Isolation and Characterization of y-Linked Genes Regulating Male Fertility in Alpacas

Principal investigator:

Terje Raudsepp, PhD
Texas A&M University

Current knowledge about the genetics of male reproduction and fertility in alpacas is limited hindering distinction between conditions caused by genes, from those affected by management. Furthermore, alpaca reference genome is from a female and does not contain sequences from the Y chromosome — the chromosome that is known to be enriched with spermatogenesis and male reproduction genes in humans, mice and several domestic species (horse, pig, cattle, cat, dog). Here we initiated research on the alpaca Y chromosome. The chromosome is present only in males and is exclusively inherited through patrilines. We isolated and characterized, for the first time, Y chromosome genes in alpacas and evaluated their expression in testis and estimated their approximate copy numbers. We identified 87 putative alpaca Y chromosome genes, confirmed male specificity of 12 genes and showed that the gene encoding for testis specific protein in Y (TSPY) has multiple copies in the alpaca Y chromosome. The study initiated Y chromosome research in alpacas and camelids in general. In long-term perspective, the finding will have applications in genetic evaluation of male fertility and for the study of the history of paternal lineages of populations and breeds in all South American camelids.

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

Matthew J. Jevit¹, Brian W. Davis¹, Caitlin Castaneda¹, Andrew Hillhouse², Rytis Juras¹,

Vladimir A. Trifonov³, Ahmed Tibary⁴, Jorge C. Pereira⁵, Malcolm A. Ferguson-Smith⁵ and Terje Raudsepp^1,*

Abstract: The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.

Genes 2021,12,105