The combination of SMRT sequencing and Illumina sequencing highlights organ-specific and age-specific expression patterns of miRNAs in Sika Deer

Boyin Jia; Xue Wang; Fuquan Ma; Xin Li; Xintong Han; Linlin Zhang; Jianming Li; Naichao Diao; Kun Shi; Chenxia Ge; Fuhe Yang; Rui Du

doi:10.3389/fvets.2022.1042445

The combination of SMRT sequencing and Illumina sequencing highlights organ-specific and age-specific expression patterns of miRNAs in Sika Deer

Front Vet Sci. 2022 Nov 14:9:1042445. doi: 10.3389/fvets.2022.1042445. eCollection 2022.

Authors

Boyin Jia^{1

2}, Xue Wang¹, Fuquan Ma¹, Xin Li¹, Xintong Han¹, Linlin Zhang¹, Jianming Li^{2

3}, Naichao Diao^{2

3}, Kun Shi^{2

3}, Chenxia Ge⁴, Fuhe Yang⁵, Rui Du^{2

3}

Affiliations

¹ College of Animal Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China.
² Laboratory of Production and Product Application of Sika Deer of Jilin Province, Jilin Agricultural University, Changchun, China.
³ College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China.
⁴ College of Vocational and Technical Education, Changchun Sci-Tech University, Changchun, China.
⁵ Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, Changchun, China.

Abstract

Due to the lack of high-quality Sika Deer (Cervus nippon) transcriptome and sRNAome across multiple organs or development stages, it is impossible to comprehensively analyze the mRNA and miRNA regulatory networks related to growth, development and immunity response. In this study, we used single molecule-real time sequencing (SMRT-seq) and Illumina sequencing methods to generate transcriptome and sRNAome from ten tissues and four age groups of Sika Deer to help us understand molecular characteristics and global miRNA expression profiles. The results showed that a total of 240,846 consensus transcripts were generated with an average length of 2,784 bp. 4,329 Transcription factors (TFs), 109,000 Simple Sequence Repeats (SSRs) and 18,987 Long non-coding RNAs (LncRNAs) were identified. Meanwhile, 306 known miRNAs and 143 novel miRNAs were obtained. A large number of miRNAs showed organ-specific and age-specific differential expression patterns. In particular, we found that the organ-specific miRNAs were enriched in the brain, some of which shared only between the brain and adrenal. These miRNAs were involved in maintaining specific functions within the brain and adrenal. By constructing miRNA96mRNA interaction networks associated with Sika Deer immunity, we found that miRNAs (miR-148a, miR-26a, miR-214, let-7b, etc.) and mRNAs (CD6, TRIM38, C3, CD163, etc.) might play an important role in the immune response of Sika Deer spleen. Together, our study generated an improved transcript annotation for Sika Deer by SMRT-seq and revealed the role of miRNA in regulating the growth, development and immunity response of Sika Deer.

Keywords: Sika Deer; age-specific; expression pattern; miRNA; organ-specific.