Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus.
Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus.
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多平台测序方法揭示了伪标记病毒中新型的转录组谱。
DOI：
10.3389/fmicb.2017.02708
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发表时间：
2017
影响因子：
5.2
通讯作者：
Boldogkői Z
中科院分区：
文献类型：
--
作者：
Moldován N;Tombácz D;Szűcs A;Csabai Z;Snyder M;Boldogkői Z
第三代测序是一种新兴技术，能够解决早期方法无法解决的几个问题，包括识别转录本异构体和重叠转录本。在这项研究中，我们使用长读段测序分析伪狂犬病病毒（PRV）转录组，包括Oxford Nanopore Technologies MinION，PacBio RS-II和Illumina HiScanSQ平台。我们还使用了来自我们之前的短读段和长读段测序研究的数据来比较结果并确认所获得的数据。我们的研究发现了19个以前未知的蛋白质编码基因，它们都是早期注释的较长PRV基因的5′截短形式。此外，我们还检测到19种非编码RNA，包括5′和3′截短的无框内ORF的转录物、反义RNA以及由病毒基因组中以前未检测到转录的部分编码的RNA分子。这项研究还导致了三个复杂的成绩单和50个不同长度的异构体，包括转录起始和结束变异的鉴定。我们还检测到121个新的转录本重叠，和两个转录本重叠的PRV复制起点。此外，计算机分析显示了145个上游ORF，其中许多位于转录本较长的5′异构体上。
Third-generation sequencing is an emerging technology that is capable of solving several problems that earlier approaches were not able to, including the identification of transcripts isoforms and overlapping transcripts. In this study, we used long-read sequencing for the analysis of pseudorabies virus (PRV) transcriptome, including Oxford Nanopore Technologies MinION, PacBio RS-II, and Illumina HiScanSQ platforms. We also used data from our previous short-read and long-read sequencing studies for the comparison of the results and in order to confirm the obtained data. Our investigations identified 19 formerly unknown putative protein-coding genes, all of which are 5′ truncated forms of earlier annotated longer PRV genes. Additionally, we detected 19 non-coding RNAs, including 5′ and 3′ truncated transcripts without in-frame ORFs, antisense RNAs, as well as RNA molecules encoded by those parts of the viral genome where no transcription had been detected before. This study has also led to the identification of three complex transcripts and 50 distinct length isoforms, including transcription start and end variants. We also detected 121 novel transcript overlaps, and two transcripts that overlap the replication origins of PRV. Furthermore, in silico analysis revealed 145 upstream ORFs, many of which are located on the longer 5′ isoforms of the transcripts.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
3.7
作者：
Boldogköi Z
通讯作者：
Boldogköi Z
影响因子：
4.6
作者：
Balázs Z;Tombácz D;Szűcs A;Csabai Z;Megyeri K;Petrov AN;Snyder M;Boldogkői Z
通讯作者：
Boldogkői Z
影响因子：
--
作者：
Card, J Patrick;Enquist, Lynn W
通讯作者：
Enquist, Lynn W
影响因子：
5.4
作者：
LUO, G;TAYLOR, J
通讯作者：
TAYLOR, J