Amphioxus, a basal chordate with highly heterozygous genomes (3.2 ~ 4.2% in sequenced species), represents a key model for understanding vertebrate origins. However, the extreme heterozygosity poses challenges for many genomic analyses, including studying meiotic recombination. Here, we present a novel bioinformatic pipeline that enables direct detection of crossover (CO) and non-crossover (NCO) recombination events using short-read whole-genome sequencing of a two-generation pedigree (two parents and 104 F1 offspring) of the amphioxus Branchiostoma floridae. Using parental assemblies generated by Platanus-allee as a custom reference for read alignment, we tracked inheritance patterns in offspring and phased contig-level haplotypes in parents, allowing us to detect recombination events. We identified 2,329 paternal and 2,288 maternal COs, yielding recombination rates of 4.66 cM/Mb and 4.57 cM/Mb, respectively. We found CO coldspots spanning > 140 Mb in each parent and these are likely associated with large-scale heterozygous inversions. CO rates were positively correlated with transposable element and gene density in both sexes, but showed weak or no correlation with GC content. We further identified ~ 10,000 paternal and ~ 5,800 maternal NCO events, predominantly shorter than 200 bp in tract length, and found evidence of GC-biased gene conversion. This work provides the first direct and genome-wide measurement of recombination in amphioxus and demonstrates how high heterozygosity, often considered a barrier, can be leveraged for fine-scale recombination mapping. Our findings illuminate conserved and divergent features of recombination in chordates and establish a framework for studying recombination in other highly heterozygous organisms.

Trypanosoma brucei, the causative agent of African trypanosomiasis, develops from the long slender (LS) to the short stumpy (SS) form in the mammalian host. The SS trypanosomes are critical for transmission to the insect vector but face significant challenges within the vertebrate host. The role of the immune response in controlling the parasitaemia is well studied, however, the mechanism underpinning the rapid degeneration of SS trypanosomes during the first parasitaemic peak in mice remains somewhat elusive. We demonstrate that fever is a critical yet underexplored factor in facilitating the clearance of SS trypanosomes, suggesting that temperature may play a critical role in regulating the natural turnover of SS trypanosomes. The elevated body temperature correlates with the parasitaemic dynamics, accelerating SS trypanosome elimination in the mammalian host. The SS trypanosomes exhibited high thermo-sensitivity to elevated temperatures, accompanied with apoptosis-like events, mitochondrial damage and oxidative stress. Metabolomic profiling also revealed disruptions in glycolysis and the TCA cycle, shedding light on the processes in compromising the SS trypanosomes. Interestingly, antibodies during the acute phase did not directly cause SS trypanosomes death, but the combination of elevated temperature and antibodies enhanced the clearance of SS trypanosomes, highlighting the critical role of fever in eliminating the first parasitaemic peak. Our findings detail the mechanism of vulnerability of SS trypanosome to elevated temperatures and suggest that host fever serves as a neglected, but critical mechanism, for T. brucei SS trypanosome clearance.

Skeletal muscle serves as a valuable source of nutrition, with distinct muscle fiber types exhibiting different physicochemical properties that influence both meat quality and muscle function. Bama miniature pigs (BM) are recognized for their superior meat quality and their relevance as models for human medical research. Therefore, investigating the differences between slow and fast muscles at various developmental stages (from 57 days post-fertilization to 120 days postnatally) in BM is crucial for both the pork industry and biomedical studies. In this study, we employed a non-targeted data-independent acquisition (nDIA) -based proteomic approach for the first time to porcine embryonic skeletal muscle fibers. A total of 616 differentially expressed genes (DEGs) and 272 differentially abundant proteins (DAPs) were identified in the fast-twitch longissimus dorsi (LD) and slow-twitch semitendinosus (SD) muscles of BM. Domain enrichment analysis and in vitro experiments demonstrated that the NEK3 gene, containing the S_TKc domain, inhibits fast-twitch muscle fiber differentiation postnatally. Additionally, cross-species analysis showed upregulation of skeletal muscle development organ genes in pigs at postnatal day 28. In summary, our results provide both fundamental data and novel insights to further uncover the mechanisms underlying pig skeletal muscle development and muscle fiber transition.