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

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.

State of the art on the physical mapping of the Y-chromosome in the Bovidae and comparison with other species — A review

“…This region is in the distal part of the Y-chromosome for all the species studied, but in BTA/OAR/CHI/SSC it is at the telomere of the p-arm, while in ECA/BBU it was reported at the telomere of the q-arm ( Figure 2 ). In addition, very recently, the same position has been confirmed also in VPA [ 75 ]. In particular, in this species, the Y-chromosome is very small and does not show distinct cytogenetic characteristic, so that it is difficult to identify the location of the centromere.…”

“…In particular, in this species, the Y-chromosome is very small and does not show distinct cytogenetic characteristic, so that it is difficult to identify the location of the centromere. Only with the use of the FISH technique by PAR BACs, it has been demonstrated that the alpaca Chr Y is submetacentric with a very small and short p-arm and the PAR located at the telomere in the long q-arm [ 75 ].…”

“…So far, no genes have been identified by cytogenetic mapping on the Y-chromosome, except for ten loci on the PAR Yq-ter region ( Table 2 ; Figure 2 ) because the CHORI-246 BAC library derives from a female alpaca [ 74 ]. The Alpaca Y-chromosome, according to the most recent physical mapping (Jevit et al [ 75 ]) is a small submetacentric, the smallest among of Old-World camels [ 76 ], and the PAR region is located in the long arm.…”