De Novo Assembly and Characterization of Bud, Leaf and Flowers Transcriptome from Juglans Regia L. for the Identification and Characterization of New EST-SSRs
De Novo Assembly and Characterization of Bud, Leaf and Flowers Transcriptome from Juglans Regia L. for the Identification and Characterization of New EST-SSRs
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核桃芽、叶和花转录组的从头组装和表征，用于新 EST-SSR 的鉴定和表征
DOI：
10.3390/f7100247
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发表时间：
2016-10-01
期刊：
影响因子：
2.9
通讯作者：
Zhao, Peng
中科院分区：
文献类型：
--
作者：
Dang, Meng;Zhang, Tian;Zhao, Peng
波斯核桃（Juglans regia L.）是原产于中亚山区的一种重要的温带树种，其坚果和木材都具有重要的生态价值。尽管它很重要，但公共数据库中关于帝王蝶的转录组学资源仍然很少，这限制了基因的发现和育种。在这里，使用Illumina测序技术对王参的四个器官（芽、叶、雌花和雄花）的转录组进行了超过4990万的测序。重新组装得到117,229个unique， N50为1955 bp。基于已知蛋白的序列相似性搜索，共鉴定和注释了20,413个（17.41%）基因。结果表明，共有27,584个具有简单序列重复序列（SSR）基序的单基因被鉴定为潜在的分子标记，并对其中77个EST-SSRs（表达序列标签）样本进行了进一步的扩增验证和多态性评估。接下来，我们开发了39个多态微卫星标记，对11个种群的88个波斯核桃个体进行了筛选。这些标记和转录组学资源将为今后研究波斯核桃和其他核桃品种的种群遗传结构、进化生态学和育种提供参考。
Persian walnut (Juglans regia L.), valued for both its nut and wood, is an ecologically important temperate tree species native to the mountainous regions of central Asia. Despite its importance, there are still few transcriptomic resources in public databases for J. regia, limiting gene discovery and breeding. Here, more than 49.9 million sequencing reads were generated using Illumina sequencing technology in the characterization of the transcriptome of four J. regia organs (bud, leaf, female flowers, and male flowers). De novo assembly yielded 117,229 unigenes with an N50 of 1955 bp. Based on sequence similarity searches against known proteins, a total of 20,413 (17.41%) genes were identified and annotated. A set of 27,584 unigenes with SSR (simple sequence repeats) motifs were identified as potential molecular markers, and a sample of 77 of these EST-SSRs (express sequence tags) were further evaluated to validate their amplification and assess their polymorphism. Next, we developed 39 polymorphic microsatellite markers to screen 88 Persian walnut individuals collected from 11 populations. These markers and transcriptomic resources will be useful for future studies of population genetic structure, evolutionary ecology, and breeding of Persian walnut and other Juglans species.