogen.

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