Single-molecule long-read (SMRT) transcriptome sequencing of Mercenaria mercenaria reveals a powerful anti-apoptotic system critical for air exposure endurance

• Published in: Comparative biochemistry and physiology. Part D, Genomics & proteomics Vol. 38; p. 100792
• Main Authors: Zhou, Cong, Song, Hao, Yang, Mei-jie, Wang, Xiao-cheng, Yu, Zheng-lin, Hu, Zhi, Shi, Pu, Zhang, Tao
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Inc 01.06.2021
• Subjects: Air exposure; Apoptosis; Environmental adaptability; Mercenaria mercenaria; SMRT sequencing; Transcriptome; SMRT sequencing; Air exposure; Mercenaria mercenaria; Environmental adaptability; Transcriptome; Apoptosis
• ISSN: 1744-117X; 1878-0407
• DOI: 10.1016/j.cbd.2021.100792

Mercenaria mercenaria is an economically important clam species and exhibits an outstanding resistance to multiple environmental stressors. However, our understanding of their stress adaptability is limited due to a lack of genomic information, such as transcriptome resources. In this study, single-molecule long-read (SMRT) mRNA sequencing was performed to obtain the full-length gill transcriptome reference sequences of M. mercenaria under air exposure stress. In all, 14.5 G subreads were obtained and assembled into 64,603 unigenes, among which 50,613 were successfully annotated. Additionally, 56,295 SSRs, 1457 transcription factors, and 5924 lncRNAs were identified in M. mercenaria transcriptome. Furthermore, numerous apoptosis-related transcripts were identified according to Swiss-Prot annotation and their numbers were counted. We also found that most apoptosis-related transcripts exhibited typical domains of a certain protein family through conserved domain prediction. Additionally, eight typical sequences related to apoptosis pathway were detected by RT-PCR, with the aim to show the sequential variation of gene expression levels under air exposure. These results implied that the complicated apoptosis system, especially the powerful anti-apoptotic system was critical for M. mercenaria to endure air exposure. [Display omitted] •This study provides full-length gill transcriptome reference sequences of Mercenaria mercenaria under air exposure using single-molecule long-read (SMRT) mRNA sequencing.•we identified numerous apoptosis-related transcripts in M. mercenaria transcriptome and quantify their expression by RT-PCR, indicating that a powerful anti-apoptosis system exists in hard clam and may enhance its endurance to air exposure.