Iandolino Alberto, Nobuta Kan, da Silva Francisco Goes, Cook Douglas R, Meyers Blake C
Department of Plant Pathology and College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616, USA.
BMC Plant Biol. 2008 May 12;8:53. doi: 10.1186/1471-2229-8-53.
Vitis vinifera (V. vinifera) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry.
The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was approximately 49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera.
The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not previously reported in grapes but comparable to that reported in other plant species. Finally, we developed a novel web-based, public resource for utilization of the grape MPSS data [1].
酿酒葡萄（Vitis vinifera）是用于葡萄酒生产的主要葡萄品种，其产业在全球每年价值数十亿美元。为了维持和增加葡萄产量，有必要了解葡萄品种的基因构成。在此，我们使用大规模平行签名测序（MPSS）进行mRNA分析，并将其与可用的表达序列标签（EST）数据相结合。这些基于标签的技术不需要基因组序列的先验知识，非常适合转录谱分析。MPSS的序列深度使我们能够捕获和定量葡萄浆果发育特定阶段的几乎所有转录本。
使用大规模平行签名测序（MPSS）确定了II期葡萄浆果转录本的数量和相对丰度。共获得了2,635,293个17碱基和2,259,286个20碱基的签名，分别代表至少30,737和26,878个不同的序列。每个签名的平均标准化丰度约为49 TPM（每百万转录本）。将MPSS签名与可用的葡萄属物种EST和单基因集进行比较表明，6,430个不同的重叠群和2,190个单拷贝与至少一个MPSS签名完全匹配。在匹配的序列中，EST是从浆果以外的组织或不同发育阶段的浆果中鉴定出来的。与已知葡萄EST不匹配的额外MPSS签名可以扩展我们对酿酒葡萄转录组的认识，特别是当这些数据用于协助注释酿酒葡萄的全基因组序列时。
此处呈现的MPSS数据不仅比以前基于EST的分析达到了更高的饱和度水平，而且在此过程中，扩展了葡萄浆果在成熟开始前独特发育阶段的已知转录本集。MPSS数据集还揭示了葡萄中以前未报道过但与其他植物物种中报道的类似的反义表达证据。最后，我们开发了一个基于网络的新型公共资源，用于利用葡萄MPSS数据[1]。
