• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Harmful Algae >Metatranscriptome profiling of a harmful algal bloom
【24h】

Metatranscriptome profiling of a harmful algal bloom

机译：有害藻华的转录组分析

获取原文
获取原文并翻译 | 示例
       
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Metagenomic methods provide a powerful means to investigate complex ecological phenomena. Developed originally for study of Bacteria and Archaea, the application of these methods to eukaryotic microorganisms is yet to be fully realized. Most prior environmental molecular studies of eukaryotes have relied heavily on PCR amplification with eukaryote-specific primers. Here we apply high throughput short-read sequencing of poly-A selected RNA to capture the metatranscriptome of an estuarine dinoflagellate bloom. To validate the metatranscriptome assembly process we simulated metatranscriptomic datasets using short-read sequencing data from clonal cultures of four algae of varying phylogenetic distance. We find that the proportion of chimeric transcripts reconstructed from community transcriptome sequencing is low, suggesting that metatranscriptomic sequencing can be used to accurately reconstruct the transcripts expressed by bloom-forming communities of eukaryotes. To further validate the bloom metatransciptome assembly we compared it to a transcriptomic assembly from a cultured, clonal isolate of the dominant bloom-causing alga and found that the two assemblies are highly similar. Eukaryote-wide phylogenetic analyses reveal the taxonomic composition of the bloom community, which is comprised of several dinoflagellates, ciliates, animals, and fungi. The assembled metatranscriptome reveals the functional genomic composition of a metabolically active community. Highlighting the potential power of these methods, we found that relative transcript abundance patterns suggest that the dominant dinoflagellate might be expressing toxin biosynthesis related genes at a higher level in the presence of competitors, predators and prey compared to it growing in monoculture.
机译：元基因组学方法为研究复杂的生态现象提供了有力的手段。这些方法最初是为研究细菌和古细菌而开发的，但这些方法在真核微生物中的应用尚未完全实现。先前大多数对真核生物的环境分子研究严重依赖于用真核生物特异性引物进行的PCR扩增。在这里我们应用高通量的poly-A选择RNA的短读测序，以捕获河口二鞭毛藻花的转录组。为了验证转录组组装过程，我们使用短读测序数据模拟了转录组数据集，该数据来自四个进化距离不同的藻类的克隆培养物。我们发现，从社区转录组测序重建的嵌合转录物的比例很低，这表明元转录组测序可以用来准确地重建真核生物的绽放形成社区表达的转录物。为了进一步验证水华元转录程序集，我们将其与来自培养的，导致水华的显性藻类的克隆分离株的转录组进行了比较，发现这两个程序集非常相似。整个真核生物的系统发育分析揭示了绽放群落的分类学组成，该群落由几种鞭毛虫，纤毛虫，动物和真菌组成。组装的转录组揭示了代谢活跃社区的功能基因组组成。强调了这些方法的潜力，我们发现相对转录物丰度模式表明，与竞争性，掠食性动物和猎物相比，优势鞭毛藻可能在更高水平上表达与毒素生物合成相关的基因，而不是单培养。

著录项

  • 来源
    《Harmful Algae》 |2014年第7期|75-83|共9页
  • 作者

    Endymion D. Cooper; Bastian Bentlage; Theodore R. Gibbons; Tsvetan R. Bachvaroff; Charles F. Delwiche;

  • 作者单位

    CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA;

    CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA;

    CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA;

    Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E Pratt St., Baltimore, MD 21202, USA;

    CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA,Maryland Agricultural Experiment Station, AGNR, University of Maryland, College Park, MD 20742, USA;

  • 收录信息
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    De novo assembly; Dinoflagellate; Flow cytometry; Harmful algal bloom; Metagenomics; Metatranscriptomics; Prorocentrum minimum; Transcriptomics;

    机译：从头组装;鞭毛藻;流式细胞仪有害的藻华;元基因组学;元转录组学最低原肠;转录组学;

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号