De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.
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使用 Illumina 平台对山茱萸叶和果实组织进行从头转录组分析
DOI：
10.1371/journal.pone.0192610
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Xu HW
中科院分区：
文献类型：
--
作者：
Hou DY;Shi LC;Yang MM;Li J;Zhou S;Zhang HX;Xu HW
山茱萸是中国和其他东亚国家数千年来最广泛使用的药用植物之一，用于治疗肝脏，肾脏，心血管疾病和尿频等疾病。它是一种三级保护物种，是中国42种国家重点保护野生动植物之一。然而，C.目前对药用植物的认识还很薄弱，这阻碍了对其代谢和利用的分子机制的研究。因此，丰富其基因组数据和信息非常重要。近年来，快速发展的新一代测序技术为获取非模式物种基因组信息提供了有效途径。本研究首次对柑橘属植物的叶和果实组织转录组进行了研究。使用Illumina HiSeq 4000平台，对药用植物进行测序。分别获得来自叶和果实的总共57，954，134和60，971，652个干净读段（GenBank编号SRP 115440）。将来自所有两个文库的合并读段组装成56，392个单基因，平均长度为856 bp。其中，41，146个unigenes与NCBI非冗余蛋白质数据库中的序列匹配。Gene Ontology数据库将24，336个unigenes与生物过程（83.26%），细胞组分（53.58%）和分子功能（83.93%）相关联。此外，10，808个unigenes被KOG数据库指定为KOG功能分类。对KEGG通路数据库的搜索表明，18，435个单基因被定位到371个KEGG通路。此外，edgeR数据库确定了4，585个显著差异表达基因（DEG），其中1，392个在果实组织中与叶组织相比上调，3，193个下调。最后，我们对50个转录因子基因家族的581个转录因子进行了研究。多数DEG和转录因子与萜类化合物的生物合成和次生代谢调控有关。本研究不仅代表了首次对C.同时也提供了其基因和生物合成途径的基本信息。这些结果将有助于我们进一步探讨白首乌萜类化合物生物合成的分子代谢机制。药用植物
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization. Hence, enriching its genomic data and information is very important. In recent years, the fast-growing technology of next generation sequencing has provided an effective path to gain genomic information from nonmodel species. This study is the first to explore the leaf and fruit tissue transcriptome of C. officinalis using the Illumina HiSeq 4000 platform. A total of 57,954,134 and 60,971,652 clean reads from leaf and fruit were acquired, respectively (GenBank number SRP115440). The pooled reads from all two libraries were assembled into 56,392 unigenes with an average length 856 bp. Among these, 41,146 unigenes matched with sequences in the NCBI nonredundant protein database. The Gene Ontology database assigned 24,336 unigenes with biological process (83.26%), cellular components (53.58%), and molecular function (83.93%). In addition, 10,808 unigenes were assigned a KOG functional classification by the KOG database. Searching against the KEGG pathway database indicated that 18,435 unigenes were mapped to 371 KEGG pathways. Moreover, the edgeR database identified 4,585 significant differentially expressed genes (DEGs), of which 1,392 were up-regulated and 3,193 were down-regulated in fruit tissue compared with leaf tissue. Finally, we explored 581 transcription factors with 50 transcription factor gene families. Most DEGs and transcription factors were related to terpene biosynthesis and secondary metabolic regulation. This study not only represented the first de novo transcriptomic analysis of C. officinalis but also provided fundamental information on its genes and biosynthetic pathway. These findings will help us explore the molecular metabolism mechanism of terpene biosynthesis in C. officinalis.
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