Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus.
Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus.
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DOI：
10.3390/v13040579
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发表时间：
2021-03-30
期刊：
影响因子：
--
通讯作者：
Boldogkői Z
中科院分区：
文献类型：
--
作者：
Torma G;Tombácz D;Csabai Z;Moldován N;Mészáros I;Zádori Z;Boldogkői Z
非洲猪瘟病毒（African swine fever virus，ASFV）是一种大DNA病毒，属于猪瘟病毒科（Asfarviridae）。尽管它在农业上很重要，但人们对这种病原体的基本分子机制知之甚少。短读段测序（SRS）可以产生大量的高精度测序读段用于转录组分析，但它对于全面注释转录组是低效的。长读段测序（LRS）可以克服SRS的一些局限性，但它也有缺点，如低覆盖率和高错误率。这两种方法的局限性可以通过结合使用这些技术来克服。在这项研究中，我们使用Illumina SRS和Oxford Nanopore Technologies LRS平台，采用多种文库制备方法（扩增和直接cDNA测序和天然RNA测序）构建ASFV转录组图谱。这项工作确定了许多新的转录本和转录异构体，并注释了先前描述的RNA的精确末端。本研究鉴定了一种新的ASFV转录物，即复制起点相关RNA。此外，我们发现了几个嵌套基因嵌入到更大的典型基因。与目前认为ASFV转录物是单顺反子的观点相反，我们检测到了显著程度的多顺反子现象，尽管这些转录物中的大部分以低丰度表达。还发现了多方面的转录重叠网络。
African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Short-read sequencing (SRS) can produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for comprehensively annotating transcriptomes. Long-read sequencing (LRS) can overcome some of SRS’s limitations, but it also has drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the ASFV transcriptomic atlas. This work identified many novel transcripts and transcript isoforms and annotated the precise termini of previously described RNAs. This study identified a novel species of ASFV transcripts, the replication origin-associated RNAs. Additionally, we discovered several nested genes embedded into larger canonical genes. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism, although a large proportion of these transcripts are expressed in low abundance. A multifaceted meshwork of transcriptional overlaps was also discovered.
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影响因子：
3.7
作者：
Boldogköi Z
通讯作者：
Boldogköi Z
DOI：
10.1073/pnas.1207846109
发表时间：
2012-09-11
影响因子：
11.1
作者：
Lee, Sooncheol;Liu, Botao;Qian, Shu-Bing
通讯作者：
Qian, Shu-Bing
多平台测序方法揭示了伪标记病毒中新型的转录组谱。
影响因子：
5.2
作者：
Moldován N;Tombácz D;Szűcs A;Csabai Z;Snyder M;Boldogkői Z
通讯作者：
Boldogkői Z
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
--
作者：
Carrascosa, Angel L;Bustos, M Jose;de Leon, Patricia
通讯作者：
de Leon, Patricia