Novel Transcripts Identified in the Bovine Y Chromosome

The mammalian Y chromosome serves as a particular genomic niche for genetic innovation due to its highly repetitive sequences in the male-specific region (MSY). The objective of this study is to characterize the transcriptome of the bovine MSY using direct testis cDNA selection and RNA-seq approaches. We identified a total of 386 novel transcripts in addition to the 17 known bovine MSY genes (families). These novel transcripts include one gene family encoding for EGLY (Envelope Glycoprotein Like, Y-linked), ten potential protein-coding genes, termed Bovid-specific Transcript, Y-linked 1-10 (BTY1-10), and 375 non-coding RNAs (ncRNAs). They were amplified on the bovine MSY with copy number ranging from 2 to ~300. EGLY shares 90% sequence similarity with the X-linked EGLX. Both EGLX and EGLY are intronless. The EGLY protein is associated with transposable elements (TEs). In addition to EGLY, we also identified 11 TE-containing ncRNAs, which may be relics after TE activity during evolution. Since TEs have been implicated in genomic duplication, the identification of these novel TE-related transcripts in the bovine Y is of significance to our understanding of the massive amplification of the MSY region. BTY1-10 encode novel proteins sharing similarity with putative proteins in remote metazoans and require further investigation. Temporal and spatial expression analyses revealed that the majority of the novel BTYs and ncRNAs were expressed predominantly in testes and were up-regulated during testis development. Gene ontology analysis indicates that the differentially expressed transcripts during testis development are primarily associated with spermatogenesis.