Characterization of EST SSRs in loblolly pine and spruce
Characterization of EST SSRs in loblolly pine and spruce
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DOI：
10.1007/s11295-006-0061-1
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发表时间：
2007-07-01
影响因子：
2.4
通讯作者：
Ritland, Kermit
中科院分区：
文献类型：
--
作者：
Berube, Yanik;Zhuang, Jun;Ritland, Kermit
在针叶树表达序列标签 - 简单序列重复（EST - SSRs）的首次大型研究中，对两个大型针叶树EST数据库的EST - SSRs进行了特征分析。一个数据库来自“内陆云杉”（不列颠哥伦比亚省南部的白云杉和恩格尔曼云杉）以及锡特卡云杉，另一个来自火炬松。我们在火炬松和云杉中分别发现了475个和629个独特的EST - SSRs。在火炬松中，3' EST所含的SSR比5' EST读数多14%，在云杉中则多41%。针叶树的EST - SSRs在几个方面与被子植物的EST - SSRs明显不同。针叶树中EST - SSRs的频率（大约每50kb一个EST - SSR）远低于被子植物（大约每20kb一个EST - SSR）。二核苷酸重复是针叶树中最丰富的重复类别，而在被子植物中，三核苷酸最为常见。最后，AT基序是两种针叶树物种中主要的基序，而AG是被子植物中最常见的二核苷酸重复。此外，由于针叶树中的这些EST - SSRs可被开发为有用的遗传标记，我们的工作证明了大规模EST测序项目对于标记开发的计算机模拟方法的价值。
In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for ESTSSRs. One database was from "interior spruce" (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3' ESTs contained 14% more SSRs than 5' EST reads in loblolly pine and 41 % more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm ESTSSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one EST-SSR every -50 kb) than in angiosperms (one EST-SSR every -20 kb). Dinucleotide repeats were the most abundant repeat class in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these ESTSSRs in conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.