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Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

机译：梅花和果实中表达的序列标签分析及简单重复序列标记的建立

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Background Expressed Sequence Tag (EST) has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST) sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047), among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs) in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65%) and low in the peach (46%), and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.
机译：背景技术表达序列标签（EST）在分子生物学中一直是一种具有成本效益的工具，代表了植物基因组注释，基因表达和比较基因组学的宝贵资源。结果在本研究中，我们构建了梅花和果实的cDNA文库，对该文库的10,123个克隆进行了测序，并获得了8,656个高质量的表达序列标签（EST）序列。 EST被组装成4,473个单基因，由1,492个重叠群和2,981个单子组成，并已存放在NCBI中（登录号：GW868575-GW873047），其中1,294个具有已知或假定功能的ESTs。此外，我们在体育梅花单基因数据集中发现了1,233个推定的简单序列重复（SSR）。我们随机测试了42对潜在SSR侧翼的PCR引物，其中14对被确定为真实型SSR基因座，可以扩增来自20个梅毒假单株植物的多态性条带。我们进一步使用了14对EST-SSR引物对来测试在桃子和李子上的可转移性。结果显示，在这两个物种中，将近89％的引物对产生了目标PCR条带。在李子物种中观察到高水平的标记多态性（65％），在桃子物种中观察到低水平的多态性（46％），对这三个物种的聚类分析表明，这些SSR标记可用于评估遗传关系和遗传多样性。在李属物种中。结论我们已经建立了第一个梅花和果实的cDNA文库，我们的数据为梅花和其他李属物种提供了分子生物学资源。这些资源将用于进一步研究，例如基因组注释，新基因发现，基因功能分析，分子育种，李子种之间的进化和比较基因组学。

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