De novo assembly and characterization of Gleditsia sinensis transcriptome and subsequent gene identification and SSR mining.
De novo assembly and characterization of Gleditsia sinensis transcriptome and subsequent gene identification and SSR mining.
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DOI：
10.4238/gmr.15017740
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发表时间：
2016-01
期刊：
影响因子：
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通讯作者：
Shiming Han;Zhenjiang Wu;X. Wang;K. Huang;Ye Jin;Wannian Yang;Huazhong Shi
中科院分区：
文献类型：
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作者：
Shiming Han;Zhenjiang Wu;X. Wang;K. Huang;Ye Jin;Wannian Yang;Huazhong Shi
皂荚是我国特有的落叶树种，具有很高的经济和药用价值。然而，由于缺乏生物信息学资源，如可用的全基因组序列，对该物种的医学特性的分子过程的了解有限。本研究利用RNA测序数据对G.利用生物信息学工具对参与重要分子生物学过程的主要基因进行了研究。从G. sinensis。使用组装工具Trinity，发现了233，751个转录本。其中，85，795个被鉴定为独特的转录物，59，326个独特的转录物被发现含有编码区。基因本体分析确定了27，637个独特的转录本，这些转录本被聚类为56个功能组。进一步分析了参与类黄酮和萜类骨架生物合成的基因以及编码转录因子的基因。序列分析表明，G.编码类黄酮生物合成酶的中华查尔酮异构酶基因（GsCHI）。GsCHI1与豆科植物查尔酮异构酶具有亲缘关系，其在不同组织中的转录水平均高于GsCHI2、GsCHI3和GsCHI4。此外，在转录本文库中发现了15，014个SSR标记，并产生了5170个SSR位点的引物。本研究所获得的遗传学和基因组学信息将有助于进一步研究G. sinensis。
Gleditsia sinensis is a Chinese native deciduous tree with a high economic and medicinal value. However, there is limited knowledge on the molecular processes responsible for the medical properties of this species owing to lack of bioinformatic resources such as available whole-genome sequences. In the present study, RNA sequencing data were used to analyze the transcriptome of G. sinensis, and a series of bioinformatic tools was used to explore the main genes involved in important molecular processes. A total of 75.57 million paired-end reads, with a length of 101 bp, were acquired from G. sinensis. Using the assembly tool Trinity, 233,751 transcripts were discovered. Among these, 85,795 were identified as unique transcripts and 59,326 unique transcripts were found to contain coding regions. Gene ontology analysis identified 27,637 unique transcripts that were clustered into 56 functional groups. Genes involved in flavonoid and terpenoid backbone biosynthesis and those encoding transcription factors were further analyzed. Sequence analysis revealed four putative G. sinensis chalcone isomerase genes (GsCHI) encoding the enzymes for flavonoid biosynthesis. GsCHI1 was found to be phylogenetically related to the chalcone isomerase of the family Leguminosae, and its transcript levels in different tissues were higher than those of GsCHI2, GsCHI3, and GsCHI4. Furthermore, 15,014 simple sequence repeat (SSR) markers were discovered in the transcript library, and 5170 primers were generated for the SSR loci. The genetic and genomic information presented in this study will be helpful for future studies on gene discovery and molecular processes in G. sinensis.