Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing

SIMPLE SUMMARY: The size of antlers varies among species; antlers of the wapiti (Cervus canadensis xanthopygus) grow much faster than those of its close relative the sika deer (Cervus nippon hortulorum) in the same growing period. This contrast provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, the reference transcriptomes of the antler reserve mesenchyme (RM) tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared, and interactive relationships and expression patterns of hub genes were identified and analysed. We identified that RNA Binding Motif Protein X-Linked (RBMX) gene was under strongly positive selection. One gene found to interact with RBMX was methyltransferase-like 3 (METTL3), an oncogene that could promote translation of cancer cell proteins. There was a contrasting relationship in expression level between RBMX and METTL3 genes in the RM tissue. We believe our study can provide a better understanding of rapid antler growth at the molecular level in particular and endochondral ossification in general. ABSTRACT: The molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference transcriptomes of antler RM tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared. The results showed that: a total of 44,485 reference full-length transcripts of antlers were obtained; 254 highly expressed transcripts (HETs) and 1936 differentially expressed genes (DEGs) were enriched and correlated principally with translation, endochondral ossification and ribosome; 228 genes were found to be under strong positive selection and would thus be important for the evolution of wapiti and sika deer; among the alternative splicing variants, 381 genes were annotated; and 4 genes with node degree values greater than 50 were identified through interaction network analysis. We identified a negative and a positive regulator for rapid antler growth, namely RNA Binding Motif Protein X-Linked (RBMX) and methyltransferase-like 3 (METTL3), respectively. Overall, we took advantage of this significant difference in growth rate and performed the comparative analyses of the antlers to identify key specific factors that might be candidates for the positive or negative regulation of phenomenal antler growth rate.