广州相思子全长转录组测序及分析

Full-length Transcriptome Sequencing of Abrus pulchellus subsp.cantoniensis(Hance)Verdc.

目的:获得广州相思子Abrus pulchellus subsp.cantoniensis(Hance)Verdc.全长转录本。方法:利用PacBio Sequel测序平台,通过对广州相思子的根、茎、叶3个部位混合样品开展三代全长转录组测序,并对测序数据进行生物信息学分析。结果:共获得原始测序数据14.55 Gb,最终获得转录本序列172829条,N50长度为1572 nt,鸟嘌呤和胞嘧啶(GC)占比为40.86%。基因注释中,共有158888(91.93%)个转录本被成功注释;基因本体(GO)数据库注释中,102457个(59.28%)转录本分为生物学过程、细胞组成和分子功能三大类46个功能组;真核生物相邻类的聚簇(KOG)数据库注释中,一般功能预测的转录本最多,为22461个;信号转导机制、翻译后修饰、蛋白反转和分子伴侣亦为其主要功能途径;京都基因与基因组百科全书(KEGG)注释到转录本有99847个,其中参与广州相思子生物合成和其他次生代谢有4530个。基因结构分析中,共得到92344条编码序列,4800个转录因子隶属于59个转录因子家族。此外,简单序列重复(SSR)标记分析表明,40050处SSR位点中单碱基重复的SSR数目最多,其次是包含腺嘌呤(A)G/C胸腺嘧啶(T)的二碱基重复SSR。结论:获得的广州相思子全长转录组数据可为后续基因功能、代谢通路调控及分子标记开发等研究提供数据支撑。

Objective:To obtain the full-length transcriptome of Abrus pulchellus subsp.cantoniensis(Hance)Verdc.Methods:PacBio Sequel was used for the third-generation full-length transcriptome sequencing of mixed root,stem,and leaf samples of A.pulchellus subsp.cantoniensis,and bioinformatics tools were used to analyze the sequencing data.Results:A total of 14.55 Gb of raw reads were obtained.The full-length transcriptome sequencing yielded 172829 transcripts,with the N50 length of 1572 nt and GC content of 40.86%,among which 158888(91.93%)transcripts were annotated.In Gene Ontology(GO)annotation,102457(59.28%)transcripts were classified into 46 functional groups of biological processes,cellular components,and molecular functions.In EuKaryotic Orthologous Groups(KOG),22461 transcripts were annotated to general functions such as signal transduction,post-translational modification,protein inversion,and molecular chaperones.In addition,99847 transcripts were annotated in the Kyoto Encyclopedia of Genes and Genomes(KEGG),among which 4530 transcripts were involved in the biosynthesis and other secondary metabolism of A.pulchellus subsp.cantoniensis.The gene structure analysis predicted 92344 coding sequences(CDSs)and 4800 transcription factors(TFs)belonging to 59 TF families.In addition,the simple sequence repeat(SSR)analysis showed that single-base repeats had the highest number,followed by two-base repeats containing AG/CT.Conclusion:The full-length transcriptome obtained in this study can provide data support for subsequent studies of the gene function,regulation of metabolic pathways,and development of molecular markers.