A general pipeline for the development of anchor markers for comparative genomics in plants.
A general pipeline for the development of anchor markers for comparative genomics in plants.
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DOI：
10.1186/1471-2164-7-207
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发表时间：
2006-08-14
期刊：
影响因子：
4.4
通讯作者：
Schauser L
中科院分区：
文献类型：
--
作者：
Fredslund J;Madsen LH;Hougaard BK;Nielsen AM;Bertioli D;Sandal N;Stougaard J;Schauser L
完整或接近完整的基因组序列信息目前仅可用于少数植物物种，这些植物物种代表了植物之间的大系统发育多样性。为了有效地将这些信息转移到缺乏序列信息的物种，需要开发比较基因组工具。允许跨物种作图的分子标记沿着共线基因组区域是比较基因组学的核心。这些“锚”标记在多个物种的遗传连锁图中定义独特的基因座，是基于基因的，并且具有使它们相对稀疏的许多特征。为了更有效地识别潜在的锚标记序列，我们建立了一个自动化的生物信息学管道，结合多物种表达序列标签（EST）和基因组序列数据。利用来自相关物种的序列数据，该管道鉴定了进化上保守的序列，这些序列可能在同一系统发育分支的大多数物种中定义独特的直向同源基因座。其关键特征是鉴定进化上保守的序列，然后自动设计内含子侧翼的聚合酶链反应（PCR）引物对。随后可以通过从作图亲本或群体扩增的PCR产物的大小或序列变异来鉴定多态性。我们说明了我们的程序在豆科植物和草，并在豆科植物，模式植物的研究和基因组和EST序列数据有潜在的影响作物品种的育种和我们的理解这个大而多样的家庭的演变。我们提供了459个候选锚基因座的数据库，这些基因座有可能在18，000多个豆类物种中作为地图锚，其中一些具有农业重要性。对于禾本科植物，该数据库包含1335个候选锚基因座。基于这个数据库，我们已经评估了76个候选锚基因座在豆科植物中的标记发展没有可用的序列信息，证明了这种方法的有效性。
Complete or near-complete genomic sequence information is presently only available for a few plant species representing a large phylogenetic diversity among plants. In order to effectively transfer this information to species lacking sequence information, comparative genomic tools need to be developed. Molecular markers permitting cross-species mapping along co-linear genomic regions are central to comparative genomics. These "anchor" markers, defining unique loci in genetic linkage maps of multiple species, are gene-based and possess a number of features that make them relatively sparse. To identify potential anchor marker sequences more efficiently, we have established an automated bioinformatic pipeline that combines multi-species Expressed Sequence Tags (EST) and genome sequence data. Taking advantage of sequence data from related species, the pipeline identifies evolutionarily conserved sequences that are likely to define unique orthologous loci in most species of the same phylogenetic clade. The key features are the identification of evolutionarily conserved sequences followed by automated design of intron-flanking Polymerase Chain Reaction (PCR) primer pairs. Polymorphisms can subsequently be identified by size- or sequence variation of PCR products, amplified from mapping parents or populations. We illustrate our procedure in legumes and grasses and exemplify its application in legumes, where model plant studies and the genome- and EST-sequence data available have a potential impact on the breeding of crop species and on our understanding of the evolution of this large and diverse family. We provide a database of 459 candidate anchor loci which have the potential to serve as map anchors in more than 18,000 legume species, a number of which are of agricultural importance. For grasses, the database contains 1335 candidate anchor loci. Based on this database, we have evaluated 76 candidate anchor loci with respect to marker development in legume species with no sequence information available, demonstrating the validity of this approach.
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影响因子：
30.8
作者：
Lyons, LA;Laughlin, TF;OBrien, SJ
通讯作者：
OBrien, SJ
DOI：
10.1073/pnas.0402251101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Choi, HK;Mun, JH;Cook, DR
通讯作者：
Cook, DR
影响因子：
11.6
作者：
Fulton, TM;Van der Hoeven, R;Tanksley, SD
通讯作者：
Tanksley, SD
影响因子：
64.8
作者：
Krusell, L;Madsen, LH;Stougaard, J
通讯作者：
Stougaard, J
PRIFI：使用相关序列的多重比对来找到用于放大同源物的引物。
影响因子：
14.9
作者：
Fredslund, J;Schauser, L;Madsen, LH;Sandal, N;Stougaard, J
通讯作者：
Stougaard, J