scholarly journals Genomic hitchhiking with moisture adaptation patterns stem prickleless in rose

2020 ◽  
Author(s):  
Mi-Cai Zhong ◽  
Xiao-Dong Jiang ◽  
Guo-Qian Yang ◽  
Wei-Hua Cui ◽  
Zhi-Quan Suo ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Regulatory Network ◽  
Molecular Basis ◽  
Reference Genome ◽  
Related Gene ◽  
High Quality ◽  
Expression Variation ◽  
Reference Genome Assembly ◽  
Gene Regulatory ◽  
Molecular Bases

Abstract“Rose with prickles” is a symbol of adversity and sacrifice but the molecular bases patterning prickle remains poorly explored. Here we generated a high-quality reference genome assembly for prickleless Rosa wichuraiana ‘Basye’s Thornless’ (BT), and identified genetic elements relating to stem prickle patterning. BT genome harbors a significant high proportion of Copia-type LTR (62.74% of LTRs) and diverges remarkably from that of R. chinensis Old Blush’, a founder genotype for rose domestication. Three negatively selected and fixed QTL were identified underlying BT prickleless. Differentially expressed genes in QTL were enriched for water-use-related genes, suggesting that prickleless might hitchhike the adaptation to moisture environments. While the prickle-related gene-regulatory-network (GRN) was highly conserved, expression variation of key candidate genes associated well with prickle-patterning divergence in roses. Our efforts provide fundamental resources and insights for Rosaceae genome evolution and molecular basis of key traits, thus should benefit rose improvement.

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

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.

scholarly journals Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China

2021 ◽  
Author(s):  
Yuanchao Liu ◽  
Longhua Huang ◽  
Huiping Hu ◽  
Manjun Cai ◽  
Xiaowei Liang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Southwest China ◽  
Reference Genome ◽  
Biological Activities ◽  
Single Copy ◽  
The Tibetan Plateau ◽  
Whole Genome ◽  
High Quality ◽  
Pharmacological Activities ◽  
Genetic Studies

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.

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

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

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

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.

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

Plant Disease ◽  
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.

scholarly journals The Chromosome-Level Reference Genome Assembly for Panax notoginseng and Insights into Ginsenoside Biosynthesis

2020 ◽  
pp. 100113 ◽  
Author(s):  
Zhouqian Jiang ◽  
Lichan Tu ◽  
Weifei Yang ◽  
Yifeng Zhang ◽  
Tianyuan Hu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Panax Notoginseng ◽  
Ginsenoside Biosynthesis ◽  
Reference Genome Assembly ◽  
Chromosome Level

scholarly journals A Short-Read Genome Assembly Resource for Leveillula taurica Causing Powdery Mildew Disease of Sweet Pepper (Capsicum annuum)

2020 ◽  
Vol 33 (6) ◽  
pp. 782-786
Author(s):  
Stefan Kusch ◽  
Márk Z. Németh ◽  
Niloofar Vaghefi ◽  
Heba M. M. Ibrahim ◽  
Ralph Panstruga ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Capsicum Annuum ◽  
Genome Assembly ◽  
Reference Genome ◽  
Gc Content ◽  
Sweet Pepper ◽  
Mesophyll Cells ◽  
Short Read ◽  
Leveillula Taurica ◽  
Reference Genome Assembly

Powdery mildew of sweet pepper (Capsicum annuum) is an economically important disease. It is caused by Leveillula taurica, an obligate biotrophic ascomycete with a partly endophytic mycelium and haustoria, i.e., feeding structures formed in the mesophyll cells of infected host plant tissues. The molecular basis of its pathogenesis is largely unknown because genomic resources only exist for epiphytically growing powdery mildew fungi with haustoria formed exclusively in epidermal cells of their plant hosts. Here, we present the first reference genome assembly for an isolate of L. taurica isolated from sweet pepper in Hungary. The short read–based assembly consists of 23,599 contigs with a total length of 187.2 Mbp; the scaffold N50 is 13,899 kbp and N90 is 3,522 kbp; and the average GC content is 39.2%. We detected at least 92,881 transposable elements covering 55.5 Mbp (30.4%). BRAKER predicted 19,751 protein-coding gene models in this assembly. Our reference genome assembly of L. taurica is the first resource to study the molecular pathogenesis and evolution of a powdery mildew fungus with a partly endophytic lifestyle.

scholarly journals Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2

2019 ◽  
Vol 102 (4) ◽  
pp. 3254-3258 ◽  
Author(s):  
T. Johnson ◽  
M. Keehan ◽  
C. Harland ◽  
T. Lopdell ◽  
R.J. Spelman ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Short Communication ◽  
Reference Genome ◽  
Pseudoautosomal Region ◽  
Reference Genome Assembly
Sign in / Sign up

Export Citation Format

Share Document