Article
Biochemical Research Methods
Quang Tran, Alexej Abyzov
Summary: The study found that different breakpoints for deletions and duplications at the same locus provide direct evidence that these multi-allelic copy number variants arise from multiple independent ancestral mutations. To address the problem of large gaps in alignment affecting single-nucleotide breakpoint resolution, a memory-efficient implementation called LongAGE was developed.
Article
Biotechnology & Applied Microbiology
Scott Hotaling, Edward R. Wilcox, Jacqueline Heckenhauer, Russell J. Stewart, Paul B. Frandsen
Summary: Highly accurate long-reads generated with HiFi or analogous technologies are crucial for improving genome assembly quality in plants and animals, especially when resources limit the choice to one type of sequencing data.
Article
Biotechnology & Applied Microbiology
Guoshun Xu, Liwen Zhang, Xiaoqing Liu, Feifei Guan, Yuquan Xu, Haitao Yue, Jin-Qun Huang, Jieyin Chen, Ningfeng Wu, Jian Tian
Summary: This study compares the application of different DNA sequencing methods in soil metagenomics research. The results show that combining long-read and short-read data can increase the length of metagenomic sequences and gene pool, and has significant advantages in studying natural product biosynthetic genes in soil microbiomes.
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Biology
Hui-su Kim, Sungwon Jeon, Yeonkyung Kim, Changjae Kim, Jihun Bhak, Jong Bhak
Summary: The study updated the previous KOREF assembly to a new chromosome-level haploid assembly, KOREF_S1v2.1, which is the first of its kind with high contiguity and accuracy. By using a trio-binning method, the parental genome information was successfully phased, achieving a near-complete haploid assembly.
Article
Biochemical Research Methods
Sandra Romain, Claire Lemaitre
Summary: SVJedi-graph is a novel method for SV genotyping that utilizes a variation graph to accurately determine the presence and copy number of SVs in sequenced individuals. Unlike other methods, SVJedi-graph avoids bias towards reference alleles when genotyping close or overlapping SVs, and consistently maintains high genotyping accuracy.
Article
Genetics & Heredity
Sigmund Ramberg, Bjorn Hoyheim, Tone-Kari Knutsdatter Ostbye, Rune Andreassen
Summary: This study successfully generated a full-length mRNA transcriptome from Atlantic salmon liver, head-kidney, and gill tissues, consisting of 71461 full-length mRNAs. Validation of 25% of known transcripts and discovery of new isoforms were achieved through the pipeline developed. The results contribute significantly to genomic research on Atlantic salmon.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Kez Cleal, Duncan M. Baird
Summary: Structural variation (SV) is important in genome evolution and disease, and Dysgu is a tool that accurately detects SVs using paired-end or long-read sequencing, with high sensitivity and fast running speed.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Jinxin Zhang, Changsheng Nie, Xinghua Li, Xiurong Zhao, Yaxiong Jia, Jianlin Han, Yu Chen, Liang Wang, Xueze Lv, Weifang Yang, Kaiyang Li, Jianwei Zhang, Zhonghua Ning, Haigang Bao, Chunjiang Zhao, Junying Li, Lujiang Qu
Summary: This study explored structural variants (SVs) in chickens using PacBio technology and detected a high number of SVs compared to Illumina short-read technology. It was found that during chicken domestication, beneficial SVs were retained while deleterious SVs were eliminated. This study contributes to our understanding of genetic characteristics and genomic diversity in chickens.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Muhammad Farooq, Rubab Zahra Naqvi, Imran Amin, Atiq Ur Rehman, Muhammad Asif, Shahid Mansoor
Summary: In this study, we sequenced the G. arboreum transcriptome and identified important events including different types of splicing, polyadenylation, and transcript fusion. We further validated some candidate transcripts, which contributes to the understanding of the resistance mechanisms in this particular germplasm.
Article
Biochemistry & Molecular Biology
Claire Merot, Kristina S. R. Stenlokk, Clare Venney, Martin Laporte, Michel Moser, Eric Normandeau, Mariann Arnyasi, Matthew Kent, Clement Rougeux, Jullien M. Flynn, Sigbjorn Lien, Louis Bernatchez
Summary: Nascent pairs of ecologically differentiated species provide an opportunity to study the genetic architecture of speciation. By utilizing long-read sequencing, we analyzed the genomic patterns of differentiation between sympatric species pairs of lake whitefish. We found that structural variants (SVs), particularly insertions and deletions of transposable elements, play a significant role in species differentiation. The integration of different sequencing technologies allows us to incorporate SVs into speciation genomics.
