Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes

Abstract

Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been recently studied in great apes, however, the diversity of splicing variants remains unexplored. Here we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2,CDY,DAZ,HSFY,PRY,RBMY,TSPY,VCY, andXKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture-probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this dataset resulted in several findings. First, we uncovered a high diversity of YAG transcripts across great apes. Second, we observed evolutionarily conserved alternative splicing patterns for most YAG families except forBPY2andPRY. Our results suggest thatBPY2transcripts and predicted proteins in several great ape species (bonobo and the two orangutans) have independent evolutionary origins and are not homologous to human reference transcripts and proteins. In contrast, our results suggest that thePRYgene family, having the highest representation of transcripts without open reading frames, has been undergoing pseudogenization. Third, even though we have identified many species-specific protein-coding YAG transcripts, we have not detected any signatures of positive selection. Overall, our work illuminates the YAG isoform landscape and its evolutionary history, and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.

Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies

“…Consistent with previous studies (Tomaszkiewicz et al 2023), our results suggest the pseudogenization of PRY. For PRY, the majority of the identified gene copies did not encode proteins and were marked as transcribed pseudogenes.…”

“…We present our YAGs transcript assemblies in comparison with previously reported findings. Consistent with Tomaszkiewicz et al (2023), we report the presence of transcripts from all nine YAG families in all great ape species, except BPY2 in bonobo (Fig. 2A).…”

“…To characterize transcript isoform diversity of YAGs in great apes, we combined targeted and untargeted long-read PacBio IsoSeq sequencing approaches with the untargeted short-read Illumina sequencing of RNA isolated from testis samples of six great ape species—bonobo, chimpanzee, gorilla, Bornean orangutan, Sumatran orangutan, and human (for human only targeted IsoSeq data were analyzed). Targeted PacBio IsoSeq data were available for two technical replicates (Tomaszkiewicz et al 2023). For our analysis, we took advantage of the T2T assemblies available for great ape Y chromosomes (Rhie et al 2023; Makova et al 2024).…”

“…Consistent with other studies (Feng et al 2019; Zhang et al 2019; Leung et al 2021), our results suggest that long-read sequencing and reference-based assembly using the T2T assemblies can improve assemblies of transcriptomes. The previous work that characterized transcript isoform diversity of YAGs in great apes used the de novo assembly approach as high-quality references were not available then (Tomaszkiewicz et al, 2023). In contrast, we utilized the recently produced T2T assemblies of Y chromosomes of great apes (Makova et al 2024).…”

“…Copy numbers of YAGs vary substantially among species and even among individuals of the same species (Vegesna et al 2019(Vegesna et al , 2020. Some YAG families, for example, PRY, underwent pseudogenization (Tomaszkiewicz et al 2023).…”