Comparison of 454-ESTs from Huperzia serrata and Phlegmariurus carinatus reveals putative genes involved in lycopodium alkaloid biosynthesis and developmental regulation.
Comparison of 454-ESTs from Huperzia serrata and Phlegmariurus carinatus reveals putative genes involved in lycopodium alkaloid biosynthesis and developmental regulation.
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锯齿石杉和红刺蛇 454-EST 的比较揭示了参与石松生物碱生物合成和发育调控的推定基因
DOI：
10.1186/1471-2229-10-209
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发表时间：
2010-09-21
影响因子：
5.3
通讯作者：
Chen S
中科院分区：
文献类型：
--
作者：
Luo H;Li Y;Sun C;Wu Q;Song J;Sun Y;Steinmetz A;Chen S
背景：石杉科植物包括石杉属和石杉属两个属，它们产生各种类型的石蒜生物碱，用于治疗许多人类疾病，如挫伤、肿胀和劳损。石杉碱甲属于石蒜碱类生物碱，已被用作抗阿尔茨海默病药物的候选药物。尽管它们在医学上很重要，但这个家族成员的基因组或转录组数据很少。我们在Roche 454-GS Flx钛平台上使用大规模并行焦磷酸测序技术生成了一个实质性的EST数据集，其中锯齿石杉和隆突石杉分别作为石杉属和石杉属的代表成员。锯缘石蒜和石蒜是研究石蒜生物碱生物合成的重要植物。结果：锯缘棘鱼从140,930个阅读数中获得了36,763个独特的推定转录本，共超过57,028,559个碱基对；而对于隆突螺旋藻，从79,920个阅读数中获得了31,812个独特的推定转录本，总阅读量超过30,498,684个碱基对。使用公共数据库的BLASTX搜索，16,274个(44.3%)锯齿鱼和14,070个(44.2%)隆突螺旋藻的独特转录本被分配到至少一个蛋白质。基因本体论(GO)和京都基因和基因组百科全书(KEGG)的正交学注释表明，这两个物种独特的假定转录本的功能涵盖了相似的广泛的分子功能、生物学过程和生化途径。特别是，通过对锯缘石蒜和石蒜454-EST-EST的比较和实时PCR分析，发现了20个在叶片中比在根中更丰富的候选细胞色素P450基因，它们可能参与石松生物碱的生物合成。通过系统发育分析，筛选出与石蒜生物碱合成相关的4个独特的细胞色素P450转录本(Hs01891、Hs04010、Hs13557和Hs00093)。在454-EST数据库中，大约有115个锯缘青霉和98个隆突青霉与三萜类、生物碱和黄酮类/黄酮类化合物的生物合成相关。还获得了与植物激素生物合成和信号转导相关的转录本以及转录因子。此外，我们还在锯缘石杉和隆突石杉454-EST中分别发现了2,729和1,573个潜在的SSR基序微卫星基因座。结论：454-EST资源为首次大规模获取锯齿石杉和隆突石杉的EST奠定了基础。我们发现了许多可能参与生物活性物质生物合成和转录调控的基因，以及大量潜在的微卫星标记。这些结果为了解石杉科植物发育调控和次生代谢物生物合成的分子基础(特别是石杉生物碱)提供了重要的资源，并为该家族的遗传多样性提供了一个概述。
Background:Plants of the Huperziaceae family, which comprise the two genera Huperzia and Phlegmariurus, produce various types of lycopodium alkaloids that are used to treat a number of human ailments, such as contusions, swellings and strains. Huperzine A, which belongs to the lycodine type of lycopodium alkaloids, has been used as an anti-Alzheimer's disease drug candidate. Despite their medical importance, little genomic or transcriptomic data are available for the members of this family. We used massive parallel pyrosequencing on the Roche 454-GS FLX Titanium platform to generate a substantial EST dataset for Huperzia serrata (H. serrata) and Phlegmariurus carinatus (P. carinatus) as representative members of the Huperzia and Phlegmariurus genera, respectively. H. serrata and P. carinatus are important plants for research on the biosynthesis of lycopodium alkaloids. We focused on gene discovery in the areas of bioactive compound biosynthesis and transcriptional regulation as well as genetic marker detection in these species.Results:For H. serrata, 36,763 unique putative transcripts were generated from 140,930 reads totaling over 57,028,559 base pairs; for P. carinatus, 31,812 unique putative transcripts were generated from 79,920 reads totaling over 30,498,684 base pairs. Using BLASTX searches of public databases, 16,274 (44.3%) unique putative transcripts from H. serrata and 14,070 (44.2%) from P. carinatus were assigned to at least one protein. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology annotations revealed that the functions of the unique putative transcripts from these two species cover a similarly broad set of molecular functions, biological processes and biochemical pathways.In particular, a total of 20 H. serrata candidate cytochrome P450 genes, which are more abundant in leaves than in roots and might be involved in lycopodium alkaloid biosynthesis, were found based on the comparison of H. serrata and P. carinatus 454-ESTs and real-time PCR analysis. Four unique putative CYP450 transcripts (Hs01891, Hs04010, Hs13557 and Hs00093) which are the most likely to be involved in the biosynthesis of lycopodium alkaloids were selected based on a phylogenetic analysis. Approximately 115 H. serrata and 98 P. carinatus unique putative transcripts associated with the biosynthesis of triterpenoids, alkaloids and flavones/flavonoids were located in the 454-EST datasets. Transcripts related to phytohormone biosynthesis and signal transduction as well as transcription factors were also obtained. In addition, we discovered 2,729 and 1,573 potential SSR-motif microsatellite loci in the H. serrata and P. carinatus 454-ESTs, respectively.Conclusions:The 454-EST resource allowed for the first large-scale acquisition of ESTs from H. serrata and P. carinatus, which are representative members of the Huperziaceae family. We discovered many genes likely to be involved in the biosynthesis of bioactive compounds and transcriptional regulation as well as a large number of potential microsatellite markers. These results constitute an essential resource for understanding the molecular basis of developmental regulation and secondary metabolite biosynthesis (especially that of lycopodium alkaloids) in the Huperziaceae, and they provide an overview of the genetic diversity of this family.
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影响因子：
5.4
作者：
Ma, XQ;Tan, CH;Gang, DR
通讯作者：
Gang, DR
影响因子：
3
作者：
Baraniuk, Richard G.;Wakin, Michael B.
通讯作者：
Wakin, Michael B.
DOI：
10.1139/v75-005
发表时间：
1975-01-01
期刊：
CANADIAN JOURNAL OF CHEMISTRY-REVUE CANADIENNE DE CHIMIE
影响因子：
--
作者：
MARSHALL, WD;NGUYEN, TT;SPENSER, ID
通讯作者：
SPENSER, ID
影响因子：
3.1
作者：
Kumpatla, SP;Mukhopadhyay, S
通讯作者：
Mukhopadhyay, S
测序的Medicago truncatula使用454个生命科学技术表达了测序标签。
影响因子：
4.4
作者：
Cheung, Foo;Haas, Brian J;Goldberg, Susanne M D;May, Gregory D;Xiao, Yongli;Town, Christopher D
通讯作者：
Town, Christopher D