Review
Biochemical Research Methods
Mian Umair Ahsan, Qian Liu, Jonathan Elliot Perdomo, Li Fang, Kai Wang
Summary: As long-read sequencing technologies become more popular, various methods have been developed for detecting and analyzing structural variants (SVs) from long reads. These methods are needed to adapt to the unique challenges and opportunities presented by long-read sequencing. This review summarizes more than 50 long-read-based methods for SV detection, genotyping, and visualization, and discusses how new telomere-to-telomere genome assemblies and pangenome efforts can enhance accuracy and drive the development of SV callers in the future.
Article
Biochemistry & Molecular Biology
Gabriele Bonetti, William Cozza, Andrea Bernini, Jurgen Kaftalli, Chiara Mareso, Francesca Cristofoli, Maria Chiara Medori, Leonardo Colombo, Salvatore Martella, Giovanni Staurenghi, Anna Paola Salvetti, Benedetto Falsini, Giorgio Placidi, Marcella Attanasio, Grazia Pertile, Mario Bengala, Francesca Bosello, Antonio Petracca, Fabiana D'Esposito, Benedetta Toschi, Paolo Lanzetta, Federico Ricci, Francesco Viola, Giuseppe Marceddu, Matteo Bertelli
Summary: This study investigates the use of PacBio sequencing to detect genetic variants in low-complexity regions, such as the ORF15 exon of RPGR, and interpret their pathogenicity through structural studies. The results show that PacBio sequencing is more accurate in detecting these variants and provides a way to predict their pathogenicity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Marek Kokot, Adam Gudys, Heng Li, Sebastian Deorowicz
Summary: The cost of maintaining a large amount of data generated by third-generation sequencing has become a significant concern in genomic research. Existing algorithms for compressing long reads have only a slight advantage over general-purpose gzip. In this study, we introduce CoLoRd, an algorithm that can significantly reduce the size of third-generation sequencing data without compromising the accuracy of downstream analyses.
Article
Biology
Jingya Yu, Mingze Xia, Yongcui Wang, Xiaofeng Chi, Hao Xu, Shilong Chen, Faqi Zhang
Summary: This study sequenced and assembled the chloroplast genome of Artemisia tangutica Pamp. and compared it with other species in the Artemisia genus. The hybrid assembly method produced the most accurate chloroplast genome, and comparative analysis revealed similarities and variations in coding regions and intergenic spacers. Phylogenetic analysis provided insights into the identification and evolution of Artemisia species.
Article
Cell & Tissue Engineering
Jingjun Li, Jing Ma, Guofeng Meng, Hong Lin, Sharon Wu, Jamie Wang, Jie Luo, Xiaohong Xu, David Tough, Matthew Lindon, Inmaculada Rioja, Jing Zhao, Hongkang Mei, Rab Prinjha, Zhong Zhong
STEM CELL RESEARCH
(2016)
Article
Biochemical Research Methods
Guofeng Meng, Axel Mosig, Martin Vingron
BMC BIOINFORMATICS
(2010)
Article
Cardiac & Cardiovascular Systems
Jianfeng Shi, Renyang Tong, Meng Zhou, Yu Gao, Yichao Zhao, Yifan Chen, Wenhua Liu, Gaoxiang Li, Dong Lu, Guofeng Meng, Liuhua Hu, Ancai Yuan, Xiyuan Lu, Jun Pu
Summary: The study revealed that the circadian protein Rev-erb alpha is functionally expressed in platelets and enhances platelet activation and thrombus formation. This suggests that Rev-erb alpha could be a promising therapeutic target for managing thrombosis-related cardiovascular diseases.
EUROPEAN HEART JOURNAL
(2022)
Article
Biochemical Research Methods
Dong Lu, Rongrong Pan, Wenxuan Wu, Yanyan Zhang, Shensuo Li, Hong Xu, Jialan Huang, Jianhua Xia, Qun Wang, Xin Luan, Chao Lv, Weidong Zhang, Guofeng Meng
Summary: Drug target discovery is crucial for understanding the mechanism of drug actions. Existing approaches are often time-consuming and unable to identify tissue-specific and weakly interacting targets. In this study, we proposed an integrated method, FL-DTD, which predicts drug interacting targets in a tissue-specific manner based on the hypothesis that cells respond to drug perturbation by activating feedback loops. Experimental results showed that FL-DTD accurately predicted drug targets and could be used for drug target discovery.
BRIEFINGS IN BIOINFORMATICS
(2022)
Meeting Abstract
Cardiac & Cardiovascular Systems
J. Shi, R. Tong, M. Zhou, Y. Gao, Y. Zhao, Y. Chen, W. Liu, G. Li, D. Lu, G. Meng, L. Hu, A. Yuan, X. Lu, J. Pu
EUROPEAN HEART JOURNAL
(2022)
Article
Biology
Axel Mosig, Meng Guofeng, Baerbel M. R. Stadler, Peter F. Stadler
THEORY IN BIOSCIENCES
(2007)
