Melon Transcriptome Characterization: Simple Sequence Repeats and Single Nucleotide Polymorphisms Discovery for High Throughput Genotyping across the Species
Melon Transcriptome Characterization: Simple Sequence Repeats and Single Nucleotide Polymorphisms Discovery for High Throughput Genotyping across the Species
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DOI：
10.3835/plantgenome2011.01.0003
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发表时间：
2011-07-01
期刊：
影响因子：
4.2
通讯作者：
Belen Pico, Maria
中科院分区：
文献类型：
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作者：
Miguel Blanca, Jose;Canizares, Joaquin;Belen Pico, Maria
甜瓜（Cucumis梅洛L.）是世界上价值最高的水果作物之一。一些基因组工具可用于这种作物，包括桑格转录组。我们报告了689，054 C的产生。梅洛高质量的表达序列标签（EST）从两个454测序运行，使用标准化和非标准化的互补DNA（cDNA）文库制备的四个基因型属于两个C.梅洛亚种和主要商业类型。将454个EST与桑格可用的EST组合并重新组装成53，252个单基因。超过63%的unigenes用Gene Ontology（GO）术语进行了功能注释，21%具有已知的拟南芥（Arabidopsis thaliana（L.）嘿注释分布遵循类似的趋势，比拟南芥的报道，这表明数据集代表了一个相当完整的甜瓜转录组。此外，我们确定了一组3298个具有微卫星基序的unigenes和14，417个具有单核苷酸变体的序列，其中11，655个单核苷酸多态性符合高通量基因分型平台的使用标准，453个可以检测到切割扩增多态性序列（CAPS）。一组标记被验证，其中90%的多态性在一些变量C。梅洛品种。这个转录组为生物学研究提供了一个宝贵的新工具，当它包括以前没有描述的转录本时更是如此。它被用于基因组注释，并提供了大量的标记，这将有助于加快培育新甜瓜品种的过程。
Melon (Cucumis melo L.) ranks among the highest-valued fruit crops worldwide. Some genomic tools are available for this crop, including a Sanger transcriptome. We report the generation of 689,054 C. melo high-quality expressed sequence tags (ESTs) from two 454 sequencing runs, using normalized and nonnormalized complementary DNA (cDNA) libraries prepared from four genotypes belonging to the two C. melo subspecies and the main commercial types. 454 ESTs were combined with the Sanger available ESTs and de novo assembled into 53,252 unigenes. Over 63% of the unigenes were functionally annotated with Gene Ontology (GO) terms and 21% had known orthologs of Arabidopsis thaliana (L.) Heynh. Annotation distribution followed similar tendencies than that reported for Arabidopsis thaliana, suggesting that the dataset represents a fairly complete melon transcriptome. Furthermore, we identified a set of 3298 unigenes with microsatellite motifs and 14,417 sequences with single nucleotide variants of which 11,655 single nucleotide polymorphism met criteria for use with high-throughput genotyping platforms, and 453 could be detected as cleaved amplified polymorphic sequence (CAPS). A set of markers were validated, 90% of them being polymorphic in a number of variable C. melo accessions. This transcriptome provides an invaluable new tool for biological research, more so when it includes transcripts not described previously. It is being used for genome annotation and has provided a large collection of markers that will allow speeding up the process of breeding new melon varieties.