Full-length Transcriptome Sequencing and Dof Transcription Factor Family Analysis of Caucasian Clover

doi:10.11733/j.issn.1007-0435.2023.11.013

Acta Agrestia Sinica ›› 2023, Vol. 31 ›› Issue (11): 3343-3354.DOI: 10.11733/j.issn.1007-0435.2023.11.013

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Full-length Transcriptome Sequencing and Dof Transcription Factor Family Analysis of Caucasian Clover

MOU Dan¹, ZHAO Qi-jun², LIU Yu-ying², LI Chang-hui², XIE Jiu-xiang²

1. State key laboratory of plateau ecology and agriculture, Qinghai University, Xining, Qinghai Province 810016, China;
2. College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province 810016, China

Received:2023-05-18 Revised:2023-07-28 Online:2023-11-15 Published:2023-12-01

高加索三叶草全长转录组测序及Dof转录因子家族分析

牟丹¹, 赵啟军², 刘玉英², 李长慧², 谢久祥²

1. 青海大学省部共建三江源生态与高原农牧业国家重点实验室, 青海西宁 810016;
2. 青海大学农牧学院, 青海西宁 810016

通讯作者: 谢久祥,E-mail:xiejiuxiagqh@163.com
作者简介:牟丹(1989-),女,汉族,四川绵阳人,助理研究员,主要从事草地植物资源方面研究,E-mail:moudan1761@163.com
基金资助:
青海省“昆仑英才·高端创新创业人才”[青人才字(2023)1号]；国家自然科学基金[32160334];青海大学2023年度青年科研基金[2023-QNY-5]资助

Abstract

Abstract: In order to explore the transcriptional characteristics of Trifolium ambiguum Bieb. under long-term low temperature stress,the full-length transcriptome was sequenced by PacBio Sequel platform,and a total of 70 590 full-length transcripts (Isoforms) were obtained. The functional annotation results of all Isoforms indicated the highest homologous similarity rate between caucasian clover and red clover existed,and the number of isoforms involving signal transduction mechanisms,stimulus response,starch and sucrose metabolism and plant hormone signal transduction pathways was the highest. Besides,the structural analysis results of all Isoforms showed that 19 693 SSRs,2 668 LncRNAs,2 788 AS,and 2 917 TFs were predicted and screened. The ERF,C3H,and Dof transcription factor families contained a larger number of isoforms. Moreover,the bioinformatics analysis of the Dof transcription factor family showed that all 42 Dof family members were hydrophilic proteins,most of which were located in the nucleus. The phylogenetic tree analysis clustered the Dof proteins of caucasian clover and Arabidopsis into 11 subfamilies. And the conserved Motif1 and Motif2 appeared more frequently. The above findings can provide a data support for the next step to cold resistance gene mining and functional verification,and lay a theoretical foundation for analyzing the physiological and biochemical mechanisms of caucasian clover tolerated to the long-term cold stress.

Key words: Caucasian clover, Low temperature, Full-length transcriptome, Dof

摘要： 为探究面临长时间低温胁迫的高加索三叶草(Trifolium ambiguum Bieb.)的转录特征，本研究通过PacBio Sequel平台进行全长转录组测序，获得70 590条全长转录本(isoforms)。Isoforms的功能注释结果为：与红三叶的同源相似率最高，涉及信号转导机制、刺激响应、淀粉和蔗糖代谢通路、植物激素信号转导通路的Isoforms较多。Isoforms的结构分析结果为：预测到19 693个SSR、2 668 条LncRNA、2 788个AS和2 917条TFs序列，TFs中的ERF,C3H,Dof等家族含序列数量较多。Dof转录因子家族的生物信息学分析结果为：42个Dof家族成员全部为亲水蛋白，大部分定位于细胞核；系统进化树分析将高加索三叶草与拟南芥Dof蛋白聚类为11个亚族；保守基序Motif1和Motif2出现的频率较高。以上发现可为下一步抗寒基因挖掘和功能验证提供数据支撑，并为解析高加索三叶草耐受长时间低温胁迫的生理生化机制奠定理论基础。

关键词: 高加索三叶草, 低温, 全长转录组, Dof

CLC Number:

Q945.78

MOU Dan, ZHAO Qi-jun, LIU Yu-ying, LI Chang-hui, XIE Jiu-xiang. Full-length Transcriptome Sequencing and Dof Transcription Factor Family Analysis of Caucasian Clover[J]. Acta Agrestia Sinica, 2023, 31(11): 3343-3354.

牟丹, 赵啟军, 刘玉英, 李长慧, 谢久祥. 高加索三叶草全长转录组测序及Dof转录因子家族分析[J]. 草地学报, 2023, 31(11): 3343-3354.

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Full-length Transcriptome Sequencing and Dof Transcription Factor Family Analysis of Caucasian Clover

高加索三叶草全长转录组测序及Dof转录因子家族分析

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