Knowledge Resource Center for Ecological Environment in Arid Area
| DOI | 10.1002/aps3.11398 |
| TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site | |
| Marx, Hannah E.; Scheidt, Stephen; Barker, Michael S.; Dlugosch, Katrina M. | |
| 通讯作者 | Dlugosch, KM |
| 来源期刊 | APPLICATIONS IN PLANT SCIENCES
 |
| ISSN | 2168-0450 |
| 出版年 | 2020 |
| 卷号 | 8期号:11 |
| 英文摘要 | Premise TagSeq is a cost-effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high-quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non-model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range National Ecological Observatory Network (NEON) core site. Methods Tissue for TagSeq was sampled from multiple individuals of four species (Bouteloua aristidoides and Eragrostis lehmanniana [Poaceae], Tidestromia lanuginosa [Amaranthaceae], and Parkinsonia florida [Fabaceae]) at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA-seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples. Results A high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species. Discussion TagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non-model plant species. |
| 英文关键词 | gene expression National Ecological Observatory Network (NEON) RNA‐ seq Sonoran Desert TagSeq transcriptome |
| 类型 | Article |
| 语种 | 英语 |
| 开放获取类型 | Green Submitted, Green Published, gold |
| 收录类别 | SCI-E |
| WOS记录号 | WOS:000591150000001 |
| WOS关键词 | GENOMICS ; DATABASE |
| WOS类目 | Plant Sciences |
| WOS研究方向 | Plant Sciences |
| 来源机构 | University of Arizona |
| 资源类型 | 期刊论文 |
| 条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/327576 |
| 作者单位 | [Marx, Hannah E.; Barker, Michael S.; Dlugosch, Katrina M.] Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA; [Marx, Hannah E.] Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA; [Scheidt, Stephen] Howard Univ, 2400 6th St NW, Washington, DC 20059 USA; [Scheidt, Stephen] NASA, Goddard Space Flight Ctr, Solar Syst Explorat Div, Greenbelt, MD 20771 USA; [Scheidt, Stephen] NASA, Goddard Space Flight Ctr, Ctr Res & Explorat Space Sci & Technol, Greenbelt, MD 20771 USA |
| 推荐引用方式 GB/T 7714 | Marx, Hannah E.,Scheidt, Stephen,Barker, Michael S.,et al. TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site[J]. University of Arizona,2020,8(11). |
| APA | Marx, Hannah E.,Scheidt, Stephen,Barker, Michael S.,&Dlugosch, Katrina M..(2020).TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site.APPLICATIONS IN PLANT SCIENCES,8(11). |
| MLA | Marx, Hannah E.,et al."TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site".APPLICATIONS IN PLANT SCIENCES 8.11(2020). |
| 条目包含的文件 | 条目无相关文件。 | |||||
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