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

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...

Full description

Saved in:
Bibliographic Details
Published in:Genes 2021-01, Vol.12 (1), p.105
Main Authors: Jevit, Matthew J, Davis, Brian W, Castaneda, Caitlin, Hillhouse, Andrew, Juras, Rytis, Trifonov, Vladimir A, Tibary, Ahmed, Pereira, Jorge C, Ferguson-Smith, Malcolm A, Raudsepp, Terje
Format: Article
Language:English
Subjects:
Alpacas
Antibiotics
Biopsy
Cell culture
Comparative analysis
Cytogenetics
Deoxyribonucleic acid
DNA
Fibroblasts
Gene expression
Genomes
Genomics
Hybridization
Mammals
Mutation
Population studies
Protocol
Sex determination
Skin
Software
Transcriptomes
Vicugna pacos
Y chromosomes
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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 ( ) 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, and are multicopy. The pseudoautosomal boundary is located between and 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 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.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes12010105