药食同源植物甘葛藤的全长转录组分析

doi:10.7668/hbnxb.20192213

摘要/Abstract

摘要： 为了深入了解甘葛藤转录组的整体水平及黄酮类生物合成通路基因。利用高通量测序PacBio Sequel平台，以甘葛藤根、茎、叶的混合样品为材料，使用单分子长读数测序技术（SMRT）对甘葛藤进行全长转录组测序及分析。平台共获得10 994 967个高质量reads和384 072条全长非嵌合序列（FLNC），测序数据经质控后获得90 856个转录本；获得的所有转录本经NR、SwissProt、KOG、KEGG、GO数据库进行注释和功能分类，结果有85 239个单基因被注释，NR注释数量最多为84 675个，占93.2%；KEGG注释的基因最少，22 330个基因被注释到132条途径，代谢途径分布的基因较多（9 368，41.95%）。预测到3 507个转录因子，bHLH转录因子家族的基因最多。14 127个基因被分配到17个R基因类别，主要为RLP类。检测到33 660个SSR序列，多为AG/CT类型。分析黄酮类生物合成途径，发现与黄酮类合成相关的基因110个，其中，26个编码HCT，3个编码CHS，7个编码CHI。PacBio测序平台能获得更长的转录本，SMRT技术能够深入挖掘甘葛藤转录数据，比第二代测序技术能够获得更高的转录本注释率。在高通量全长转录组水平对甘葛藤进行了研究，为甘葛藤的分子生物学研究提供了较可靠、全面的转录组数据，为进一步开发甘葛藤的分子标记和挖掘优良基因提供了科学依据。

关键词: 甘葛藤, 药食同源, 全长转录组, 育种

Abstract: In order to in-depth understand the overall level of transcriptome and the flavonoid biosynthesis pathway genes of Pueraria thomsonii Benth. The mixed sample of root, stem and leaf of Pueraria thomsonii was used as materials for sequencing analysis using the single-molecule long read sequencing technology(SMRT) of Pacific Biosciences Sequel platform. A total of 10 994 967 high quality reads and 384 072 full-length non-chimeric(FLNC) were obtained. Sequencing data after quality control, 90 856 isoforms were obtained. There were 85 239 isoforms annotated by NR, SwissProt, KOG, KEGG and GO databases, and the number of NR annotation was 84 675, accounting for 93.2%;In KEGG database, only 22 330 genes were annotated in 132 pathways, and 9 368 genes were distributed more in metabolic pathway, accounting for 41.95%. A total of 3 507 transcription factors(TF) were predicted, and bHLH TF family was the most annotated genes. Besides, 14 127 genes were assigned to 17 R gene classes, mainly RLP. 33 660 SSR sequences were detected, most of them were AG/CT type. By analyzing the biosynthesis pathway of flavonoids, 110 genes were found, including 26 genes encoding HCT, 3 genes encoding CHS and 7 genes encoding CHI. Compared with Illumina HiSeq^TM2500, PacBio platform obtained longer transcripts and higher annotation rates. This research intensively studied the Pueraria thomsonii at the full-length transcriptome level, which provided more reliable transcriptome data for molecular biology research and scientific basis for further development of molecular markers and mining excellent genes of Pueraria thomsonii.

Key words: Pueraria thomsonii, Homology of medicine and food, Full-length transcriptome, Breeding

中图分类号:

S567.19

梅瑜, 李向荣, 蔡时可, 顾艳, 王继华. 药食同源植物甘葛藤的全长转录组分析[J]. 华北农学报, 2021, 36(5): 10-17. doi: 10.7668/hbnxb.20192213.

MEI Yu, LI Xiangrong, CAI Shike, GU Yan, WANG Jihua. Full-length Transcriptome Analysis of a Homology of Medicine and Food of Pueraria thomsonii[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2021, 36(5): 10-17. doi: 10.7668/hbnxb.20192213.

http://www.hbnxb.net/CN/Y2021/V36/I5/10

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