Eukaryotic genomes are generally organized in multiple chromosomes. Here we have created a functional single-chromosome yeast from a Saccharomyces cerevisiae haploid cell containing sixteen linear chromosomes, by successive end-to-end chromosome fusions and centromere deletions. The fusion of sixteen native linear chromosomes into a single chromosome results in marked changes to the global three-dimensional structure of the chromosome due to the loss of all centromere-associated inter-chromosomal interactions, most telomere-associated inter-chromosomal interactions and 67.4% of intra-chromosomal interactions. However, the single-chromosome and wild-type yeast cells have nearly identical transcriptome and similar phenome profiles. The giant single chromosome can support cell life, although this strain shows reduced growth across environments, competitiveness, gamete production and viability. This synthetic biology study demonstrates an approach to exploration of eukaryote evolution with respect to chromosome structure and function.

Assembly of complete Y chromosome is a significant challenge in animals with XX/XY sex determination system. Recently, we created YY supermale yellow catfish by crossing XY males with sex-reversed XY females, providing a valuable model for Y chromosome assembly and evolution. Here, we assembled highly homomorphic Y and X chromosomes by sequencing genomes of the YY supermale and XX female in yellow catfish, revealing their nucleotide divergences with only less than 1% and with the same gene compositions. The sex-determining region (SDR) was identified to locate within a physical distance of 0.3 Mb by FST scanning. Strikingly, the incipient sex chromosomes were revealed to originate via autosome-autosome fusion and were characterized by a highly rearranged region with an SDR downstream of the fusion site. We found that the Y chromosome was at a very early stage of differentiation, as no clear evidence of evolutionary strata and classical structure features of recombination suppression for a rather late stage of Y chromosome evolution were observed. Significantly, a number of sex-antagonistic mutations and the accumulation of repetitive elements were discovered in the SDR, which might be the main driver of the initial establishment of recombination suppression between young X and Y chromosomes. Moreover, distinct three-dimensional chromatin organizations of the Y and X chromosomes were identified in the YY supermales and XX females, as the X chromosome exhibited denser chromatin structure than the Y chromosome, while they respectively have significantly spatial interactions with female- and male-related genes compared with other autosomes. The chromatin configuration of the sex chromosomes as well as the nucleus spatial organization of the XX-neomale were remodelled after sex reversal and similar to those in YY supermales, and a male-specific loop containing the SDR was found in the open chromatin region. Our results elucidate the origin of young sex chromosomes and the chromatin remodelling configuration in the catfish sexual plasticity.

The effect of thermal changes on the physiology and behavior of fish is a major research focus in the face of ongoing global warming. There is little information about the effects of temperature increase on fish in the wild. However, the consequences of temperature increase on fish in controlled laboratory conditions can provide insights into what can be expected in the wild. Triplophysa bleekeri, a high-plateau fish, exhibits high sensitivity to high temperatures, suggesting it to be a good model to investigate the impact of temperature increase on fish. In this study, we analyzed the effect of gradual temperature increase on transcriptional and metabolic levels of T. bleekeri subjected to a gradual temperature change of 0.5°C/day until temperatures of 10°C, 13°C, 16°C, and 19°C were reached. Transcriptomics results of the liver, gut, spleen, and trunk kidney showed that metabolic pathways are widely involved in the response to increased temperatures in T. bleekeri. Lipidomics results further indicated that the lipid composition was altered by increased temperatures, and three lipids (PC 14:0e/22:1, PC 18:0e/22:5, and TAG 14:3-21:2-21:2) were identified as potential biomarkers of heat stress in T. bleekeri. Moreover, a decline in unsaturated fatty acid levels was observed in T. bleekeri under high temperatures. These results suggest that high temperatures modify the metabolomic pathways. Overall, our results help improve the understanding of physiological responses in fish to increased temperatures, and provide valuable information predicting the consequences of global warming on fish.