ScTrio-seq identifies colon cancer lineages: To better design treatments for cancer, it is important to understand the heterogeneity in tumors and how this contributes to metastasis. To examine this process, Bian et al. used a single-cell triple omics sequencing (scTrio-seq) technique to examine the mutations, transcriptome, and methylome within colorectal cancer tumors and metastases from 10 individual patients. The analysis provided insights into tumor evolution, linked DNA methylation to genetic lineages, and showed that DNA methylation levels are consistent within lineages but can differ substantially among clones. Science , this issue p. 1060

A single-cell survey of developing human CC was performed with comprehensive temporal and spatial information.

Gonadal somatic cells are the main players in gonad development and are important for sex determination and germ cell development. Here, using a time-series single-cell RNA sequencing (scRNA-seq) strategy, we analyzed fetal germ cells (FGCs) and gonadal somatic cells in human embryos and fetuses. Clustering analysis of testes and ovaries revealed several novel cell subsets, including POU5F1+SPARC+ FGCs and KRT19+ somatic cells. Furthermore, our data indicated that the bone morphogenetic protein (BMP) signaling pathway plays cell type-specific and developmental stage-specific roles in testis development and promotes the gonocyte-to-spermatogonium transition (GST) in late-stage testicular mitotic arrest FGCs. Intriguingly, testosterone synthesis function transitioned from fetal Sertoli cells to adult Leydig cells in a stepwise manner. In our study, potential interactions between gonadal somatic cells were systematically explored and we identified cell type-specific developmental defects in both FGCs and gonadal somatic cells in a Turner syndrome embryo (45, XO). Our work provides a blueprint of the complex yet highly ordered development of and the interactions among human FGCs and gonadal somatic cells.

Background: The common carp (Cyprinus carpio) is a key species in global freshwater aquaculture. One of its variants, the koi carp, is particularly prized for its aesthetic appeal. However, lacking a high-quality genome has limited genetic research and breeding efforts for common carp and koi carp. Findings: This study presents a gap-free genome for the Taisho Sansyoku koi carp strain (C. carpio). The assembly achieved a total size of 1,555.86 Mb with a contig N50 of 30.45 Mb, comprising 50 gap-free pseudochromosomes ranging in length from 20.70 to 49.02 Mb. The BUSCO completeness score reached 99.20%, and the Genome Continuity Inspector score was 85.82, indicating high genome integrity and accuracy. Notably, 83 out of 100 telomeres were detected, resulting in 33 chromosomes possessing complete telomeres. Comparative genomic analysis showed that the expanded gene families and unique genes play essential roles in various biological traits, such as energy metabolism, endocrine regulation, cell proliferation, and immune response, potentially related to multiple metabolic diseases and health conditions. The positively selected genes are linked to various biological processes, such as the metalloendopeptidase activity, which plays a significant role in the central nervous system and is associated with diseases. Conclusions: The koi carp genome assembly (CC 4.0) fills a critical gap in understanding common carp’s biology and adaptation. It provides an invaluable resource for molecular-guided breeding and genetic enhancement strategies, underscoring the importance of common carp and koi carp in aquaculture and ecological research.