Rapid microsatellite development for tree peony and its implications.
Rapid microsatellite development for tree peony and its implications.
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牡丹微卫星快速发展及其意义
DOI：
10.1186/1471-2164-14-886
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发表时间：
2013-12-16
期刊：
影响因子：
4.4
通讯作者：
Shu Q
中科院分区：
文献类型：
--
作者：
Gao Z;Wu J;Liu Z;Wang L;Ren H;Shu Q
微卫星普遍存在于各种生物的基因组中。随着认识到它们在发育和生理过程中发挥作用，而不是作为“垃圾”DNA存在，微卫星正受到越来越多的关注。下一代测序允许获得大规模的微卫星信息，并且对于没有参考基因组序列的植物特别有用。本研究利用454 GS-FLX Titanium焦磷酸测序技术，以牡丹为材料，构建高通量的微卫星引物。我们获得了675，221个读数，平均长度为356 bp。共检测到240，672，018 bp的序列，鉴定出237，134个SSR。在这些序列中，164，043个含有SSR，其中27%具有一个以上的SSR。有趣的是，高比例的SSR（43%）存在于化合物的形成。重复基序为1-4 bp（单、二、三和四核苷酸重复）的SSR占99.8%。二核苷酸重复是最丰富的。与大多数植物一样，牡丹的主要基序是（A/T）n，（G/C）n较少见。SSR长度分为11组。最短的SSR（10 bp）占总数的1%，而21-30和101-110 bp的SSR分别占所有SSR的26%和29%。许多序列（42，111）被定位到CDS（编码结构域序列）区域，使用拟南芥作为参考。GO注释分析预测具有SSR的CDS执行与细胞组分、分子功能和生物过程相关的各种功能。100个验证的引物对，24个被选为多态性分析之间的23个基因型;聚类分析所得到的数据分组的基因型，根据已知的关系，确认开发的SSR标记的有用性。本研究以牡丹为材料进行的大规模SSR标记开发结果，对于研究植物基因组结构进化、阐明牡丹在进化和人工选择过程中的表型变异具有重要意义。这些新发现的SSR标记可用于遗传连锁图谱的构建、QTL定位、基因定位与克隆以及分子标记辅助育种。此外，本研究所获得的全基因组标记资源也为牡丹及其近缘种的基因组研究提供了参考。
Microsatellites are ubiquitous in genomes of various organisms. With the realization that they play roles in developmental and physiological processes, rather than exist as ‘junk’ DNA, microsatellites are receiving increasing attention. Next-generation sequencing allows acquisition of large-scale microsatellite information, and is especially useful for plants without reference genome sequences. In this study, enriched DNA libraries of tree peony, a well-known ornamental woody shrub, were used for high-throughput microsatellite development by 454 GS-FLX Titanium pyrosequencing. We obtained 675,221 reads with an average length of 356 bp. The total size of examined sequences was 240,672,018 bp, from which 237,134 SSRs were identified. Of these sequences, 164,043 contained SSRs, with 27% featuring more than one SSR. Interestingly, a high proportion of SSRs (43%) were present in compound formation. SSRs with repeat motifs of 1–4 bp (mono-, di-, tri-, and tetra-nucleotide repeats) accounted for 99.8% of SSRs. Di-nucleotide repeats were the most abundant. As in most plants, the predominant motif in tree peony was (A/T)n, with (G/C)n less common. The lengths of SSRs were classified into 11 groups. The shortest SSRs (10 bp) represented 1% of the total number, whereas SSRs 21–30 and 101–110 bp long accounted for 26% and 29%, respectively, of all SSRs. Many sequences (42,111) were mapped to CDS (coding domain sequence) regions using Arabidopsis as a reference. GO annotation analysis predicted that CDSs with SSRs performed various functions associated with cellular components, molecular functions, and biological processes. Of 100 validated primer pairs, 24 were selected for polymorphism analysis among 23 genotypes; cluster analysis of the resulting data grouped genotypes according to known relationships, confirming the usefulness of the developed SSR markers. The results of our large-scale SSR marker development using tree peony are valuable for investigating plant genomic structural evolution and elucidating phenotypic variation in this species during its evolution and artificial selection. The newly identified SSRs should be useful for genetic linkage map construction, QTL mapping, gene location and cloning, and molecular marker-assisted breeding. In addition, the genome-wide marker resources generated in this study should aid genomic studies of tree peony and related species.
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影响因子：
2.4
作者：
Han, Xiao Yan;Wang, Liang Sheng;Tetsumura, Takuya
通讯作者：
Tetsumura, Takuya
DOI：
10.1093/bioinformatics/btp527
发表时间：
2009-11-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Lassmann T;Hayashizaki Y;Daub CO
通讯作者：
Daub CO
影响因子：
7.7
作者：
Castoe TA;Poole AW;Gu W;Jason de Koning AP;Daza JM;Smith EN;Pollock DD
通讯作者：
Pollock DD
DOI：
10.1073/pnas.91.1.88
发表时间：
1994-01-04
影响因子：
11.1
作者：
KANDPAL, RP;KANDPAL, G;WEISSMAN, SM
通讯作者：
WEISSMAN, SM
影响因子：
2.7
作者：
Abdelkrim, Jawad;Robertson, Bruce C.;Gemmell, Neil J.
通讯作者：
Gemmell, Neil J.