基于RNA-Seq高通量测序技术的法螺差异表达基因分析

doi:10.11978/2022197

热带海洋学报 ›› 2023, Vol. 42 ›› Issue (4): 146-154.doi: 10.11978/2022197CSTR: 32234.14.2022197

基于RNA-Seq高通量测序技术的法螺差异表达基因分析

刘文广¹(), 张格格¹^,², 岑希彤¹^,², 何毛贤¹()

1.中国科学院热带海洋生物资源与生态重点实验室, 广东省应用海洋生物学重点实验室, 中国科学院南海海洋研究所, 广东广州 510301
2.中国科学院大学, 北京 100049

收稿日期:2022-09-20 修回日期:2022-10-17 出版日期:2023-07-10 发布日期:2022-10-13
作者简介:
刘文广(1978—), 山东省聊城市人, 副研究员, 主要从事贝类育种及环境适应性研究。email: lwg@scsio.ac.cn
基金资助:
国家自然科学基金项目(42176129); 广东省自然科学基金项目(2022A1515010779)

Analysis of differential expressed genes from Charonia tritonis based on transcriptome sequencing

LIU Wenguang¹(), ZHANG Gege¹^,², CEN Xitong¹^,², HE Maoxian¹()

1. CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
2. University of Chinese Academy of Sciences, Beijing 100049, China

Received:2022-09-20 Revised:2022-10-17 Online:2023-07-10 Published:2022-10-13
Supported by:
National Natural Science Foundation of China(42176129); Natural Science Foundation of Guangdong Province(2022A1515010779)

摘要/Abstract

摘要：

法螺是珊瑚礁“杀手”长棘海星为数不多的自然捕食者之一, 是珊瑚礁生态系统的重要保卫者。但是, 由于海洋环境变化、人类的过度捕捞、珊瑚礁栖息地被破坏等因素, 法螺的自然资源遭受严重破坏, 已长期处于濒临灭绝的状态。尽快开展法螺基础研究迫在眉睫, 但是该物种的基因组资源有限, 阻碍了如生物矿化等分子机制的深入研究。本研究借助于Illumina HiSeq^TM2000测序平台完成了法螺两种组织(肌肉与外套膜)的高通量测序工作。测序所得原始序列经筛选、组装之后比对到NR、NT、Swissprot、KEGG、GO和InterPro数据库中获得注释结果, 并进行差异基因聚类分析。结果表明, 测序共获得109722个Unigene, 其中有46239个Unigene得到功能注释, 共获得7994个差异表达基因, 其中在法螺外套膜组织中有 3196个上调, 4798个下调。对差异表达基因(differentially expressed genes, DEG)的GO注释和KEGG富集分析显示, 高表达的DEG显著富集在典型的生物矿化相关通路中, 如糖胺聚糖生物合成硫酸软骨素通路(glycosaminoglycan biosynthesis chondroitin sulfase dermatan sulfate)、磺基转移酶活性(sulfotransferase activity)、钙离子结合(calcium ion binding)等。通过实时定量荧光聚合酶链反应(RT-qPCR)对8个与矿化相关的DEG基因的表达情况进行验证表明, 其表达趋势与转录组测序结果一致。本研究中所获得丰富的转录本和全面的转录组信息, 增加了法螺基因信息的同时, 还为法螺矿化机制的解析提供了一定的数据支持。

关键词: 法螺, 转录组, 差异表达基因

Abstract:

The giant triton snail (Charonia tritonis), an endangered gastropod species of ecological and economic importance, is widely distributed in coral reef ecosystems of the Indo-West Pacific region and the tropical waters of the South China Sea. Research on molecular mechanisms is limited due to the lack of complete genomic data for this species. In the present work, transcriptome sequencing of foot muscle and mantle in C. tritonis were obtained by Illumina HiSeq sequencing platform, from which 7994 (3196 upregulated and 4798 downregulated) differentially expressed genes (DEGs) containing biomineralization sequences were identified. The top 20 GO terms in the molecular function category were considered to be related to biomineralization. In KEGG classifications, DEGs are primarily enriched in some pathways that may be involved in biomineralization. The results of qPCR showed that three of the eight genes examined are significantly up-regulated in the mantle. Our results improve the understanding of biomineralization in C. tritonis and provide fundamental transcriptome information to study other molecular mechanisms, such as reproduction.

Key words: Charonia tritonis, transcriptome, DEG

刘文广, 张格格, 岑希彤, 何毛贤. 基于RNA-Seq高通量测序技术的法螺差异表达基因分析[J]. 热带海洋学报, 2023, 42(4): 146-154.

LIU Wenguang, ZHANG Gege, CEN Xitong, HE Maoxian. Analysis of differential expressed genes from Charonia tritonis based on transcriptome sequencing[J]. Journal of Tropical Oceanography, 2023, 42(4): 146-154.

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样本名称	总数/个	总长度/bp	平均长度/bp	N50长度/bp	N70长度/bp	GC碱基对数量/%
法螺肌肉	87443	50845674	581	799	426	43.26
法螺外套膜	81100	48450379	597	843	442	43.78
All-Unigene	109722	70289861	640	995	485	43.43

	总数	NR	NT	Swissport	KEGG	KOG	InterPro	GO	Intersection	Overall
基因个数	109722	26050	27059	16944	18705	15319	17617	9788	2712	46239
注释比例	100%	23.74%	24.66%	15.44%	17.05%	13.96%	16.06%	8.92%	2.47%	42.14%

基于RNA-Seq高通量测序技术的法螺差异表达基因分析

Analysis of differential expressed genes from Charonia tritonis based on transcriptome sequencing

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