基于单分子纳米孔测序技术揭示大白菜抽薹期全长转录组差异的复杂性  

Complexity of Differences in Full-Length Transcriptome at Bolting Stage between Late-and Early-Bolting Chinese Cabbage Lines Revealed by Single-Molecule Nanopore DNA Sequencing Technology

作　　者：王树彬 张志刚[1] 王荣花 李巧云[1] 王立华[1] 胡新新[1] 赵智中[1] 刘栓桃[1] Wang Shubin;Zhang Zhigang;Wang Ronghua;Li Qiaoyun;Wang Lihua;Hu Xinxin;Zhao Zhizhong;Liu Shuantao(Vegetable Institute of Shandong Academy of Agricultural Sciences/Shandong Branch of National Center for Vegetables Improvement/Shandong Key Laboratory for Biology of Greenhouse Vegetables/Huang￣Huai Region Scientific Observation and Experimental Station of Vegetables in Shandong,Ministry of Agriculture and Rural Affairs,Jinan 250100,China)

机构地区：[1]山东省农业科学院蔬菜研究所/国家蔬菜改良中心山东分中心/山东省设施蔬菜生物学重点实验室/农业部黄淮地区蔬菜科学观测实验站(山东),山东济南250100

出　　处：《山东农业科学》2024年第11期1-12,共12页Shandong Agricultural Sciences

基　　金：山东省自然科学基金项目(ZR2021QC228,ZR2019BC048);山东省农业良种工程项目(2022LZGCQY005,2019LZGC006);山东省农业科学院农业科技创新工程项目(CXGC2021B17,CXGC2021A30-2)。

摘　　要：为了解春白菜抽薹相关转录组的结构和表达差异,采用单分子纳米孔测序技术对早抽薹材料He102与晚抽薹材料06-247带叶片的花序轴进行了全长转录组分析。与大白菜参考基因组V3.0比对后,He102与06-247分别得到了6051557条和4844987条有效读段以及37309条和30415条非冗余全长转录本。两材料中共鉴定到46485个非冗余基因,其中包括1688个新基因。从He102与06-247中分别鉴定出2421个和993个独有的可变剪切事件,内含子保留是最常见的可变剪切类型;分别鉴定到3286个和2646个独有的可变多聚酰胺酸位点。共筛选出453个lncRNA,80%以上的lncRNA属于基因间区非编码RNA,分别鉴定到81个和55个He102和06-247独有的lncRNA。在两材料中筛选到5197个差异表达基因,其中He102中上调的有2453个,下调的有2744个,结合功能富集分析获得了41个与抽薹有关的候选基因。本研究结果揭示了不同抽薹期大白菜材料转录组在结构和表达上存在复杂的差异,这为阐释大白菜抽薹分子机理提供了新的线索。To learn about the transcriptomic structure and expression pattern related to bolting in spring Chinese cabbage,the full-length transcriptomes were analyzed with samples of floral axis connected with one piece of leaf from early-bolting line He102 and late-bolting line 06-247.By aligning reads to reference genome V3.0 of Chinese cabbage,6051557 and 4844987 clean full-length mapped reads along with 37309 and 30415 non-redundant full-length transcripts were identified in He102 and 06-247,respectively.By integrating non-redundant full-length transcripts from the two lines,a total of 46485 unigenes were obtained,which in-cluded 1688 novel genes.Through alternative splicing(AS)analysis,2421 and 993 AS events were found only occurred in He102 and 06-247 respectively,and intron retention was the most common type of the AS e-vents.He102 and 06-247 harbored 3286 and 2646 specific alternative polyadenylation(APA)events,re-spectively.In total,453 long non-coding RNAs(lncRNA)were identified with 81 ones only from He102 and 55 ones only from 06-247,and more than 80%of them were long intergenic non-coding RNAs.There were 5197 differentially expressed genes were selected by comparing He102 and 06-247,and 2744 ones were down regulated and 2453 ones were up regulated in He102.Combined with information from GO annotation,41 potential candidate genes related to bolting were identified.These results suggested the differences in struc-ture and expression of transcriptome between late-and early-bolting Chinese cabbage lines were very complex,and offered new information for elucidating the molecular mechanism of Chinese cabbage bolting.

关 键 词：第三代高通量测序技术 单分子纳米孔测序技术 大白菜 抽薹期 全长转录本 

分 类 号：S634.1[农业科学—蔬菜学]