Comparative genomics provides insights into the aquatic adaptations of mammals.

The ancestors of marine mammals once roamed the land and independently committed to an aquatic lifestyle. These macroevolutionary transitions have intrigued scientists for centuries. Here, we generated high-quality genome assemblies of 17 marine mammals (11 cetaceans and six pinnipeds), including eight assemblies at the chromosome level. Incorporating previously published data, we reconstructed the marine mammal phylogeny and population histories and identified numerous idiosyncratic and convergent genomic variations that possibly contributed to the transition from land to water in marine mammal lineages. Genes associated with the formation of blubber (NFIA), vascular development (SEMA3E), and heat production by brown adipose tissue (UCP1) had unique changes that may contribute to marine mammal thermoregulation. We also observed many lineage-specific changes in the marine mammals, including genes associated with deep diving and navigation. Our study advances understanding of the timing, pattern, and molecular changes associated with the evolution of mammalian lineages adapting to aquatic life.

Taxonomic composition and functional potentials of gastrointestinal microbiota in 12 wild-stranded cetaceans.

Cetaceans play a crucial role in marine ecosystems; however, research on their gastrointestinal microbiota remains limited due to sampling constraints. In this study, we collected hindgut samples from 12 stranded cetaceans and performed 16S rRNA gene amplicon sequencing to investigate microbial composition and functional potentials. Analysis of ZOTUs profiles revealed that the phyla Firmicutes, Proteobacteria, and Bacteroidetes dominated all hindgut samples. However, unique microbial profiles were observed among different cetacean species, with significant separation of gut microbiota communities according to biological evolutionary lineages. Different genera that contain pathogens were observed distinguishing delphinids from physeteroids/ziphiids. Delphinid samples exhibited higher abundances of Vibrio, Escherichia, and Paeniclostridium, whereas physeteroid and ziphiid samples showed higher abundances of Pseudomonas, Enterococcus, and Intestinimonas. Functional analysis indicated convergence in the gut microbiota among all cetaceans, with shared bacterial infection pathways across hindgut samples. In addition, a comparison of the gastrointestinal microbial composition between a stranded short-finned pilot whale (Globicephala macrorhynchus) and a stranded rough-toothed dolphin (Steno bredanensis) using 16S rRNA gene sequencing revealed distinct microbial community structures and functional capacities. To the best of our knowledge, this study represents the first report on the gastrointestinal microbiota of the pantropical spotted dolphin (Stenella attenuata), Blainville's beaked whale (Mesoplodon densirostris), and rough-toothed dolphin, with various comparisons conducted among different cetacean species. Our findings enhance the understanding of microbial composition and diversity in cetacean gastrointestinal microbiota, providing new insights into co-evolution and complex interactions between cetacean microbes and hosts.

Depletion of chop suppresses procedural apoptosis and enhances innate immunity in loach Misgurnus anguillicaudatus under ammonia nitrogen stress.

Ammonia nitrogen is highly toxic to fish, and it can easily cause fish poisoning or even high mortality. So far, many studies have been conducted on the damages to fish under ammonia nitrogen stress. However, there are few studies of ammonia tolerance improvement in fish. In this study, the effects of ammonia nitrogen exposure on apoptosis, endoplasmic reticulum (ER) stress, and immune cells in loach Misgurnus anguillicaudatus were investigated. Loaches (60 d post fertilization) were exposed to different concentrations of NH4Cl, and their survival rates were examined every 6 h. The results showed that high-concentration and long-time NH4Cl exposure (20 mM + 18 h; 15 mM + 36 h) induced apoptosis and gill tissue damages, finally causing a decline in survival. chop plays an important role in ER stress-induced apoptosis, and thus we constructed a model of chop-depleted loach by using CRISPR/Cas9 technology to investigate its response to ammonia nitrogen stress. The results showed that ammonia nitrogen stress down-regulated the expressions of apoptosis-related genes in chop+/- loach gills, while wildtype (WT) exhibited an opposite gene expression regulation pattern, suggesting that the depletion of chop suppressed apoptosis level. In addition, chop+/- loach showed a larger number of immunity-related cells and higher survival rate than WT under the NH4Cl exposure, indicating that the inhibition of chop function strengthened the innate immune barrier in general, thus increasing survival. Our findings provide the theoretical basis for developing high ammonia nitrogen-tolerant germplasm with aquaculture potential.

Ammonia nitrogen can easily cause fish poisoning or even death. In this study, the effects of ammonia nitrogen exposure on endoplasmic reticulum (ER) stress, apoptosis, and immune cells in loach Misgurnus anguillicaudatus were investigated. chop plays an important role in ER stress-induced apoptosis, and thus we constructed a model of chop-depleted loach to investigate its response to ammonia nitrogen stress. The results showed that the inhibition of chop function reduced apoptosis and strengthened the innate immune barrier in general, thus increasing survival. Our findings provide the theoretical basis for developing high ammonia nitrogen-tolerant germplasm with aquaculture potential.

