A chromosome-assigned Mongolian gerbil genome with sequenced centromeres provides evidence of a new chromosome

Abstract

Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil (Meriones unguiculatus) have distinct underpinnings: chromosome 5 has a large block of intra-arm heterochromatin as the result of a massive expansion of centromeric repeats (probably due to centromeric drive); while chromosome 13 is comprised of extremely large (>150kb) repeated sequences. We suggest that chromosome 13 originated when a functionally important "seed" broke off from another chromosome and underwent multiple breakage-fusion-bridge cycles. Genes with the most extreme GC skew are encoded on this chromosome, most likely due to the restriction of recombination to a narrow permissive region (since GC bias is linked with recombination-associated processes). Our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data, and highlight novel patterns involved in the evolution of chromosomes.

Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits

“…The Y chromosome of goats features a unique centromeric repeat, CenY, which was not found on the other chromosomes with centromeric SatI-SatIII. A unique centromeric repeat unit on the Y chromosome was also found in the other animals; for example, a 1747-bp repeat unit was found in the Mongolian gerbil 44 .…”

“…To date, T2T-goat1.0 is one of several complete seamless mammal genomes, similar to those of human 10,11 , gerbil 44 and cattle 45 . With the advancement of T2T-goat1.0, a black box corresponding to highly repetitive regions was uncovered, especially for centromeric regions.…”

“…The linguistic sequence complexity was calculated with the program NeSSie 89 in a window size of 10 kb. The locations of the centromeres were subsequently determined based on the lower sequence complexity due to the enrichment of repetitive sequences 44 . Sequence identity heatmaps for centromeric repeats were generated by StainedGlass 90 (v0.5), with similar repeats colored according to percentage identity.…”

“…We generated a total of 328. 44 Gb of ultralong ONT (114.8× coverage), 141.03 Gb of PacBio HiFi (49.3× coverage), 435. 76 Gb of Hi-C data (152.2× coverage), and 1188.9 Gb of Bionano optical mapping data (Supplementary Table 1).…”

Telomere-to-telomere sheep genome assembly reveals new variants associated with wool fineness trait

“…Since the release of human T2T-CHM13, T2T genome assemblies have become popular and available for several species 16,44,45 . Nevertheless, several gaps are still present in recent nearly complete animal genome assemblies, including those of chicken 46 , duck 47 , Mongolian gerbil 48 , and cattle 49 . The T2T-sheep1.0 genome assembled here represents the first gap-free T2T genome of a ruminant, which we obtained by resolving PURs, particularly those in centromeres and on the Y chromosome (T2T-sheep-chrY).…”