Chromosomal Rearrangements And Speciation Of Subterranean Myospalax In China

Speciation is the core of biodiversity and plays an important role in the generation and maintenance of biodiversity.Speciation is often accompanied by genomic differentiation,including nucleotide variation,chromosomal variation and 3D genomic variation.In this study,we investigated the genomic differentiation of the Myospalax species in China during the process of speciation.Taking advance of the Hi Fi long-read sequencing and HiC technology,we assembled the chromosome-level genomes of the Myospalax psilurus and the Myospalax aspalax,revealing the role of gene family expansion and contraction and conserved non-coding elements in the adaptation of the Myospalax genus to underground life.We clarified the population differentiation and demographic history of the two species,and discussed the role of chromosome fission and structural variation in the process of speciation.The detailed results are as follows.(1)We assembled high-quality chromosome-level genomes of M.aspalax and M.psilurus.They were anchored to 31(M.aspalax)and 32(M.psilurus)pseudochromosomes respectively,which are consistent with the previously reported karyotype.The evaluation indicated that our genome assembly ensured a high continuity and completeness,which provided a good reference base for subsequent studies.(2)Comparative genomic analysis revealed that M.aspalax and M.psilurus diverged around three million years ago.Rapidly evolving genes,positively selected genes and conserved non-coding element-related genes are significantly enriched for eye degeneration,ear degeneration,tumor and heart development,which were typically adaptive characteristics to underground life.Testing M.aspalax as the foreground branch we identified genes related to kidney development and hormone regulation,which are relevant to its adaptation to arid habitats with low precipitation;Also using M.psilurus as the foreground branch,we screened for genes related to bitter taste receptors and reproduction.(3)Based on the single nucleotide polymorphic loci of 27 individuals,we performed population genetics analyses.Principal component analysis and neighbor-joining trees showed that the two species are highly divergent in genetic structure.Ancestral component analysis revealed mixed ancestral components in some individuals,which indirectly suggests that gene flow may exist between the two species.Population history simulations showed that the two species diverged into species at about 3 million years,with secondary contact occurring at about 1.7 million years,and PSMC showed that the two species had distinctly different population histories.In summary,we suggest that the speciation of M.aspalax and the M.psilurus is due to early geographic barriers.At the same time,we did not detect significantly reduced recombination and elevated differentiation in the fission region,suggesting that chromosome breaks did not hamper interspecific gene flow.(4)Based on genomic collinearity analysis,we identified that the Chromosomal 1 of M.aspalax chromosome was broken into Chromosomal 1 and Chromosomal 32 of M.psilurus.From 3D genomic perspective,we found that the interactions between the anterior and posterior parts(Chr1＿a,Chr1＿b)of the Chr1 of M.aspalax were significantly reduced,and the inter-chromosomal interactions of Chr1＿b were significantly higher.Meanwhile,the intactness of the TAD of Chr1 was lowest in the M.aspalax compared with that of Chr1 and Chr32 in the M.psilurus.In addition,it was observed from the Spearman correlation matrix that the chromosomal conformation of Chr32 was more ordered compared to that of Chr1＿b before fission,which revealed that the fission occurred perhaps due to the unstable three-dimensional conformation of the chromosome.In addition,we identified a region enriched in internal telomeric sequences at 169M-172 M,which is weakly reciprocal,and this sequence is likely to be the location where the break occurs.At the same time,we found that this ITS region might cause the hotspot region of rearrangement of the entire zoker subfamily.(5)To characterize the mechanism of the 40 interspecific large inversions identified based on the genome,we found that segmental duplication appeared near all inversion breakpoints,suggesting that large inversions were mediated through a non-allelic homologous recombination mechanism.We didn’t find evidence showing inversions caused high genetic load.From a three-dimensional genomic perspective,we found that the occurrence of large inversions led to the rearrangement of some TADs.At the same time,most of the large inversions are overlapped with highly differentiated regions,suggesting that large inversions may be the initiation point for species differentiation.Genes of these large inversions exhibit functional enrichment with respect to regulation of reproduction,metabolism and histone modifications.In summary,the chromosome fission between M.aspalax and M.psilurus did not lead to species differentiation by suppressing gene flow in the region near the breakpoint.The secondary contact demographic history of the two species indicated that early geographic isolation may have been responsible for species differentiation,and that chromosome fission have occurred by accident.Based on the detection of a 2.7 Mb internal telomeric sequence to the right of the breakpoint region,which is also a hotspot for rearrangements in the subfamily Myospalacinae,we proposed a hypothesis for the occurrence of the chromosome fission in this study.There were also differences in the chromatin threedimensional organization before and after the fission.Furtherly,most of the 40 large inversions detected between the two species intersected with highly differentiated island regions.Genes in large inversions were associated with reproduction,regulation and metabolism,suggesting that the large inversions may have been the initial point for differentiation between the two species.