Journal of Guangxi Normal University(Natural Science Edition) ›› 2022, Vol. 40 ›› Issue (6): 247-256.doi: 10.16088/j.issn.1001-6600.2021080902

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Sequencing and Bioinformatic Analysis for Transcriptome of Shandan Sphallerocarpus racills Leaf

ZHANG Chunmei1,2*, YAN Fang2,3, SONG Hai2, ZHANG Xifeng1,2 , CHEN Ye1,2   

  1. 1. College of Agriculture and Ecological Engineering, Hexi University, Zhangye Gansu 734000, China;
    2. Key Laboratory of Hexi Corridor Resources Utilization of GanSu, Zhangye Gansu 734000, China;
    3. Ecological & Oasis Agricultural Research Institute of Hexi University, Zhangye Gansu 734000,China
  • Received:2021-08-09 Revised:2021-09-17 Online:2022-11-25 Published:2023-01-17

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Abstract: Sphallerocarpusg racilis is considered as “second Panax Ginseng” in Compendium of Materia Medica. The high-throughput sequencing platform BGISEQ-500 was used to sequence the transcriptome of Huangshen (S. racills) leaf and transcriptome analysis software was used for assembly, and annotation. The results showed: 1) A total of 99 981 unigenes were obtained through de novo assembly,with total length of 113 850 816 bp, an average length of 1 138 bp and N50 of 1 874 bp. GC content accounted for 39.93%. 2) The unigenes were functionally annotated by searching against seven protein databases. There were 49 390 (NT:49.40%), 48 281 (SwissProt:48.29%), 61 116 (KOGdatabase:61.13%) and 55 859 (Pfam:55.87%) Unigenes for functional annotation,respectively. 3) Compared with NR database, 66 451 Unigene were annotated in the NR. It was found that S. gracilis had higher homology with Daucus carota subsp. sativus, but lower homology with other species. 4) 78 040 Unigeneswere annotated within 40 terms of three main GO (Gene Ontology) categories. According to function, they were divided into biological process, cellular component and molecular function, which included 15, 11 and 14 subclasses respectively, with the largest proportion of classes performing biological process. 5) For KEGG(Kyoto Encyclopedia of Genes and Genomes)analysis, 51 479 Unigenes were assigned to 20 known metabolic pathways. 6) 61 116 Unigenes were annotated in the KOG database and a total of 26 gene functional categories were obtained.Among them, the genes involved in general function, signal transduction mechanisms, translation, modification and protein transportation were the most abundant categories. 7) A total of 62 323 CDSs were detected by Transdecoder from the transcriptome. Moreover, a total of 17 308 SSRs(simple sequence repeats) from 13 256 Unigenes were identified from the transcriptome. Di-nucleotidere peat motif was the most abundant SSR, accounting for 38.83% (6 721 SSRs). 2 370 Unigenes encoding transcription factors were predicted. Conclusion: The study provided valuable information and abundant resources for revealing its genetic background, future functional genome analysis, molecular marker developmentand laid a foundation for comprehensive utilization and protection of S. racills.

Key words: Sphallerocarpusg racilis, transcriptome, functional gene, bioinformatics, SSR markers

CLC Number: 

  • S567.239
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