马铃薯转录组数据中的病毒序列挖掘

Identification of Virus Sequences in Potato Transcriptome Data

摘要

转录组测序数据中包含寄主所感染的病毒序列信息。为分析和验证马铃薯转录组数据中存在的病毒序列，试验收集了关于马铃薯块茎发育、抗病、抗逆等研究的9个马铃薯转录组测序数据样本，过滤掉来源于马铃薯转录本的读段，组装并与病毒数据库进行本地比对，获得样本中相关病毒序列的种类和数量信息。病毒来源的读段在各样本中普遍存在，占总读段的0.12%~20.24%。这些读段组装得到10种植物病毒，包括9种RNA病毒和1种DNA病毒。其中来源于马铃薯S病毒（Potato virus S，PVS）的序列最多，组装得到28条近全长序列。进一步系统进化分析表明，这些样品中同时存在PVS^A和PVS O两种株系类型。此外，通过RT-PCR对转录组数据原始样本中的马铃薯H病毒（Potato virus H，PVH）、马铃薯卷叶病毒（Potato leafroll virus，PLRV）、马铃薯 M 病毒（Potato virus M，PVM）、PVS、马铃薯 X 病毒（Potato virus X，PVX）和马铃薯 Y 病毒（Potato virus Y，PVY）6 种病毒进行检测，结果显示RT-PCR 验证结果与测序数据组装结果基本一致。该研究为马铃薯病毒多样性和进化分析提供一种高通量测序的方法。

Abstract

Transcriptome sequencing data often contain valuable information about viruses infecting the host. In order to analyze and validate the presence of virus sequences in potato transcriptome data, nine transcriptome sequencing data samples related to potato tuber development, disease resistance, and stress tolerance were collected. After filtering out reads originating from potato transcripts, the remaining unmapped reads were assembled and locally aligned against a virus database to obtain information on the types and quantities of virus sequences in these samples. The results revealed that reads originating from viruses were commonly present in all samples, accounting for 0.12% to 20.24% of the total reads. These reads were assembled into sequences representing 10 different plant viruses, including nine RNA viruses and one DNA virus. Among them, sequences derived from potato virus S (PVS) were the most abundant, with 28 nearly full-length sequences assembled. Further phylogenetic analysis indicated the coexistence of two strain types, PVS^A and PVS O, in these samples. Additionally, reverse transcription-polymerase chain reaction (RT-PCR) was performed to detect six viruses including potato virus H (PVH), potato leafroll virus (PLRV), potato virus M (PVM), potato virus S (PVS), potato virus X (PVX), and potato virus Y (PVY) in the original transcriptome data samples. The RT-PCR validation results were generally consistent with the assembly results from the sequencing data. Overall, this study provides a high-throughput approach for analyzing the diversity and evolution of viruses in potatoes.

关键词

马铃薯 / 病毒 / 高通量测序 / 转录组 / RT-PCR

Key words

potato / virus / high-throughput sequencing / transcriptome / RT-PCR

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基金资助

国家自然科学基金(31971989)

国家马铃薯产业技术体系(CARS-09-P07)