Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.
Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.
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基因组，功能性基因注释和核核酸藻Nannochloropsis Oceanica CCMP1779的基因组和核转化。
DOI：
10.1371/journal.pgen.1003064
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Benning C
中科院分区：
文献类型：
--
作者：
Vieler A;Wu G;Tsai CH;Bullard B;Cornish AJ;Harvey C;Reca IB;Thornburg C;Achawanantakun R;Buehl CJ;Campbell MS;Cavalier D;Childs KL;Clark TJ;Deshpande R;Erickson E;Armenia Ferguson A;Handee W;Kong Q;Li X;Liu B;Lundback S;Peng C;Roston RL;Sanjaya;Simpson JP;Terbush A;Warakanont J;Zäuner S;Farre EM;Hegg EL;Jiang N;Kuo MH;Lu Y;Niyogi KK;Ohlrogge J;Osteryoung KW;Shachar-Hill Y;Sears BB;Sun Y;Takahashi H;Yandell M;Shiu SH;Benning C
单细胞海洋藻类有希望提供可持续和可扩展的生物燃料原料，尽管没有单一物种成为首选生物。此外，大多数候选物种缺乏合理改造海藻原料所需的足够的分子和遗传资源。微拟球藻属的异鞭毛藻天然具有高细胞油含量，并且已经用于高价值脂质产品的工业生产。通过靶向基因置换应用反向遗传学的首次成功使海洋微绿球藻成为研究这一迷人生物群的细胞和分子生物学以及生物化学的有吸引力的模型。本文报道了N. oceanica CCMP 1779.来自氮充足和氮耗尽生长条件的RNA测序数据支持总共11，973个基因，其中除了自动注释外，还手动检查了一些基因以预测该生物体的生化库。其中，100多个与脂质代谢相关的基因、114个预测的转录因子和109个转录调控因子被注释。N. oceanica CCMP 1779基因库与最近发表的N. gaditana基因组鉴定了2，649个可能是N. oceanica CCMP 1779.许多N。海洋生物特有的基因在其他物种中具有推定的直系同源物，或者得到转录证据的支持。然而，由于基于相似性的注释是有限的，大多数这些物种特异性基因的功能仍然未知。除了基因组序列及其分析，转化N。oceanica CCMP 1779的。海洋微拟球藻CCMP 1779的基因组和转录组学数据的可用性，沿着高效的转化方案，为未来详细的基因功能分析和微拟球藻属的基因工程提供了蓝图。藻类是一种高度多样化的生物体，由于其生产生物燃料原料、营养保健品和生物材料的潜力，已成为重新关注的焦点。它们的高光合产量和在不适合农业的地区生长的能力，为利用传统农作物生产生物燃料提供了潜在的可持续替代方案。由于目前使用的藻类都没有驯化历史，并且藻类的生物工程仍处于起步阶段，因此需要开发适于工业大规模生产所需化合物的培养的藻类菌株。从小鼠到面包酵母的模式生物在提供对基本生物结构和功能的见解方面发挥了重要作用。藻类领域需要多功能的模型来发展对单细胞、海洋、产油藻类物种的生物量和有价值化合物的光合作用生产的基本理解。为了有助于这种藻类模型系统的发展，我们对N. oceanica CCMP 1779，组装基因组序列，鉴定推定基因，并开始解释选定基因的功能。选择该物种是因为它很容易用外源DNA转化，并且在培养中生长良好。
Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogen-depleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica–specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis species by a growing academic community focused on this genus. Algae are a highly diverse group of organisms that have become the focus of renewed interest due to their potential for producing biofuel feedstocks, nutraceuticals, and biomaterials. Their high photosynthetic yields and ability to grow in areas unsuitable for agriculture provide a potential sustainable alternative to using traditional agricultural crops for biofuels. Because none of the algae currently in use have a history of domestication, and bioengineering of algae is still in its infancy, there is a need to develop algal strains adapted to cultivation for industrial large-scale production of desired compounds. Model organisms ranging from mice to baker's yeast have been instrumental in providing insights into fundamental biological structures and functions. The algal field needs versatile models to develop a fundamental understanding of photosynthetic production of biomass and valuable compounds in unicellular, marine, oleaginous algal species. To contribute to the development of such an algal model system for basic discovery, we sequenced the genome and two sets of transcriptomes of N. oceanica CCMP1779, assembled the genomic sequence, identified putative genes, and began to interpret the function of selected genes. This species was chosen because it is readily transformable with foreign DNA and grows well in culture.
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影响因子：
7.4
作者：
BROWN, JS
通讯作者：
BROWN, JS
影响因子：
56.9
作者：
Armbrust, EV;Berges, JA;Rokhsar, DS
通讯作者：
Rokhsar, DS
影响因子：
5.8
作者：
Adryan, Boris;Teichmann, Sarah A.
通讯作者：
Teichmann, Sarah A.
DOI：
10.1199/tab.0137
发表时间：
2010-01-01
期刊：
The arabidopsis book
影响因子：
--
作者：
Binder, Stefan
通讯作者：
Binder, Stefan
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A