Nematodes play key roles in marine ecosystem. Although oceans cover 71% of the Earth’s surface, none of marine model nematode has been reported. Here, we constructed the first inbred line of free-living marine nematode Litoditis marina , sequenced and assembled its genome. Furthermore, we successfully applied CRISPR/Cas9 genome editing in L. marina . Comparative genomics revealed that immunity and oxygen regulation genes are expanded, which is probably central to its sediment adaptation. While L. marina exhibits massive gene contractions in NHRs, chemoreceptors, xenobiotics detoxification and core histones, which could explain the more defined marine environment. Our experiments showed that dozens of H4 genes in Caenorhabditis elegans might contribute to its adaptation to the complex terrestrial environments, while two H4 genes in L. marina are involved in salinity stress adaptation. Additionally, ninety-two conserved genes appear to be positively selected in L. marina , which may underpin its osmotic, neuronal and epigenetic changes in the sea. With short generation time, highly inbred lines, and genomic resources, our report brings L. marina a promising marine animal model, and a unique satellite marine model to the well-known biomedical model nematode C. elegans . This study will underpin ongoing work on animal functional genomics, environmental adaptation and developmental evolution.

Coral reef ecosystems in the South China Sea are one of the globally important marine biodiversity hotspots. However, there are few studies on nematode biodiversity in coral reef sediments. Here, we assessed nematode biodiversity in coral reef sediments in the South China Sea using eDNA metabarcoding. Eight sampling stations were set up in the region north of the South China Sea Basin (Xisha and Zhongsha Islands) and south of it (Nansha Islands), respectively. We also compared and analysed the nematode biodiversity and community structure in different regions, as well as the effects of environmental factors on the community structure. The results showed that a total of 503 operational taxonomic units (OTUs) were detected in 16 sediment samples. The nematodes identified belong to two classes, 10 orders, 37 families, 51 genera and 61 species, and all of them were Enoplea and Chromadorea, except for the unidentified taxa, which accounted for 97.26% of the total abundance. The analyses showed that the northern region had higher nematode abundance and diversity relative to the southern region. However, there was no significant difference in the nematode community structure between the two regions, which was less affected by geographic location. Similarly, environmental factors (total nitrogen, total phosphorus, copper, zinc, cadmium, lead and arsenic) have an effect on the abundance of specific nematode groups but not on the overall community structure. In summary, this study initially reveals the composition and diversity of nematode communities in coral reef sediments in the South China Sea and provides an important reference for further in-depth study of the South China Sea ecosystem.

The sister species Caenorhabditis briggsae and Caenorhabditis nigoni are the first Caenorhabditis nematode pair known to produce viable F1 hybrids, making them an ideal model for speciation study. Male F1 hybrids are lethal or sterile depending on the parent of origin, while F1 females, though viable, exhibit distinct phenotypes in fecundity and viability. Besides, both female hybrids could mate with C. nigoni males to produce viable progeny but experience hybrid breakdown when crossed with C. briggsae males. The molecular mechanisms driving these phenotype variations in F1 females remain unknown. Here, we analyzed the transcriptomes of F1 female hybrids from both crossing directions to examine whether a parent-specific haplotype dominates gene expression in the hybrids and to explore the mechanisms underlying the distinct phenotypes. We showed that in female hybrids from both directions, the C. nigoni haplotype was more abundantly expressed and maintained the parental expression patterns better than that of C. briggsae. We also observed an upregulation of female-biased genes in the C. nigoni haplotype of F1 females, which may explain their compatibility with C. nigoni males for producing viable progeny, suggesting a haplotype-specific influence on female reproductive traits. Our mitochondrial gene analysis suggested a nuclear–cytoplasmic incompatibility marked by cis-dominated expression patterns of mitochondrial genes, which may contribute to the reduced viability in F1 females. This research provides insights into the expression pattern of interspecies F1 female hybrids and the mechanisms underlying nonlethal hybrid incompatibility defects.