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三代测序探索者每周文献精选(08.22-08.28)

作者: 点击:226 发布时间:2022-08-30

三代测序探索者每周文献精选

(08.22-08.28)


01

Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres
https://doi.org/10.1186/s13059-022-02751-6
杂志:Genome Biology(IF=17.906)
发表时间:2022.08.26
作者:Kar-Tong Tan(Dana-Farber Cancer Institute)
通讯作者:李恒(Dana-Farber Cancer Institute)
解读链接:GB | Nanopore测序数据中端粒所在处序列repeat-calling错误的鉴定和纠正


三代测序探索者每周文献精选(08.22-08.28)

Fig1. Strand-specific nanopore basecalling errors are pervasive at telomeres.


亮点:作者在将nanopore序列比对到近测序和组装的人类基因组CHM13中的端粒区域进行分析时发现,基因组端粒区域经常以链特异性的方式被错误地标记为其他类型的重复。为了解决端粒上的这些碱基calling错误,作者通过提供更多的端粒训练示例来调整nanopore碱基calling程序。在训练数据上可以看到在端粒和亚端粒区域的basecalls准确性显著改善,并在染色体末端的错误明显减少。



02

Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis
https://www.nature.com/articles/s41589-022-01102-7
杂志:Nature Chemical Biology(IF=16.174)
发表时间:2022.08.22
作者:Yu Imai(Shinshu University
通讯作者:Frédéric J. Veyrier(INRS-Centre Armand-Frappier Santé Biotechnologie)
三代测序探索者每周文献精选(08.22-08.28)

Fig2. The BGC of evybactin. Gene alignment of the BGC of evybactin in the producer strain. A–E are NRPS genes, and T1 and T2 are transporter genes.


亮点:The biosynthetic gene cluster (BGC) of evybactin was determined using bioinformatic analysis of the genome. The genome was sequenced by a combination of Nanopore and Illumina reads (Microbial Genome Sequencing Center (MiGS)) and assembled into two contigs with a total size of 5.5megabases.The BGC of evybactin was identified as NRPS with a core BGC spanning 49.6 kilobases.



03

Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci
https://www.nature.com/articles/s41467-022-32358-1
杂志:Nature Communications(IF=17.694)
发表时间:2022.08.24
作者:Kensuke Yamaguchi(Tokyo Medical and Dental University)
通讯作者:Yuta Kochi(Tokyo Medical and Dental University)
三代测序探索者每周文献精选(08.22-08.28)

Fig3. Long-read capture RNA-sequencing for CDS incomplete isoforms.


亮点:We conducted long-read RNA-sequencing for the CDSI isoforms (37 isoforms in total), whose i-rQTL signals were co-localized with disease GWAS signals and whose unique splice junctions showed significant sQTL signals in LeafCutter analysis (FDR ≤ 0.05). The cDNAs were sequenced by MinION (Oxford Nanopore Technologies). We performed conventional long-read RNA-seq using 300 ng of total RNA from LCL and THP-1, then sequenced them using GridION X5 (Oxford Nanopore Technologies).



04

Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family
https://www.nature.com/articles/s41467-022-32260-w
杂志:Nature Communications(IF=17.694)
发表时间:2022.08.22
作者:Sammy Nyongesa(INRS-Centre Armand-Frappier Santé Biotechnologie)
通讯作者:Frédéric J. Veyrier(INRS-Centre Armand-Frappier Santé Biotechnologie)
三代测序探索者每周文献精选(08.22-08.28)

Fig4.Core genome-based phylogeny of rod-shaped, coccoid and MuLDi Neisseriaceae.


亮点: The Neisseriales order comprises the family Chromobacteriaceae and the family Neisseriaceae and more recently three additional families have been suggested, AquaspirillaceaeChitinibacteraceae and Leeiaceae. The family Neisseriaceae includes 12 genera . We selected species from each of these Neisseriaceae genera and used SMRT (PacBio) and Minion (Nanopore) technologies to obtain 21 closed genomes . Genomes obtained in this study were combined with Neisseriaceae draft genomes from the NCBI database to calculate the Average Nucleotide Identity (ANI). This enabled us to identify 75 Neisseriaceae species with genome ANI > 96%. 


05

Genomic Variation in the Tea Leafhopper Reveals the Basis of Adaptive Evolution
https://doi.org/10.1016/j.gpb.2022.05.011
杂志:Genomics, Proteomics & Bioinformatics(IF=6.409)
发表时间:2022.08.28
作者:Qian Zhao(福建农林大学)
通讯作者:Minsheng You(福建农林大学)
三代测序探索者每周文献精选(08.22-08.28)

Fig5. Genomic characterization of Empoasca onukii and comparison with other insect genomes. A. Genomic characterization of the sequenced E. onukii. Track


亮点: In Asia, the tea green leafhopper (TGL), Empoasca onukii (Hemiptera: Cicadellidae), represents the most devastating pest across tea plantations, causing up to 50% economic loss of tea production annually. We generated a chromosome-level genome assembly of the E. onukii by integrating Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and high-throughput chromosome conformation capture (Hi-C). This high-quality genome resource enabled us to investigate the genetic basis of chemoreception and detoxification in this insect, key to adapting to new environments.



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