De novo transcriptome analysis of an aerial microalga Trentepohlia jolithus: pathway description and gene discovery for carbon fixation and carotenoid biosynthesis.
De novo transcriptome analysis of an aerial microalga Trentepohlia jolithus: pathway description and gene discovery for carbon fixation and carotenoid biosynthesis.
复制标题
空中微藻 Trentepohlia jolithus 的从头转录组分析：碳固定和类胡萝卜素生物合成的途径描述和基因发现
DOI：
10.1371/journal.pone.0108488
复制
发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Liu Q
中科院分区：
文献类型：
--
作者：
Li Q;Liu J;Zhang L;Liu Q
橘色藻目（Trentepohliales）的藻类地理分布广泛，通常以富含β - 胡萝卜素为特征。到目前为止发表的许多专著主要关注其形态、分类、系统发育、分布和繁殖；对该目的分子研究仍然很少。高通量RNA测序（RNA - Seq）技术为朱红橘色藻（Trentepohlia jolithus）的转录本分析和基因发现提供了一种强大而有效的方法。
Illumina HiSeq 2000测序产生了55,007,830条Illumina双端原始读段，这些读段被组装成41,328个组装的单基因。基于非冗余蛋白质数据库（NR）注释，53.28%的单基因（22,018个）可被归类到具有54个子类和161,451个功能术语的基因本体类别中。共有26,217个（63.44%）组装的单基因被定位到128个京都基因与基因组百科全书（KEGG）通路。此外，在5,206个单基因中鉴定出5,798个简单重复序列（SSR）以及131,478个假定的单核苷酸多态性（SNP）。而且，朱红橘色藻中存在所有C4光合作用基因这一事实表明其具有复杂的碳获取和固定系统。还深入描述了朱红橘色藻与其他藻类在类胡萝卜素生物合成方面的异同。
这是首次对朱红橘色藻进行广泛的转录组研究，增加了绿藻纲（Ulvophyceae）可用的分子数据量。除了为功能基因组学研究提供资源外，这里鉴定出的功能基因和假定的通路将有助于更好地理解朱红橘色藻中的碳固定以及脂肪酸和类胡萝卜素的生物合成。
Background:Algae in the order Trentepohliales have a broad geographic distribution and are generally characterized by the presence of abundant β-carotene. The many monographs published to date have mainly focused on their morphology, taxonomy, phylogeny, distribution and reproduction; molecular studies of this order are still rare. High-throughput RNA sequencing (RNA-Seq) technology provides a powerful and efficient method for transcript analysis and gene discovery in Trentepohlia jolithus.Methods/principal findings:Illumina HiSeq 2000 sequencing generated 55,007,830 Illumina PE raw reads, which were assembled into 41,328 assembled unigenes. Based on NR annotation, 53.28% of the unigenes (22,018) could be assigned to gene ontology classes with 54 subcategories and 161,451 functional terms. A total of 26,217 (63.44%) assembled unigenes were mapped to 128 KEGG pathways. Furthermore, a set of 5,798 SSRs in 5,206 unigenes and 131,478 putative SNPs were identified. Moreover, the fact that all of the C4 photosynthesis genes exist in T. jolithus suggests a complex carbon acquisition and fixation system. Similarities and differences between T. jolithus and other algae in carotenoid biosynthesis are also described in depth.Conclusions/significance:This is the first broad transcriptome survey for T. jolithus, increasing the amount of molecular data available for the class Ulvophyceae. As well as providing resources for functional genomics studies, the functional genes and putative pathways identified here will contribute to a better understanding of carbon fixation and fatty acid and carotenoid biosynthesis in T. jolithus.
登录
查看更多内容
影响因子：
56.9
作者：
Armbrust, EV;Berges, JA;Rokhsar, DS
通讯作者：
Rokhsar, DS
影响因子：
2.6
作者：
Gupta, S;Agrawal, SC
通讯作者：
Agrawal, SC
通过454转录组测序发现SNP。
影响因子：
7.2
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
通讯作者：
Schnable, Patrick S
影响因子：
3.3
作者：
Abe, Katsuya;Takahashi, Emi;Hirano, Morio
通讯作者：
Hirano, Morio
影响因子：
6.2
作者：
Aragon, C.;Pascual, P.;Amancio, S.
通讯作者：
Amancio, S.