RT Journal
A1 Lu, Yuan
A1 Rice, Edward
A1 Du, Kang
A1 Kneitz, Susanne
A1 Naville, Magali
A1 Dechaud, Corentin
A1 Volff, Jean-Nicolas
A1 Boswell, Mikki
A1 Boswell, William
A1 Hillier, LaDeana
A1 Tomlinson, Chad
A1 Milin, Kremitzki
A1 Walter, Ronald B.
A1 Schartl, Manfred
A1 Warren, Wesley C.
T1 High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
JF Genome Research 
JO Genome Research 
YR 2023 
FD April 01 
VO 33 
IS 4 
SP 557 
OP 571 
DO 10.1101/gr.277434.122 
UL http://genome.cshlp.org/content/33/4/557.abstract 
AB Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species, namely, X. maculatus, X. couchianus, and X. hellerii. Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorus species and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten–Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.