De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots.
De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots.
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从头转录组分析和比较转录组分析解释了三七主根的形态差异。
DOI：
10.1186/s12864-021-08283-w
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发表时间：
2022-01-31
期刊：
影响因子：
4.4
通讯作者：
Liu Y
中科院分区：
文献类型：
--
作者：
Yang L;Wang H;Wang P;Gao M;Huang L;Cui X;Liu Y
三七(Panax notogiseng(Burk.)人参为五加科人参属植物，广泛用于治疗多种疾病。Pn主根作为生物活性成分积累的最重要器官，即使在相同的环境中，也呈现出不同的形态(椭圆形或长形)。然而，目前还没有相关研究解释表型差异的分子机制。为了探讨主根表型差异的原因，对Pn主根进行了从头分析和比较转录分析。基于对椭圆形和长直根样本的高通量测序，分别获得了133,730,886和114,761,595对末端清洁读数。利用从头组装转录组获得121,955个单基因，重叠群N50=1,774个碱基，BLAST获得63,133个注释。然后，根据综合注释结果，确定了42个基因属于III类过氧化物酶基因家族，8个基因属于L抗坏血酸过氧化物酶基因家族，55个基因属于一系列丝裂原活化蛋白激酶基因家族。差异表达基因分析表明，与活性氧代谢相关的PnAPX3和PnPRX45基因以及与细胞增殖和植物根发育相关的PnMPK3基因在长主根中的表达显著高于椭圆形主根。此外，实时定量聚合酶链式反应、酶活性和过氧化氢含量的测定结果验证了转录分析结果。这些结果表明，ROS代谢和PnMPK3基因可能在调节Pn主根表型中起重要作用。这项研究为人参属其他物种表型差异的遗传机制提供了进一步的见解。网上版载有补充材料，可在10.1186/s12864-021-08283-w查阅。
Panax notoginseng (Burk.) F. H. Chen (PN) belonging to the genus Panax of family Araliaceae is widely used in traditional Chinese medicine to treat various diseases. PN taproot, as the most vital organ for the accumulation of bioactive components, presents a variable morphology (oval or long), even within the same environment. However, no related studies have yet explained the molecular mechanism of phenotypic differences. To investigate the cause of differences in the taproot phenotype, de novo and comparative transcriptomic analysis on PN taproot was performed. A total of 133,730,886 and 114,761,595 paired-end clean reads were obtained based on high-throughput sequencing from oval and long taproot samples, respectively. 121,955 unigenes with contig N50 = 1,774 bp were generated by using the de novo assembly transcriptome, 63,133 annotations were obtained with the BLAST. And then, 42 genes belong to class III peroxidase (PRX) gene family, 8 genes belong to L-Ascorbate peroxidase (APX) gene family, and 55 genes belong to a series of mitogen-activated protein kinase (MAPK) gene family were identified based on integrated annotation results. Differentially expressed genes analysis indicated substantial up-regulation of PnAPX3 and PnPRX45, which are related to reactive oxygen species metabolism, and the PnMPK3 gene, which is related to cell proliferation and plant root development, in long taproots compared with that in oval taproots. Furthermore, the determination results of real-time quantitative PCR, enzyme activity, and H2O2 content verified transcriptomic analysis results. These results collectively demonstrate that reactive oxygen species (ROS) metabolism and the PnMPK3 gene may play vital roles in regulating the taproot phenotype of PN. This study provides further insights into the genetic mechanisms of phenotypic differences in other species of the genus Panax. The online version contains supplementary material available at 10.1186/s12864-021-08283-w.
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影响因子：
4.3
作者：
Herrero, Joaquin;Fernandez-Perez, Francisco;Miguel Zapata, Jose
通讯作者：
Miguel Zapata, Jose
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
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影响因子：
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作者：
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影响因子：
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