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首页> 外文期刊>Journal of genetics >De novotranscriptome assembly and mining of EST-SSR markers inGloriosa superba
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De novotranscriptome assembly and mining of EST-SSR markers inGloriosa superba

机译：De Novotrovercriptome组装和挖掘Est-SSR标记Ingloriosa Superba

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Gloriosa superbais an economical source of pharmaceutical colchicine, which is a mitotic poison used to treat gout, cancer and inflammatory diseases. It is important to study the genetic variations in this plant, but the progress is impeded due to limited number of molecular markers. In this study, we developed the expressed sequence tag-derived simple sequence repeat (EST-SSR) markers from the transcriptome sequence of the leaf samples of three different ecotypes ofG. superba.De novoassembly was performed on these sequencing data to generate a total of 65,579 unigenes and 38,200 coding sequences (CDSs). These CDSs were annotated using NCBI Nr protein database, gene ontology terms and KEGG pathways. Differential gene expression was studied to yield differences in these ecotypes at the molecular level. Finally, a total of 14,672 potential EST-SSRs were identified from these unigenes, among which the dinucleotide (5754, 39.22%) and trinucleotide (5421, 36.95%) repeats were most abundant types followed by mononucleotides (3213, 21.83%). The most frequent motifs were CT/GA (1392, 9.48%), AG/TC (1219, 8.31%), and GA/CT (1146, 7.82%) among the dinucleotide repeats and CCG/CGG (1487, 10.13%), AGG/CCT (1421, 9.68%), AGC/CTG (697, 4.75%) and AAG/CTT (621, 4.23%) among the trinucleotide repeats. Polymorphism study using a random set of 20 newly developed EST-SSRs revealed polymorphic information content value ranging from 0 to 0.5926 with an average of 0.4021. The large-scale ESTs developed in the current study will be useful as a genomic resource for further investigation of the genetic variations in this species.
机译：Gloriosa superbais是药用秋水仙碱的经济来源，秋水仙碱是一种有丝分裂毒素，用于治疗痛风、癌症和炎症疾病。研究这种植物的遗传变异很重要，但由于分子标记数量有限，研究进展受阻。在本研究中，我们从三种不同生态型的银杏叶片样本的转录组序列中开发了表达序列标签衍生的简单序列重复（EST-SSR）标记。superba。对这些测序数据进行从头组装，共产生65579个单基因和38200个编码序列（CDS）。使用NCBI Nr蛋白质数据库、基因本体术语和KEGG途径对这些CDS进行注释。为了在分子水平上产生这些生态型的差异，对差异基因表达进行了研究。最后，从这些单基因中鉴定出14672个潜在的EST SSR，其中二核苷酸（5754,39.22%）和三核苷酸（5421,36.95%）重复序列最丰富，其次是单核苷酸（3213,21.83%）。在二核苷酸重复序列中，最常见的基序是CT/GA（1392,9.48%）、AG/TC（1219,8.31%）和GA/CT（1146,7.82%），在三核苷酸重复序列中，最常见的基序是CCG/CGG（1487,10.13%）、AGG/CCT（1421,9.68%）、AGC/CTG（697,4.75%）和AAG/CTT（621,4.23%）。利用20个新开发的EST-ssr进行多态性研究，发现多态信息含量值在0到0.5926之间，平均值为0.4021。本研究中开发的大规模EST将作为进一步研究该物种遗传变异的基因组资源。

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