Complex genome assembly based on long-read sequencing

Zhang, Tianjiao; Jie, Zhou; Gao, Wentao; Jia, Yuran; Wei, Yanan; Wang, Guohua

doi:10.1093/bib/bbac305

Cited by 17 publications

(13 citation statements)

References 64 publications

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“…These repetitive sequences complicate genome sequencing and assembly, making it difficult to accurately obtain or assemble sequences in certain genomic regions [86] . Although second-generation sequencing technologies produce numerous short-read sequences, they are insufficient for obtaining the long-read fragments required for accurate genome assembly, variant detection, and comprehensive annotation of gene structure and function [87] . Therefore, development of long-read sequencing technologies remains a priority.…”

Section: Discussionmentioning

confidence: 99%

Genome sequencing provides potential strategies for drug discovery and synthesis

Zhao,

Zhang,

Sun

et al. 2023

Acupuncture and Herbal Medicine

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Medicinal plants are renowned for their abundant production of secondary metabolites, which exhibit notable pharmacological activities and great potential for drug development. The biosynthesis of secondary metabolites is highly intricate and influenced by various intrinsic and extrinsic factors, resulting in substantial species diversity and content variation. Consequently, precise regulation of secondary metabolite synthesis is of utmost importance. In recent years, genome sequencing has emerged as a valuable tool for investigating the synthesis and regulation of secondary metabolites in medicinal plants, facilitated by the widespread use of high-throughput sequencing technologies. This review highlights the latest advancements in genome sequencing within this field and presents several strategies for studying secondary metabolites. Specifically, the article elucidates how genome sequencing can unravel the pathways for secondary-metabolite synthesis in medicinal plants, offering insights into the functions and regulatory mechanisms of participating enzymes. Comparative analyses of plant genomes allow identification of shared pathways of metabolite synthesis among species, thereby providing novel avenues for obtaining cost-effective biosynthetic intermediates. By examining individual genomic variations, genes or gene clusters associated with the synthesis of specific compounds can be discovered, indicating potential targets and directions for drug development and the exploration of alternative compound sources. Moreover, the advent of gene-editing technology has enabled the precise modifications of medicinal plant genomes. Optimization of specific secondary metabolite synthesis pathways becomes thus feasible, enabling the precise editing of target genes to regulate secondary metabolite production within cells. These findings serve as valuable references and lessons for future drug development endeavors, conservation of rare resources, and the exploration of new resources.

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Section: Discussionmentioning

confidence: 99%

Genome sequencing provides potential strategies for drug discovery and synthesis

Zhao,

Zhang,

Sun

et al. 2023

Acupuncture and Herbal Medicine

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“…Computational tools have been tested for different purposes to study cancer and polyploidy [ 133 , 134 ]. Among these approaches, we would like to highlight studies on nucleotide polymorphisms (SNPs), structural variants (SVs), unique somatic tumor-specific variants [ 135 ], genome annotation, mutation detection, evolutionary analysis, gene function, comparative genomics [ 136 , 137 ], identification of haplotypes, subgenomes, and assembly of whole genomes [ 137 ].…”

Section: Computational Perspectivesmentioning

confidence: 99%

Computational Biology Helps Understand How Polyploid Giant Cancer Cells Drive Tumor Success

Casotti

Meira

Zetum

et al. 2023

Genes

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Precision and organization govern the cell cycle, ensuring normal proliferation. However, some cells may undergo abnormal cell divisions (neosis) or variations of mitotic cycles (endopolyploidy). Consequently, the formation of polyploid giant cancer cells (PGCCs), critical for tumor survival, resistance, and immortalization, can occur. Newly formed cells end up accessing numerous multicellular and unicellular programs that enable metastasis, drug resistance, tumor recurrence, and self-renewal or diverse clone formation. An integrative literature review was carried out, searching articles in several sites, including: PUBMED, NCBI-PMC, and Google Academic, published in English, indexed in referenced databases and without a publication time filter, but prioritizing articles from the last 3 years, to answer the following questions: (i) “What is the current knowledge about polyploidy in tumors?”; (ii) “What are the applications of computational studies for the understanding of cancer polyploidy?”; and (iii) “How do PGCCs contribute to tumorigenesis?”.

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“…Moreover, NGS only sequences short fragments of DNA, which has limitations in producing a complete genome, especially among cases with complex genome or genes with a high rate of duplication and multiple heterozygosities. 6 Third-generation sequencing (TGS) is a new approach adopted in DNA sequencing, which is desired for long molecules. 7 Long-range PCR can generate longer PCR fragments that include intergenic and intragenic regions to identify sequence variants.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Thalassemia screening by third-generation sequencing: Pilot study in a Thai population

Traisrisilp,

Zheng,

Choy

et al. 2023

Obstet Med

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Background Conventional thalassemia screening takes a stepwise approach and has limitations in comprehensively identifying all spectrums of mutations. This study aimed to investigate the performance of third-generation sequencing (TGS) compared to conventional molecular testing. Methods TGS was applied to validate all known variants detected by conventional testing and to detect missing variants in undiagnosed cases. The study was conducted at Maharaj Nakorn Chiang Mai Hospital between December 2021 and April 2022. Results In total, 19 cases were included in this study, among which 52.6% (10/19) had known thalassemia variants, while 47.7% (9/19) cases were undiagnosed by conventional methods. All 16 variants previously detected were validated by TGS, and TGS additionally detected 43.8% (7/16) thalassemia variants for 36.8% (7/19) cases. Conclusion TGS could provide additional genetic diagnoses compared with conventional methods. Further cost-effectiveness studies with a larger sample size are needed to explore the role of TGS in clinical practices.

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Complex genome assembly based on long-read sequencing

Cited by 17 publications

References 64 publications

Genome sequencing provides potential strategies for drug discovery and synthesis

Genome sequencing provides potential strategies for drug discovery and synthesis

Computational Biology Helps Understand How Polyploid Giant Cancer Cells Drive Tumor Success

Thalassemia screening by third-generation sequencing: Pilot study in a Thai population

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