A Hitchhiker's Guide to long-read genomic analysis

Genome Research, Journal Year: 2025, Volume and Issue: 35(4), P. 545 - 558

Published: April 1, 2025

Over the past decade, long-read sequencing has evolved into a pivotal technology for uncovering hidden and complex regions of genome. Significant cost efficiency, scalability, accuracy advancements have driven this evolution. Concurrently, novel analytical methods emerged to harness full potential long reads. These enabled milestones such as first fully completed human genome, enhanced identification understanding genomic variants, deeper insights interplay between epigenetics variation. This mini-review provides comprehensive overview latest developments in DNA analysis, encompassing reference-based de novo assembly approaches. We explore entire workflow, from initial data processing variant calling annotation, focusing on how these improve our ability interpret wide array variants. Additionally, we discuss current challenges, limitations, future directions field, offering detailed examination state-of-the-art bioinformatics sequencing.

Language: Английский

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Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics

Genome Research, Journal Year: 2024, Volume and Issue: 34(11), P. 1735 - 1746

Published: Nov. 1, 2024

RNA isoform diversity, produced via alternative splicing, and usage of transcription start poly(A) sites, results in varied transcripts being derived from the same gene. Distinct isoforms can play important biological roles, including by changing sequences or expression levels protein products. The first single-cell approaches to sequencing—and later, spatial approaches—which are now widely used for identification differentially expressed genes, rely on short reads offer ability transcriptomically compare different cell types but limited their measure differential expression. More recently, long-read sequencing methods have been combined with technologies order characterize In this review, we provide an overview emergence discuss challenges associated implementation these interpretation data. We opportunities they understanding relationships between distinct variable elements transcript molecules highlight some ways which isoforms’ roles development pathology. Single-nucleus sequencing, a special case approach, is also discussed. attempt cover both limitations significant potential expanding our still-limited isoforms.

Language: Английский

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Direct RNA sequencing in plants: practical applications and future perspectives

Plant Communications, Journal Year: 2024, Volume and Issue: 5(11), P. 101064 - 101064

Published: Aug. 18, 2024

The transcriptome serves as a bridge that links genomic variation to phenotypic diversity. A vast number of studies using next-generation RNA sequencing (RNA-seq) over the last 2 decades have emphasized essential roles plant in response developmental and environmental conditions, providing numerous insights into dynamic changes, evolutionary traces, elaborate regulation transcriptome. With substantial improvement accuracy throughput, direct (DRS) has emerged new powerful platform for precise detection native full-length transcripts, overcoming many limitations such read length PCR bias are inherent short-read RNA-seq. Here, we review recent advances dissecting complexity diversity transcriptomes DRS main technological approach, covering aspects metabolism, including novel isoforms, poly(A) tails, modification, propose comprehensive workflow processing data. Many challenges application plants, need machine learning tools tailored transcriptomes, remain be overcome, together outline future biological questions can addressed by DRS, allele-specific modification. This technology provides convenient support on which connection distinct features is tightly built, sustainably refining our understanding functions

Language: Английский

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Revolutionizing genomics and medicine—one long molecule at a time

Genome Research, Journal Year: 2024, Volume and Issue: 34(11), P. ix - xi

Published: Nov. 1, 2024

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