Chen Gang, Lin Qiu-Mei, Zeng Lin, Zou Yi-Ping
Key Laboratory of Natural Active Pharmaceutical Constituents, College of Chemistry and Biology Engineering, Yichun University, Yichun 336000, China.
College of Life Sciences and Resource Environment, Yichun University, Yichun 336000, China.
Chin Herb Med. 2020 Mar 27;12(2):133-141. doi: 10.1016/j.chmed.2020.03.001. eCollection 2020 Apr.
a fern of the Lycopodiaceae family, is a traditional Chinese medicine, which has similar efficacy to that of in treating rheumatoid arthritis (RA). However, they are different in the contents and compositions of lycopodium alkaloids. In this study, the biosynthesis related genes of lycopodium alkaloids and genetic markers are discovered in transcriptome.
The plant of was collected and was subjected to the RNA isolation, cDNA library construction, high throughput RNA sequencing and bioinformatics analysis.
Totally 124, 524 high-quality unigenes were assembled from RNA sequencing reads, with an average sequence length of 601 bp. Among the transcripts, 61,304 shared the significant similarity (E-value < 10) with existing protein sequences in the public databases. From 124,524 unigenes, 47,538 open reading frames (ORFs) were predicted. Based on the bioinformatics analysis, all possible enzyme genes involved in the lycodine-type alkaloids biosynthetic pathway of were identified, including lysine decarboxylase (LDC), primary amine oxidase (PAO), malonyl-CoA decarboxylase, etc. Sixty-four putative cytochrome p450 (CYP) and 827 putative transcription factors were selected from the transcriptome unigenes as the candidates of lycodine-type alkaloids biosynthesis modifiers. Furthermore, 13,352 simple sequence repeats (SSRs) were identified from 124,524 unigenes, of which dinucleotide motifs AG/CT were the most abundant (50.1%). Meanwhile, we confirmed the amplification effectiveness of 25 PCR primer pairs for randomly selected SSRs.
We obtained the comprehensive transcriptomic information from the high throughput RNA sequencing and bioinformatics analysis, which provided a valuable resource of transcript sequences of in public databases.
石松科的一种蕨类植物，是一种传统中药，在治疗类风湿性关节炎（RA）方面具有与[未提及的某种植物或物质]相似的功效。然而，它们在石松生物碱的含量和组成上有所不同。在本研究中，从[该蕨类植物名称未给出]转录组中发现了石松生物碱生物合成相关基因和遗传标记。
采集[该蕨类植物名称未给出]植株，进行RNA分离、cDNA文库构建、高通量RNA测序及生物信息学分析。
从RNA测序读数中总共组装了124,524个高质量单基因，平均序列长度为601 bp。在这些转录本中，61,304个与公共数据库中现有的蛋白质序列具有显著相似性（E值<10）。从124,524个单基因中预测出47,538个开放阅读框（ORF）。基于生物信息学分析，鉴定出了参与[该蕨类植物名称未给出]石松碱型生物碱生物合成途径的所有可能的酶基因，包括赖氨酸脱羧酶（LDC）、伯胺氧化酶（PAO）、丙二酰辅酶A脱羧酶等。从转录组单基因中筛选出64个假定的细胞色素P450（CYP）和827个假定的转录因子作为石松碱型生物碱生物合成修饰剂的候选者。此外，从124,524个单基因中鉴定出13,352个简单序列重复（SSR），其中二核苷酸基序AG/CT最为丰富（50.1%）。同时，我们证实了随机选择的25对SSR的PCR引物对的扩增有效性。
通过高通量RNA测序和生物信息学分析，我们获得了全面的转录组信息，为公共数据库提供了[该蕨类植物名称未给出]有价值的转录序列资源。
