基于SMRT技术的水杉全长转录组分析及基因功能注释

Characterization of the full-length transcriptome using SMRT technology and functional annotation of the genes in Metasequoia glyptostroboides

以水杉原生种为材料,提取其幼嫩植株的根、茎和叶的总RNA,经mRNA纯化、反转录、全长转录组文库构建等过程,再采用SMRT技术测定其全长转录本序列,运用生物信息学对获得的原始转录组数据进行分析。结果显示:提取的总RNA符合建库要求;全长转录组测序共获得了包含5914711个亚读段(subreads)的14.0 Gb的数据,质量控制处理后包括236130个全长非嵌合读段(reads)和97626个一致性reads;转录本经去冗余处理后共获得61057个全长一致性读段(unigenes),其中有54099个被成功注释到7个数据库中,注释比达88.60%;对水杉unigenes作CDS(coding sequence)长度分布及转录因子分析,其CDS长度范围为144~6477 nt,平均长度约为679 nt;共检测到2386个转录因子,这些转录因子可以归类为29个家族。

This study selected the young roots,stems and leaves of the native species Metasequoia glyptostroboides(M.glyptostroboides)as material and the total RNA was extracted from them,respectively.The RNA products were equally mixed and then was used for mRNA purification,reverse transcription and full-length transcriptome library construction.The SMRT(single-molecule real-time)technology was employed to sequence transcriptome library,and bioinformatics methods were used to analyze transcriptome data.The results showed that the extracted total RNA could meet the requirements of library construction;a total of 14.0 Gb of data containing 5914711 subreads were obtained,including 236130 full-length non-chimeric reads and 97626 consensus reads after quality control treatment.After redundancy removal,a total of 61057 full-length unigenes were identified,among which 54099 were successfully annotated into seven databases,accounting for 88.60%.In addition,CDS(coding sequence)length distribution and TFs(transcription factors)of these unigenes were analyzed.The CDS length ranged from 144 to 6477 nt,with an average length of 679 nt;a total of 2386 transcription factors were detected,which could be classified into 29 families.