Short Communication: New alleles at the BoLA-DQA1 locus in Holstein–Fresian cattle

2015 ◽  
Vol 95 (2) ◽  
pp. 161-164
Author(s):  
Dominika Kułaj ◽  
Joanna Pokorska ◽  
Marian Ormian ◽  
Magdalena Dusza
Keyword(s):  
Short Communication ◽  
Cattle Population ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Holstein Friesian ◽  
Dqa1 Locus ◽  
First Time ◽  
Friesian Cattle ◽  
Generation Sequencing ◽  
New Alleles

Kułajaj, D., Pokorska, J., Ormian, M. and Dusza, M. 2015. Short Communication: New alleles at the BoLA-DQA1 locus in Holstein Fresian cattle. Can. J. Anim. Sci. 95: 161–164. The aim of the study was to analyze genetic polymorphism at locus BoLA-DQA1 in Polish Holstein-Friesian cattle, using next generation sequencing technology (Miseq sequencer – Illumina). In the studied cattle population we identified 14 alleles, of which three were determined for the first time (BoLA-DQA1*0106, BoLA-DQA1*3201, BoLA-DQA1*3301). The frequencies of these alleles were respectively: 0.0423, 0.0282, 0.0282. At locus BoLA-DQA1 the highest frequency was found for the BoLA-DQA1*10011 and BoLA-DQA1*0101 alleles and their frequencies were respectively: 0.3592 and 0.2606. The frequencies of other alleles identified in the studied population ranged from 0.0070 to 0.0704. The results obtained in this study indicate that the BoLA-DQA1 locus is highly polymorphic and new alleles are still identifiable.

scholarly journals Identification of a Novel Papillomavirus Type (MfoiPV1) Associated with Acrochordon in a Stone Marten (Martes foina)

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 539
Author(s):  
Urška Kuhar ◽  
Diana Žele Vengušt ◽  
Urška Jamnikar-Ciglenečki ◽  
Gorazd Vengušt
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Manifestation ◽  
Skin Tumor ◽  
Wild Animals ◽  
Stone Marten ◽  
Sequencing Technology ◽  
Martes Foina ◽  
Tumor Sample ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Papillomaviruses (PVs) are an extremely large group of viruses that cause skin and mucosal infections in humans and various domestic and wild animals. Nevertheless, there is limited knowledge about PVs in wildlife hosts, including mustelid species. This study describes a case in stone marten (Martes foina) with a clinical manifestation of skin tumor, which is rather atypical for infections with PVs. The result of the papillomavirus PCR performed on the skin tumor sample was positive, and the complete PV genome was determined in the studied sample using next-generation sequencing technology. The analysis of the PV genome revealed infection of the stone marten with a putative new PV type belonging to the Dyonupapillomavirus genus. The proposed new stone marten PV type was named MfoiPV1.

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.

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