RT Journal
A1 Maggiolini, Flavia Angela Maria
A1 Sanders, Ashley D.
A1 Shew, Colin James
A1 Sulovari, Arvis
A1 Mao, Yafei
A1 Puig, Marta
A1 Catacchio, Claudia Rita
A1 Dellino, Maria
A1 Palmisano, Donato
A1 Mercuri, Ludovica
A1 Bitonto, Miriana
A1 Porubský, David
A1 Cáceres, Mario
A1 Eichler, Evan E.
A1 Ventura, Mario
A1 Dennis, Megan Y.
A1 Korbel, 
Jan O.
A1 Antonacci, Francesca
T1 Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
JF Genome Research 
JO Genome Research 
YR 2020 
FD November 01 
VO 30 
IS 11 
SP 1680 
OP 1693 
DO 10.1101/gr.265322.120 
UL http://genome.cshlp.org/content/30/11/1680.abstract 
AB Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.