Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites.
Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites.
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苔藓基因 SSR 标记的鉴定以及 24 种藻类和植物基因指数的比较分析揭示了微卫星的物种特异性而不是群体特异性特征。
DOI：
10.1186/1471-2229-6-9
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发表时间：
2006-05-30
影响因子：
5.3
通讯作者：
Reski R
中科院分区：
文献类型：
--
作者：
von Stackelberg M;Rensing SA;Reski R
小壶藓（Physcomitrella patens）是比较植物科学中一种新兴的模式。目前，小立壶菌基因组的测序工作由美国联合基因组研究所完成。本文介绍了小立碗藻表达序列标记微卫星标记的研究进展，以及它们在种内和种间的分类和应用。由于不同的微卫星搜索标准和有限的分析物种选择，我们在将小壶菌的研究结果与其他植物物种的早期研究进行比较时受到了严格的限制。因此，我们对24种植物中表达序列标签衍生的微卫星进行了并排分析，涵盖了广泛的系统发育范围，并根据观察到的频率给出了我们的结果。我们使用MISA软件在一个包含超过37兆碱基核苷酸信息的非冗余小碗藻表达序列标签数据库中鉴定了3,723颗微卫星。导出了2951颗微卫星的附属引物序列。376个微卫星的PCR结果显示，两个小壶菌的扩增成功率为88%，多态性超过30%。64颗微卫星的多态性信息含量较高，平均值为0.47 +/- 0.17。在64个小立小藻微卫星标记中，分别有34%和79.7%的标记在两个亲缘关系较近的苔藓物种中具有跨种适用性。在对两种绿藻、两种苔藓、一种蕨类植物、一种蕨类植物、一种蕨类棕榈、银杏树、两种针叶树、十种双子树和五种单子树的调查中，我们检测到总体频率的变化高达7倍，每megabbase最小微卫星37到最大微卫星258，并且不同微卫星类别和基序频率之间存在很大的差异。许多特定物种的微卫星频率变得明显，并确定了与早先报告的一些偏差。小立壶菌微卫星标记的建立为进一步在种内和种间水平上的遗传和基因组学应用提供了一个有价值的工具。植物界中表达序列标签衍生的微卫星的比较调查很适合于未来植物微卫星研究的分类。
The moss Physcomitrella patens is an emerging model in comparative plant science. At present, the Physcomitrella genome is sequenced at the Joint Genome Institute (USA). In this study we present our results on the development of expressed sequence tag-derived microsatellite markers for Physcomitrella patens, their classification and applicability as genetic markers on the intra- as well as on the interspecies level. We experienced severe restrictions to compare our results on Physcomitrella with earlier studies for other plant species due to varying microsatellite search criteria and a limited selection of analysed species. As a consequence, we performed a side by side analysis of expressed sequence tag-derived microsatellites among 24 plant species covering a broad phylogenetic range and present our results on the observed frequencies. We identified 3,723 microsatellites using the software MISA in a non-redundant Physcomitrella expressed sequence tag database comprising more than 37 megabases of nucleotide information. For 2,951 microsatellites appendant primer sequences have been derived. PCR of 376 microsatellites yielded 88 % successful amplicons and over 30 % polymorphisms between two Physcomitrella accessions. The polymorphism information content of 64 microsatellites based on 21 different Physcomitrella accessions was comparably high with a mean of 0.47 +/- 0.17. Of the 64 Physcomitrella microsatellite markers, 34 % respectively 79.7 % revealed cross-species applicability in two closely related moss species. In our survey of two green algae, two mosses, a fern, a fern palm, the ginkgo tree, two conifers, ten dicots and five monocots we detected an up to sevenfold variation in the overall frequency with a minimum of 37 up to maximal 258 microsatellites per megabase and a high variability among the different microsatellite class and motif frequencies. Numerous species-specific microsatellite frequencies became evident and several deviations to earlier reports were ascertained. With the Physcomitrella microsatellite marker set a valuable tool has been made available for further genetic and genomic applications on the intra- as well as on the interspecies level. The comparative survey of expressed sequence tag-derived microsatellites among the plant kingdom is well suited for a classification of future studies on plant microsatellites.
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影响因子：
4.4
作者：
Brenner ED;Katari MS;Stevenson DW;Rudd SA;Douglas AW;Moss WN;Twigg RW;Runko SJ;Stellari GM;McCombie WR;Coruzzi GM
通讯作者：
Coruzzi GM
影响因子：
14.9
作者：
Rudd S;Schoof H;Mayer K
通讯作者：
Mayer K
影响因子：
3.4
作者：
Hedges, SB;Blair, JE;Shoe, JL
通讯作者：
Shoe, JL
影响因子：
7.4
作者：
Dong, QF;Lawrence, CJ;Brendel, V
通讯作者：
Brendel, V
影响因子：
12.3
作者：
Brenner ED;Stevenson DW;McCombie RW;Katari MS;Rudd SA;Mayer KF;Palenchar PM;Runko SJ;Twigg RW;Dai G;Martienssen RA;Benfey PN;Coruzzi GM
通讯作者：
Coruzzi GM