Comparative transcriptome analyses of drought-resistant and - susceptible Brassica napus L. and development of EST-SSR markers by RNA-Seq
Comparative transcriptome analyses of drought-resistant and - susceptible Brassica napus L. and development of EST-SSR markers by RNA-Seq
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DOI：
10.1007/s12374-015-0113-x
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发表时间：
2015-07
影响因子：
2.9
通讯作者：
Daojie Wang;Cuiling Yang;L. Dong;Jiacheng Zhu;Jianping Wang;Shufen Zhang
中科院分区：
文献类型：
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作者：
Daojie Wang;Cuiling Yang;L. Dong;Jiacheng Zhu;Jianping Wang;Shufen Zhang
甘蓝型油菜（Brassica napusis）是菊科双子叶植物。它是一种重要的油料作物，在世界各地广泛种植。干旱胁迫是一个非常重要的威胁。油菜生产在这项研究中，两个B。用200 g/L PEG-6000作为干旱模拟剂处理不同抗旱性的油菜品系（标记为S、R），用1/2 Hoagland培养基处理两个对照（标记为ST、RT）。借助Illumina配对末端RNA-seq技术和Trinity的从头组装，我们获得了107,294个Unigenes（综合四个样本结果），平均长度为834 bp，N50为1245。在这些Unigenes中，分别有84，768、92，545、54，857、28，129、75，278个被分配到NR、NT、Swiss-Prot、COG和GO数据库。通过与KEGG数据库的BLAST比较，总共将46，861个定位到128个通路。为了全面了解四个样本中独特基因的表达差异，我们利用RPKM计算Unigene表达，并识别差异表达基因。此外，本研究还开发了22，414个SSR。
Brassica napusis a dicotyledonous plant in the familyBrassicaceae. It is an important oil crop which has been widely cultivated over the world. However, drought stress is a very important threatening toB. napusproduction. In this study, twoB. napusstrains with different resistance to drought stress were treated with 200 g/L PEG-6000 as drought simulation agent (marked as S, R)and two controls were treated with 1/2 Hoagland medium(marked as ST, RT). With the help of Illumina paired-end RNA-seq technology and de novo assembly by Trinity, we obtained 107,294 Unigenes (integrated four sample results) with an average length of 834 bp and N50 1245. Of these Unigenes, 84,768, 92,545, 54,857, 28,129, 75,278 were assigned to NR, NT, Swiss-Prot, COG and GO database respectively. A total of 46,861 were mapped to 128 pathways by BLAST comparison against the KEGG database. In order to have an overall understanding of the unique genes’ expression difference among four samples, we utilized RPKM to calculate Unigene expression, and to identify differentially expressed genes. Besides, 22,414 SSRs were developed in this study.