Gene expression profiling of flax (Linum usitatissimum L.) under edaphic stress.
Gene expression profiling of flax (Linum usitatissimum L.) under edaphic stress.
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DOI：
10.1186/s12870-016-0927-9
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发表时间：
2016-11-16
影响因子：
5.3
通讯作者：
Melnikova NV
中科院分区：
文献类型：
--
作者：
Dmitriev AA;Kudryavtseva AV;Krasnov GS;Koroban NV;Speranskaya AS;Krinitsina AA;Belenikin MS;Snezhkina AV;Sadritdinova AF;Kishlyan NV;Rozhmina TA;Yurkevich OY;Muravenko OV;Bolsheva NL;Melnikova NV
栽培亚麻（Linum usitatissimum L.）广泛用于生产纺织品、食品、化学和医药产品。然而，各种压力会降低亚麻产量。寻找与应激反应有关的基因对于培育适应性品种是必要的。土壤中营养元素浓度不平衡会降低亚麻产量，还会导致某些亚麻品系发生遗传变化。 Linum 插入序列 1 (LIS-1) 的出现是研究最多的修饰。然而，LIS-1的功能仍不清楚。使用 Illumina 平台对正常 (N)、磷缺乏 (P) 和营养过剩 (NPK) 条件下生长的亚麻植物的转录组进行高通量测序。进行转录组组装，分别鉴定出 N、P 和 NPK 测序文库的总共 34924、33797 和 33698 个独特转录本。我们的测序数据中没有透露任何 LIS-1 衍生的 mRNA。高通量测序数据的分析使我们能够识别在营养不平衡下具有潜在差异表达的基因。为了进一步使用 qPCR 研究，选择了 15 个基因，并在 31 株亚麻植物的扩展采样中评估了它们的表达水平。在 P 和 NPK 条件下，编码 WRKY 和 JAZ 蛋白家族的基因出现了显着的表达变化。此外，WRKY家族基因的改变根据亚麻植物基因组中LIS-1的存在而不同。此外，我们还发现，在营养胁迫下，与 LIS-1 相邻的 KRP2 和 ING1 基因的 mRNA 水平发生轻微且不依赖于 LIS-1 的变化。基于高通量测序和 qPCR 数据，鉴定了在磷缺乏和营养过剩条件下生长的亚麻植物中的差异表达基因。我们发现 WRKY 和 JAS 基因家族参与亚麻对土壤养分含量不平衡的反应。此外，在我们的转录组测序数据中，我们尚未鉴定出任何可能源自 LIS-1 的 mRNA。 LIS-1 侧翼基因 ING1 和 KRP2 的表达被认为不是由营养胁迫诱导的。获得的结果为亚麻土壤应激反应以及 LIS-1 在这些过程中的作用提供了新的见解。本文的在线版本 (doi:10.1186/s12870-016-0927-9) 包含补充材料，可供授权用户使用。
Cultivated flax (Linum usitatissimum L.) is widely used for production of textile, food, chemical and pharmaceutical products. However, various stresses decrease flax production. Search for genes, which are involved in stress response, is necessary for breeding of adaptive cultivars. Imbalanced concentration of nutrient elements in soil decrease flax yields and also results in heritable changes in some flax lines. The appearance of Linum Insertion Sequence 1 (LIS-1) is the most studied modification. However, LIS-1 function is still unclear. High-throughput sequencing of transcriptome of flax plants grown under normal (N), phosphate deficient (P), and nutrient excess (NPK) conditions was carried out using Illumina platform. The assembly of transcriptome was performed, and a total of 34924, 33797, and 33698 unique transcripts for N, P, and NPK sequencing libraries were identified, respectively. We have not revealed any LIS-1 derived mRNA in our sequencing data. The analysis of high-throughput sequencing data allowed us to identify genes with potentially differential expression under imbalanced nutrition. For further investigation with qPCR, 15 genes were chosen and their expression levels were evaluated in the extended sampling of 31 flax plants. Significant expression alterations were revealed for genes encoding WRKY and JAZ protein families under P and NPK conditions. Moreover, the alterations of WRKY family genes differed depending on LIS-1 presence in flax plant genome. Besides, we revealed slight and LIS-1 independent mRNA level changes of KRP2 and ING1 genes, which are adjacent to LIS-1, under nutrition stress. Differentially expressed genes were identified in flax plants, which were grown under phosphate deficiency and excess nutrition, on the basis of high-throughput sequencing and qPCR data. We showed that WRKY and JAS gene families participate in flax response to imbalanced nutrient content in soil. Besides, we have not identified any mRNA, which could be derived from LIS-1, in our transcriptome sequencing data. Expression of LIS-1 flanking genes, ING1 and KRP2, was suggested not to be nutrient stress-induced. Obtained results provide new insights into edaphic stress response in flax and the role of LIS-1 in these process. The online version of this article (doi:10.1186/s12870-016-0927-9) contains supplementary material, which is available to authorized users.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.2147/rrb.s27198
发表时间：
2012-01-01
期刊：
RESEARCH AND REPORTS IN BIOLOGY
影响因子：
--
作者：
Bickel, Cory L.;Lukacs, Marshall;Cullis, Christopher A.
通讯作者：
Cullis, Christopher A.
影响因子：
3.9
作者：
Melnikova, Nataliya V.;Dmitriev, Alexey A.;Kudryavtseva, Anna V.
通讯作者：
Kudryavtseva, Anna V.
影响因子：
2.4
作者：
TYSON, H;FIELDES, MA
通讯作者：
FIELDES, MA
影响因子：
--
作者：
Melnikova NV;Kudryavtseva AV;Zelenin AV;Lakunina VA;Yurkevich OY;Speranskaya AS;Dmitriev AA;Krinitsina AA;Belenikin MS;Uroshlev LA;Snezhkina AV;Sadritdinova AF;Koroban NV;Amosova AV;Samatadze TE;Guzenko EV;Lemesh VA;Savilova AM;Rachinskaia OA;Kishlyan NV;Rozhmina TA;Bolsheva NL;Muravenko OV
通讯作者：
Muravenko OV