Global transcriptome sequencing using the Illumina platform and the development of EST-SSR markers in autotetraploid alfalfa.
Global transcriptome sequencing using the Illumina platform and the development of EST-SSR markers in autotetraploid alfalfa.
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DOI：
10.1371/journal.pone.0083549
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Wang Y
中科院分区：
文献类型：
--
作者：
Liu Z;Chen T;Ma L;Zhao Z;Zhao PX;Nan Z;Wang Y
苜蓿是世界上种植最广泛的豆科牧草，也是经济价值最高的作物之一。苜蓿基因组庞大且复杂，这延缓了苜蓿研究的基因组资源开发。第二代Illumina转录组测序是一种为苜蓿基因发现和分子标记开发生成全局转录组序列数据集的有效方法。
通过Illumina双端测序从15种不同的苜蓿组织样本中产生了超过2800万条测序读长（56.4亿个干净的核苷酸）。通过从头组装共获得了40433个平均长度为803bp的单基因。基于对已知蛋白质的序列相似性搜索，共有36684个（90.73%）单基因得到注释。此外，从长度超过1kb的单基因中鉴定出1649个潜在的EST - SSR作为潜在的分子标记。随机选取100对PCR引物以验证组装质量并从基因组DNA中开发EST - SSR标记。在这些引物对中，82对在初步筛选试验中能够扩增序列，27对引物成功扩增DNA片段，并在10个苜蓿品种中检测到大量多态性。
本研究为同源四倍体苜蓿提供了全局序列数据，并证明Illumina平台是一种在苜蓿中开发EST - SSR标记的快速有效的方法。这些转录组数据集的使用将作为一个有价值的公共信息平台，加速苜蓿基因组的研究。
Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. The large size and complexity of the alfalfa genome has delayed the development of genomic resources for alfalfa research. Second-generation Illumina transcriptome sequencing is an efficient method for generating a global transcriptome sequence dataset for gene discovery and molecular marker development in alfalfa. More than 28 million sequencing reads (5.64 Gb of clean nucleotides) were generated by Illumina paired-end sequencing from 15 different alfalfa tissue samples. In total, 40,433 unigenes with an average length of 803 bp were obtained by de novo assembly. Based on a sequence similarity search of known proteins, a total of 36,684 (90.73%) unigenes were annotated. In addition, 1,649 potential EST-SSRs were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 100 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 82 were able to amplify sequences in initial screening tests, and 27 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 10 alfalfa accessions. The present study provided global sequence data for autotetraploid alfalfa and demonstrates the Illumina platform is a fast and effective approach to EST-SSR markers development in alfalfa. The use of these transcriptome datasets will serve as a valuable public information platform to accelerate studies of the alfalfa genome.
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使用 Illumina 测序对橡胶树 (Hevea brasiliensis Muell. Arg.) 中的树皮转录组进行从头组装和表征以及 EST-SSR 标记的开发
影响因子：
4.4
作者：
Li D;Deng Z;Qin B;Liu X;Men Z
通讯作者：
Men Z
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：
4.4
作者：
Chen, Wei-Hua;Wei, Wu;Lercher, Martin J.
通讯作者：
Lercher, Martin J.
影响因子：
5.4
作者：
BRUMMER, EC;BOUTON, JH;KOCHERT, G
通讯作者：
KOCHERT, G
影响因子：
5.4
作者：
Kaló, P;Endre, G;Kiss, GB
通讯作者：
Kiss, GB