Full-length Transcriptome Sequencing and Heat Shock Transcription Factor Family （HSFs） Analysis of Littledalea racemosa（Poaceae） Based on PacBio Platform

doi:10.11733/j.issn.1007-0435.2025.02.005

Acta Agrestia Sinica ›› 2025, Vol. 33 ›› Issue (2): 370-381.DOI: 10.11733/j.issn.1007-0435.2025.02.005

Full-length Transcriptome Sequencing and Heat Shock Transcription Factor Family （HSFs） Analysis of Littledalea racemosa（Poaceae） Based on PacBio Platform

QU Rong-ju¹, LIU Yu-ping^1,2, SU Xu^1,2,3, FU Gui¹, JIN Jia-rui¹, YANG Qian¹, ZHANG Peng-hui¹, YU Ming-jun¹, SUN Cheng-lin¹, MAO Xuan-rui¹

1. School of Life Sciences, Qinghai Normal University, Xining, Qinghai Province 810008, China;
2. Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, Qinghai Province 810008, China;
3. Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, Qinghai Province 810016, China

Received:2024-06-19 Revised:2024-09-04 Published:2025-03-01

基于PacBio平台的扇穗茅全长转录组测序及热激转录因子家族（HSFs）分析

曲荣举¹, 刘玉萍^1,2, 苏旭^1,2,3, 富贵¹, 靳佳瑞¹, 杨倩¹, 张朋辉¹, 余明君¹, 孙成林¹, 毛轩睿¹

1. 青海师范大学生命科学学院, 青海西宁 810008;
2. 青海师范大学青海省青藏高原生物多样性形成机制与综合利用重点实验室, 青海西宁 810008;
3. 青海师范大学高原科学与可持续发展研究院, 青海西宁 810016

通讯作者: 苏旭,E-mail:xusu8527972@126.com
作者简介:曲荣举（2000-）,男,汉族,山东聊城人,硕士研究生,主要从事高山植物系统与进化方面研究,E-mail:QU203462@163.com
基金资助:
国家自然科学基金项目（32160297,32360305）;2023年中央林业草原生态保护恢复资金野生动植物保护项目（QHSY-2023-016）;2023年省级财政林业改革发展资金林草新技术推广项目（QSCZ-2023-001）资助

Abstract

Abstract: In order to clarify the transcriptome characteristics of Littledalea racemosa and the function and systematic location of the heat shock transcription factor family （HSFs）, we sequenced and analyzed the full-length transcriptome based on the PacBio platform in this study. The results indicated that we obtained 62 016 high quality unigenes with an average length of 2752 bp, the length of N50 of 2971 bp, 48 127 protein coding region sequences （CDS） and 8 858 simple repeat sequences （SSR）. The number of unigenes annotations in five public databases was 27 566 （NR）, 17 961 （GO）, 18 300 （KOG）, 17 381 （KEGG） and 23 737 （SwissProt）, and 7663 unigenes （12.36%） were annotated in all five databases. 1165 transcription factors were identified in transcriptome of L. racemosa, belonging to 48 transcription factor families, the majority of which were related to the adaptation to the extreme environment of the plateau. The transcriptome contained 17 HSF transcription factors, most of which were located in the nucleus and hydrophilic proteins, and HSF cDNA usually contained from 5 to 10 motifs. Phylogenetic tree showed HSF transcription factors of L. racemosa and Arabidopsis thaliana were clustered into nine clades （Clade A-I）, most of which were composed of HSF transcription factors from the same species and were closely related to each other. 11 HSFs of L.racemosa and HSFA2 of A.thaliana were clustered into one clade, which was closely related to each other and might have similar functions. This study enriched the genetic information for Littledalea and provided a theoretical basis for the mining of key functional genes in the future.

Key words: Littledalea racemosa, Full-length transcriptome, Function annotation, Transcription factor, HSFs

摘要： 为了明晰扇穗茅（Littledalearacemosa）的转录组特征和热激转录因子家族（HSFs）的功能与系统位置,本研究基于PacBio平台对扇穗茅全长转录组进行了测序和生物信息学分析。结果表明：测序获得高质量的Unigenes 62 016条,平均长度为2752 bp,N50长度为2971 bp,蛋白编码区序列（CDS）48 127个,简单重复序列（SSR）8858个；扇穗茅Unigenes在5大公共数据库中的注释量分别为27 566（NR）、17 961（GO）、18 300（KOG）、17 381（KEGG）和23 737（SwissProt）,有7663条Unigenes在5个数据库中均得到注释；扇穗茅转录本鉴定到1165个转录因子,隶属于48个转录因子家族,大多与高原极端环境适应有关；其中包含17个热激转录因子（HSF）,大部分位于细胞核,为亲水蛋白,cDNA常包含5~10个保守结构域；系统发育研究表明扇穗茅和拟南芥（Arabidopsis thaliana）HSF转录因子聚为9个分支（CladeA-I）,扇穗茅的11个HSF与HSFA2聚为一支,彼此具有较近的亲缘关系,可能具有相似的功能。本研究丰富了扇穗茅属物种的遗传信息,为后续关键功能基因的挖掘提供了理论依据。

关键词: 扇穗茅, 全长转录组, 功能注释, 转录因子, HSFs

CLC Number:

Q949.71

QU Rong-ju, LIU Yu-ping, SU Xu, FU Gui, JIN Jia-rui, YANG Qian, ZHANG Peng-hui, YU Ming-jun, SUN Cheng-lin, MAO Xuan-rui. Full-length Transcriptome Sequencing and Heat Shock Transcription Factor Family （HSFs） Analysis of Littledalea racemosa（Poaceae） Based on PacBio Platform[J]. Acta Agrestia Sinica, 2025, 33(2): 370-381.

曲荣举, 刘玉萍, 苏旭, 富贵, 靳佳瑞, 杨倩, 张朋辉, 余明君, 孙成林, 毛轩睿. 基于PacBio平台的扇穗茅全长转录组测序及热激转录因子家族（HSFs）分析[J]. 草地学报, 2025, 33(2): 370-381.

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Full-length Transcriptome Sequencing and Heat Shock Transcription Factor Family （HSFs） Analysis of Littledalea racemosa（Poaceae） Based on PacBio Platform

基于PacBio平台的扇穗茅全长转录组测序及热激转录因子家族（HSFs）分析

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