A high-quality reference genome of wild Cannabis sativa

Abstract Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. G. leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with a N50 scaﬀold size of 3.06 Mb, 78,206 coding sequences and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and G. lucidum. G. leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.

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De Novo Genome Assembly of a Foxtail Millet Cultivar Huagu11 Uncovered the Genetic Difference to the Cultivar Yugu1, and the Genetic Mechanism of Imazethapyr Tolerance

10.21203/rs.3.rs-143813/v1 ◽

2021 ◽

Author(s):

Jie Wang ◽

Shiming Li ◽

Lei Lan ◽

Mushan Xie ◽

Shu Cheng ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genome Sequence ◽

Reference Genome ◽

Foxtail Millet ◽

Setaria Italica ◽

Genome Comparison ◽

Sequencing Technology ◽

High Quality ◽

Next Generation Sequencing Technology ◽

Generation Sequencing

Abstract Background: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97% and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was found that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

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Improved Reference Genome for Cyclotella Cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

10.1101/2020.05.19.103069 ◽

2020 ◽

Author(s):

Wade R. Roberts ◽

Kala M. Downey ◽

Elizabeth C. Ruck ◽

Jesse C. Traller ◽

Andrew J. Alverson

Keyword(s):

Reference Genome ◽

Lipid Production ◽

Fold Increase ◽

High Quality ◽

Short Read Sequencing ◽

Large Size ◽

Reference Genome Assembly ◽

Cell Wall Morphogenesis ◽

Cyclotella Cryptica

ABSTRACTThe diatom, Cyclotella cryptica, is a well-established experimental model for physiological studies and, more recently, biotechnology applications of diatoms. To further facilitate its use as a model diatom species, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms.Data available fromNCBI BioProjects PRJNA628076 and PRJNA589195

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Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

10.1101/2021.11.23.469778 ◽

2021 ◽

Author(s):

Xinxin Yi ◽

Jing Liu ◽

Shengcai Chen ◽

Hao Wu ◽

Min Liu ◽

...

Keyword(s):

Nitrogen Fixation ◽

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Genomic Analysis ◽

Comparative Genomic ◽

High Quality ◽

Genome Wide ◽

A Genome ◽

Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

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A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-20-0060-a ◽

2020 ◽

Vol 33 (7) ◽

pp. 880-883

Author(s):

Stefan Kusch ◽

Heba M. M. Ibrahim ◽

Catherine Zanchetta ◽

Celine Lopez-Roques ◽

Cecile Donnadieu ◽

...

Keyword(s):

Host Range ◽

Sclerotinia Sclerotiorum ◽

Genome Assembly ◽

Plant Pathogens ◽

Reference Genome ◽

Close Relative ◽

High Quality ◽

Protein Coding ◽

Protein Coding Genes ◽

Reference Genome Assembly

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.

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Genome Assembly and Annotation of Botryosphaeria dothidea sdau11-99, a Latent Pathogen of Apple Fruit Ring Rot in China

Plant Disease ◽

10.1094/pdis-06-20-1182-a ◽

2020 ◽

Author(s):

Chengming Yu ◽

Yufei Diao ◽

Quan Lu ◽

Jiaping Zhao ◽

Shengnan Cui ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Fungal Pathogen ◽

Woody Plants ◽

Reference Genome ◽

Apple Fruit ◽

Botryosphaeria Dothidea ◽

High Quality ◽

Ring Rot ◽

Wide Range

Botryosphaeria dothidea is a latent and important fungal pathogen on a wide range of woody plants. Fruit ring rot caused by B. dothidea is a major disease in China on apple. This study establishes a high quality, nearly complete and well annotated genome sequence of B. dothidea strain sdau11-99. The findings of this research provide a reference genome resource for further research on the apple fruit ring rot pathogen on apple and other hosts.

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De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries

Genes ◽

10.3390/genes10060426 ◽

2019 ◽

Vol 10 (6) ◽

pp. 426 ◽

Cited By ~ 3

Author(s):

Daniel Berner ◽

Marius Roesti ◽

Steven Bilobram ◽

Simon K. Chan ◽

Heather Kirk ◽

...

Keyword(s):

Reference Genome ◽

De Novo ◽

Gene Annotation ◽

Model System ◽

Threespine Stickleback ◽

Evolutionary Genomics ◽

Digital Repository ◽

High Quality ◽

De Novo Gene ◽

Dna Libraries

The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7).

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Extraction of High Quality RNA from Cannabis sativa Bast Fibres: A Vademecum for Molecular Biologists

Fibers ◽

10.3390/fib4030023 ◽

2016 ◽

Vol 4 (4) ◽

pp. 23 ◽

Cited By ~ 6

Author(s):

Gea Guerriero ◽

Lauralie Mangeot-Peter ◽

Jean-Francois Hausman ◽

Sylvain Legay

Keyword(s):

Cannabis Sativa ◽

High Quality

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Fully resolved assembly of Cryptosporidium parvum

10.1101/2021.07.07.451495 ◽

2021 ◽

Author(s):

Vipin K. Menon ◽

Pablo C. Okhuysen ◽

Cynthia Chappell ◽

Medhat Mahmoud ◽

Qingchang Meng ◽

...

Keyword(s):

Cryptosporidium Parvum ◽

Reference Genome ◽

Single Copy ◽

Comparative Genomic ◽

Infection Prevalence ◽

High Quality ◽

Apicomplexan Parasites ◽

Oxford Nanopore ◽

Genomic Study ◽

Genomic Studies

Background Cryptosporidium parvum are apicomplexan parasites commonly found across many species with a global infection prevalence of 7.6%. As such it is important to understand the diversity and genomic makeup of this prevalent parasite to prohibit further spread and to fight an infection. The general basis of every genomic study is a high quality reference genome that has continuity and completeness, and is of high quality and thus enables comprehensive comparative studies. Findings Here we provide a highly accurate and complete reference genome of Cryptosporidium spp.. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall the assembly shows a high completion rate with 98.4% single copy Busco genes. This is also shown by the identification of 13 telomeric regions across the 8 chromosomes. The consensus accuracy of the established reference genome was further validated by sequence alignment of established genetic markers for C.parvum. Conclusions This high quality reference genome provides the basis for subsequent studies and comparative genomic studies across the Cryptosporidium clade.

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A new and improved genome sequence of Cannabis sativa

Gigabyte ◽

10.46471/gigabyte.10 ◽

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.

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