scholarly journals A high‐quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes

2020 ◽  
Vol 13 (3) ◽  
Author(s):  
Zhenqiao Song ◽  
Caicai Lin ◽  
Piyi Xing ◽  
Yuanyuan Fen ◽  
Hua Jin ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Salvia Miltiorrhiza ◽  
High Quality ◽  
Reference Genome Sequence

scholarly journals Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring

2019 ◽  
Vol 20 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Susan B. Altenbach ◽  
Han-Chang Chang ◽  
Annamaria Simon-Buss ◽  
Toni Mohr ◽  
Naxin Huo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Hexaploid Wheat ◽  
Chinese Spring ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Proteomic Study

scholarly journals 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

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.

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 A novel genome-wide microsatellite resource for species ofEucalyptuswith linkage-to-physical correspondence on the reference genome sequence

2014 ◽  
Vol 15 (2) ◽  
pp. 437-448 ◽  
Author(s):  
Dario Grattapaglia ◽  
Eva M. C. Mamani ◽  
Orzenil B. Silva-Junior ◽  
Danielle A. Faria
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Genome Wide

scholarly journals Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers

2020 ◽  
Vol 7 (3) ◽  
pp. 88
Author(s):  
Rachael Thomas ◽  
Joan U Pontius ◽  
Luke B Borst ◽  
Matthew Breen
Keyword(s):  
Genome Sequence ◽  
Copy Number ◽  
Reference Genome ◽  
Microarray Platform ◽  
Domestic Cat ◽  
Dna Copy Number ◽  
Reference Genome Sequence ◽  
Copy Number Aberrations ◽  
Genome Sequence Assembly ◽  
Dna Copy Number Aberrations

The utility of the domestic cat as a model system for biomedical studies was constrained for many years by the absence of a comprehensive feline reference genome sequence assembly. While such a resource now exists, the cat continues to lag behind the domestic dog in terms of integration into the ‘One Health’ era of molecular medicine. Stimulated by the advances being made within the evolving field of comparative cancer genomics, we developed a microarray platform that allows rapid and sensitive detection of DNA copy number aberrations in feline tumors using comparative genomic hybridization analysis. The microarray comprises 110,456 unique oligonucleotide probes anchored at mean intervals of 22.6 kb throughout the feline reference genome sequence assembly, providing ~350-fold higher resolution than was previously possible using this technique. We demonstrate the utility of this resource through genomic profiling of a feline injection-site sarcoma case, revealing a highly disrupted profile of DNA copy number imbalance involving several key cancer-associated genes including KIT, TP53, PTEN, FAS and RB1. These findings were supported by targeted fluorescence in-situ hybridization analysis, which identified major alterations in chromosome structure, including complex intrachromosomal reorganization events typical of those seen in aggressive soft-tissue sarcomas of other species. We then characterized a second mass that was identified at a nearby site in the same patient almost 12 months later. This mass demonstrated a remarkably conserved genomic profile consistent with a recurrence of the original tumor; however the detection of subtle differences reflected evolution of the tumor over time. These findings exemplify the diverse potential of this microarray platform to incorporate domestic cat cancers into comparative and translational research efforts in molecular oncology.

scholarly journals Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana (Musa Spp.)

2019 ◽  
Vol 10 ◽  
Author(s):  
Denisa Šimoníková ◽  
Alžbeěta Němečková ◽  
Miroslava Karafiátová ◽  
Brigitte Uwimana ◽  
Rony Swennen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Chromosome Painting ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Musa Spp
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