Transcriptome Responses to Different Salinity Conditions in <i>Litoditis marina,</i> Revealed by Long-Read Sequencing

doi:10.3390/genes15030317

IOCAS-IR > 实验海洋生物学重点实验室

	*Transcriptome Responses to Different Salinity Conditions in Litoditis marina,* Revealed by Long-Read Sequencing**
	Zhang, Pengchi1,2,3,4,5 ; Xue, Beining 1,2,3,4,5; Yang, Hanwen 1,2,3,4; Zhang, Liusuo 1,2,3,4
	2024-03-01
发表期刊	GENES
卷号	15 期号:3 页码:15
通讯作者	Zhang, Liusuo([email protected])
摘要	The marine nematode Litoditis marina is widely distributed in intertidal zones around the globe, yet the mechanisms underlying its broad adaptation to salinity remain elusive. In this study, we applied ONT long-read sequencing technology to unravel the transcriptome responses to different salinity conditions in L. marina. Through ONT sequencing under 3 parts per thousand, 30 parts per thousand and 60 parts per thousand salinity environments, we obtained 131.78 G clean data and 26,647 non-redundant long-read transcripts, including 6464 novel transcripts. The DEGs obtained from the current ONT lrRNA-seq were highly correlated with those identified in our previously reported Illumina short-read RNA sequencing data. When we compared the 30 parts per thousand to the 3 parts per thousand salinity condition, we found that GO terms such as oxidoreductase activity, cation transmembrane transport and ion transmembrane transport were shared between the ONT lrRNA-seq and Illumina data. Similarly, GO terms including extracellular space, structural constituents of cuticle, substrate-specific channel activity, ion transport and substrate-specific transmembrane transporter activity were shared between the ONT and Illumina data under 60 parts per thousand compared to 30 parts per thousand salinity. In addition, we found that 79 genes significantly increased, while 119 genes significantly decreased, as the salinity increased. Furthermore, through the GO enrichment analysis of 214 genes containing DAS, in 30 parts per thousand compared to 3 parts per thousand salinity, we found that GO terms such as cellular component assembly and coenzyme biosynthetic process were enriched. Additionally, we observed that GO terms such as cellular component assembly and coenzyme biosynthetic process were also enriched in 60 parts per thousand compared to 30 parts per thousand salinity. Moreover, we found that 86, 125, and 81 genes that contained DAS were also DEGs, in comparisons between 30 parts per thousand and 3 parts per thousand, 60 parts per thousand and 30 parts per thousand, and 60 parts per thousand and 3 parts per thousand salinity, respectively. In addition, we demonstrated the landscape of alternative polyadenylation in marine nematode under different salinity conditions This report provides several novel insights for the further study of the mechanisms by which euryhalinity formed and evolved, and it might also contribute to the investigation of salinity dynamics induced by global climate change.
关键词	marine nematode Litoditis marina ONT long-read sequencing technology salinity alternative splicing alternative polyadenylation (APA)
DOI	10.3390/genes15030317
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:001193412400001
出版者	MDPI
WOS关键词	3' UNTRANSLATED REGIONS ; ALTERNATIVE POLYADENYLATION ; MESSENGER-RNAS ; ELEGANS ; CLEAVAGE
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/185086
专题	实验海洋生物学重点实验室
通讯作者	Zhang, Liusuo
作者单位	1.Chinese Acad Sci, Qingdao 266071, Peoples R China 2.Chinese Acad Sci, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 3.Lab Marine Biol & Biotechnol, Qingdao Natl Lab Marine Sci & Technol, Qingdao 266237, Peoples R China 4.Chinese Acad Sci, Ctr Ocean Mega Sci, 7 Nanhai Rd, Qingdao 266071, Peoples R China 5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Zhang, Pengchi,Xue, Beining,Yang, Hanwen,et al. Transcriptome Responses to Different Salinity Conditions in Litoditis marina, Revealed by Long-Read Sequencing[J]. GENES,2024,15(3):15.
APA	Zhang, Pengchi,Xue, Beining,Yang, Hanwen,&Zhang, Liusuo.(2024).Transcriptome Responses to Different Salinity Conditions in Litoditis marina, Revealed by Long-Read Sequencing.GENES,15(3),15.
MLA	Zhang, Pengchi,et al."Transcriptome Responses to Different Salinity Conditions in Litoditis marina, Revealed by Long-Read Sequencing".GENES 15.3(2024):15.