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

文献类型：期刊论文

作者Zhang, Pengchi1,2,3,4,5; Xue, Beining1,2,3,4,5; Yang, Hanwen2,3,4,5; Zhang, Liusuo2,3,4,5
刊名GENES
出版日期2024-03-01
卷号15期号:3页码:15
关键词marine nematode Litoditis marina ONT long-read sequencing technology salinity alternative splicing alternative polyadenylation (APA)
DOI10.3390/genes15030317
通讯作者Zhang, Liusuo(lzhang@qdio.ac.cn)
英文摘要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.
WOS关键词3' UNTRANSLATED REGIONS ; ALTERNATIVE POLYADENYLATION ; MESSENGER-RNAS ; ELEGANS ; CLEAVAGE
资助项目National Natural Science Foundation of China
WOS研究方向Genetics & Heredity
语种英语
WOS记录号WOS:001193412400001
出版者MDPI
源URL[http://ir.qdio.ac.cn/handle/337002/185085]  
专题海洋研究所_实验海洋生物学重点实验室
通讯作者Zhang, Liusuo
作者单位1.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
2.Chinese Acad Sci, Ctr Ocean Mega Sci, 7 Nanhai Rd, 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, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
5.Chinese Acad Sci, Qingdao 266071, Peoples R China
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.

入库方式： OAI收割

来源：海洋研究所

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