甘肃省农业科学院机构知识库

De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

收藏
分享
全文链接

文献类型：外文期刊

作者： Long, Yan ¹ ; Zhang, Jingwen ¹ ; Tian, Xinjie ¹ ; Wu, Shanshan ¹ ; Zhang, Qiong ² ; Zhang, Jianping ² ; Dang, Zhanhai; ¹ ;

作者机构： 1.Chinese Acad Agr Sci, Inst Biotechnol, Beijing 100081, Peoples R China

2.Gansu Agr Acad, Crop Inst, Lanzhou 730070, Peoples R China

关键词： Haloxylon ammodendron;Drought;Transcriptome;Digital gene expression;EST-SSR

期刊名称：BMC GENOMICS （影响因子：3.969；五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2014 年 15 卷

页码：

收录情况： SCI

摘要： Background: Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no genomic information or expressed sequence tag-simple sequence repeat (EST-SSR) marker has been reported for H. ammodendron plants. Results: Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length = 728 bp). Based on similarity searches comparing these unigenes with known proteins in the non-redundant (nr) protein database, 25,619 unigenes were functionally annotated with a cut-off E-value of 10(-5). In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. Among these genes, 356 genes were upregulated after drought treatment, and 704 genes were downregulated. We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members. Conclusions: Our study is the first to provide a transcriptome sequence resource for H. ammodendron plants and to determine its digital gene expression profile under drought conditions using the assembled transcriptome data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions.

相关文献

[1]轮叶党参EST-SSR标记的开发及在党参属中的应用. 刘新星,石有太,罗俊杰,欧巧明,陈子萱,李忠旺. 2018

[2]辣椒EST-SSRs的分布特征及在品种多样性研究中的应用. 魏兵强,刘飞云,马宗桓,陈灵芝,张茹. 2013

[3]Histopathology combined with transcriptome analyses reveals the mechanism of resistance to Meloidogyne incognita in Cucumis metuliferus. Ye, De-You,Wei, Bing-Qiang,Zhang, Hua-Sheng,Qi, Yong-Hong,Cao, Su-Fang.

作者其他论文更多>>

Vis-NIR and NIR hyperspectral imaging combined with convolutional neural network with attention module for flaxseed varieties identification

作者：Zhu, Dongyu;Han, Junying;Liu, Chengzhong;Zhang, Jianping;Qi, Yanni

关键词：Hyperspectral imaging; Flaxseed; Identification; Convolutional neural network; Channel attention and transformer modules
Genome-Wide Identification and Expression Profiling of Dehydration-Responsive Element-Binding Family Genes in Flax (Linum usitatissimum L.)

作者：Wang, Yan;Niu, Yamin;Lu, Nan;Hu, Zuyu;Liu, Zigang;Zhang, Jianping;Wang, Yan;Qi, Yanni;Wang, Limin;Xu, Chenmeng;Li, Wenjuan;Dang, Zhao;Zhao, Wei;Wang, Ping;Xie, Yaping;Niu, Yamin;Lu, Nan;Hu, Zuyu;Zhang, Jianping;Liu, Zigang

关键词：flax; DREB; transcription factors; abiotic stress; expression analysis
Genetic analysis and identification of major locus and candidate genes linked to thousand-seed weight in flax (Linum usitatissimum)

作者：Qi, Yanni;Wang, Limin;Li, Wenjuan;Dang, Zhao;Zhao, Wei;Wang, Ping;Xie, Yaping;Xu, Chenmeng;Wang, Yan;Zhang, Jianping;Wang, Wei

关键词：Flax; TSW; BSA-seq; Fine mapping; qRT-PCR
Flaxseed protein content prediction based on hyperspectral wavelength selection with fractional order ant colony optimization

作者：Wang, Bo;Han, Junying;Liu, Chengzhong;Zhang, Jianping;Qi, Yanni

关键词：hyperspectral imaging; wavelength selection; visible-near infrared; protein content; fractional order ant colony optimization
LEHP-DETR: A model with backbone improved and hybrid encoding innovated for flax capsule detection

作者：Wang, Changshun;Han, Junying;Liu, Chengzhong;Zhang, Jianping;Qi, Yanni

关键词：
Combining Vis-NIR and NIR hyperspectral imaging techniques with a data fusion strategy for rapid and nondestructive determination of multiple nutritional qualities in flaxseed

作者：Zhu, Dongyu;Han, Junying;Liu, Chengzhong;Zhang, Jianping;Qi, Yanni

关键词：Hyperspectral imaging; Flaxseed; Data fusion; Multiple nutritional qualities; Visualization
Effect of foliar spray selenium on antioxidant defense system, yields, fatty acid composition, and mineral concentrations in flax (Linum usitatissimum L.)

作者：Xie, Yaping;Wang, Limin;Li, Wenjuan;Zhao, Wei;Dang, Zhao;Wang, Xingzhen;Duan, Yanqiao;Zhang, Jianping;Yuan, Minlu;Wang, Gang;Xie, Yaping;Zhou, Yangchen

关键词：flax; selenium; antioxidant; productivity; quality; biofortification

De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

作者其他论文 更多>>

Vis-NIR and NIR hyperspectral imaging combined with convolutional neural network with attention module for flaxseed varieties identification

Genome-Wide Identification and Expression Profiling of Dehydration-Responsive Element-Binding Family Genes in Flax (Linum usitatissimum L.)

Genetic analysis and identification of major locus and candidate genes linked to thousand-seed weight in flax (Linum usitatissimum)

Flaxseed protein content prediction based on hyperspectral wavelength selection with fractional order ant colony optimization

LEHP-DETR: A model with backbone improved and hybrid encoding innovated for flax capsule detection

Combining Vis-NIR and NIR hyperspectral imaging techniques with a data fusion strategy for rapid and nondestructive determination of multiple nutritional qualities in flaxseed

Effect of foliar spray selenium on antioxidant defense system, yields, fatty acid composition, and mineral concentrations in flax (Linum usitatissimum L.)

意 见 箱

作者其他论文更多>>

意见箱