Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research 长读测序-病毒转录组研究中的一个强大工具
Highlights
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Long-read sequencing (LRS) has revolutionized genomics and transcriptomics. These third-generation approaches have a relatively low throughput compared to short-read sequencing, but they can solve problems that used to be a challenge for earlier techniques.
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The PacBio and ONT sequencing are able to read full-length transcripts and allow the direct study of base modifications on both DNA and RNA molecules. Nanopore technology is able to sequence RNA directly.
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LRS has revealed a much more complex viral transcriptome. Among other capabilities, these techniques allow the discrimination between multispliced transcript variants, RNA length isoforms, embedded RNAs, and polycistronic RNA molecules.
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The viral genomes express a highly complex pattern of transcriptional overlaps, the function of which continues to remain unknown.
Long-read sequencing (LRS) has become increasingly popular due to its strengths in de novo assembly and in resolving complex DNA regions as well as in determining full-length RNA molecules. Two important LRS technologies have been developed during the past few years, including single-molecule, real-time sequencing by Pacific Biosciences, and nanopore sequencing by Oxford Nanopore Technologies. Although current LRS methods produce lower coverage, and are more error prone than short-read sequencing, these methods continue to be superior in identifying transcript isoforms including multispliced RNAs and transcript-length variants as well as overlapping transcripts and alternative polycistronic RNA molecules. Viruses have small, compact genomes and therefore these organisms are ideal subjects for transcriptome analysis with the relatively low-throughput LRS techniques. Recent LRS studies have multiplied the number of previously known transcripts and have revealed complex networks of transcriptional overlaps in the examined viruses.
长读测序(LRS)彻底改变了基因组学和转录组学。
与短读测序相比，这些第三代测序方法的通量相对较低，但它们可以解决以前技术面临的挑战。
PacBio和ONT测序能够读取全长转录本，并允许直接研究DNA和RNA分子上的碱基修饰。
纳米孔技术能够直接对RNA进行测序。
LRS揭示了一个更为复杂的病毒转录组。
在其他功能中，这些技术允许区分多条带转录变种、RNA长度亚型、嵌入RNA和多顺反子RNA分子。
病毒基因组表达一种高度复杂的转录重叠模式，其功能仍不清楚。
长读测序(LRS)由于其在从头组装、解析复杂DNA区域以及确定全长RNA分子方面的优势而越来越受欢迎。
在过去的几年中，两项重要的LRS技术得到了发展，包括太平洋生物科学公司的单分子实时测序和牛津纳米孔技术公司的纳米孔测序。
尽管目前的LRS方法的覆盖率较低，而且比短读测序更容易出错，但这些方法在识别转录子异构体方面仍然具有优势，这些异构体包括多组织序列RNA和转录长度变异，以及重叠转录本和替代的多顺反子RNA分子。
病毒具有小而紧凑的基因组，因此这些生物体是使用相对低通量LRS技术进行转录组分析的理想对象。
最近的LRS研究增加了已知转录本的数量，并揭示了被检测病毒中复杂的转录重叠网络。