A comprehensive analysis of 124 transcriptomes from 31 tissues in developing, juvenile, and adult Japanese Black cattle

Omics analyses of economically important animals, including Japanese Black cattle, are underway worldwide. Particularly, tissue and developmental stage-specific transcriptome characterization is essential for understanding the molecular mechanisms underlying phenotypic expression of genetic disorders and economical traits. Here, we conducted a comprehensive analysis of 124 transcriptomes across 31 major tissues from fetus, juvenile calf, and adult cattle using short-read sequencing. We found that genes showing high tissue-specific expression tended to gradually increase with development after 60 days of fertilization and significantly reflected the tissue-relevant biology. Based on the variation and inflection points of gene expression during development, we categorized gene expression pattern into stable, increased, decreased, temporary, or complex in each tissue. We also analyzed the expression profiles of causative genes (e.g., SLC12A1, ANXA10, MYH6) for genetic disorders in cattle, revealing disease-relevant expression patterns. Additionally, to directly analyze the structure of full-length transcripts without transcript reconstruction, we performed RNAseq analysis with 22 tissues using long-read sequencing and identified 232 novel non-RefSeq isoforms. Collectively, our comprehensive transcriptomic analysis can serve as an important resource for biological and functional interpretation of gene expression and will enable a mechanistic interpretation of genetic disorders and economical traits in Japanese Black cattle.