Microplastics are transferred by soil fauna and regulate soil function as material carriers.

The ecotoxicological effects of microplastics, a new and widespread ecosystem pollutant, have been extensively reported. However, it remains unclear whether soil fauna transfer microplastics and whether migration behaviours influence subsequent ecological functions in terrestrial ecosystems. We investigated the transfer patterns of microplastics and their adsorbed substances by soil animals (the springtail, Folsomia candida) and the effect of the transfer on the decomposition of soil organic matter through a standardized cotton strip assay. The results showed that springtails had a strong ability to transfer microplastics into the soil. The adsorbed nutrient (nitrogen; N), pollutant (cadmium; Cd), and green fluorescent Escherichia coli (GFP-E. coli) were also transferred with the microplastics. In addition, cotton strip decomposition was accelerated when the microplastics adsorbed N, but the adsorption of Cd decreased decomposition. These ecological effects were particularly strong for small microplastics. Microplastic transfer regulated soil bacterial communities, promoting the growth of Ascomycota fungi and inhibiting that of Basidiomycota, leading to cotton strip decomposition. Thus, microplastic pollution may occur at one site, but microplastics can be transferred anywhere in terrestrial ecosystems by soil animals and adsorb other substances, including nutrients and pollutants, that affect ecosystem function. Therefore, more studies on the migration behaviour of microplastics are necessary.

Mitotic defects lead to unreduced sperm formation in cdk1-/- mutants.

Unreduced gametes, that are important for species evolution and agricultural development, are generally believed to be formed by meiotic defects. However, we found that male diploid loach (Misgurnus anguillicaudatus) could produce not only haploid sperms, but also unreduced sperms, after cyclin-dependent kinase 1 gene (cdk1, one of the most important kinases in regulating cell mitosis) deletion. Observations on synaptonemal complexes of spermatocyte in prophase of meiosis and spermatogonia suggested that the number of chromosomes in some spermatogonia of cdk1-/- loach doubled, leading to unreduced diploid sperm production. Then, transcriptome analysis revealed aberrant expressions of some cell cycle-related genes (such as ppp1c and gadd45) in spermatogonia of cdk1-/- loach relative to wild-type loach. An in vitro and in vivo experiment further validated that Cdk1 deletion in diploid loach resulted in mitotic defects, leading to unreduced diploid sperm formation. In addition, we found that cdk1-/- zebrafish could also produce unreduced diploid sperms. This study provides important information on revealing the molecular mechanisms behind unreduced gamete formation through mitotic defects, and lays the foundation for a novel strategy for fish polyploidy creation by using cdk1 mutants to produce unreduced sperms, which can then be used to obtain polyploidy, proposed to benefit aquaculture.

Grazing Effects of Soil Fauna on White-Rot Fungi: Biomass, Enzyme Production and Litter Decomposition Ability.

Soil invertebrates and microorganisms are two major drivers of litter decomposition. Even though the importance of invertebrates and microorganisms in biogeochemical soil cycles and soil food webs has been studied, the effects of invertebrates on fungi are not well understood compared to other organisms. In this work, we investigated the effects of soil invertebrates on fungi as a factor that cannot be ignored in the study of nutrient cycling. The result showed the grazing of isopods on white-rot fungi was transitive and persistent. The grazed fungi appeared "compensatory" growing. The biomass of fungi increased after grazing. The activities of enzymes associated with nutrient cycling were increased under grazing. The zymography images showed the enzyme hotspots and activities also increased significantly in the grazing area. The results suggest that invertebrate grazing can significantly increase the fungal biomass and enzyme activity, accelerating litter decomposition in the unreached grazer area. The grazing effects of invertebrate plays an important role in promoting the nutrient cycling of the forest ecosystem. We believe that this study will be a good reference related to showing the relationship between soil invertebrates, fungi and soil biogeochemical cycles.

A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon.

Anglerfishes are a highly diverse group of species with unique characteristics. Here, we report the first chromosome-level genome of a species in the order Lophiiformes, the yellow goosefish (Lophius litulon), obtained by whole genome shotgun sequencing and high-throughput chromatin conformation capture. Approximately 97.20% of the assembly spanning 709.23 Mb could be anchored to 23 chromosomes with a contig N50 of 164.91 kb. The BUSCO value was 95.4%, suggesting that the quality of the assembly was high. A comparative gene family analysis identified expanded and contracted gene families, and these may be associated with adaptation to the benthic environment and the lack of scales in the species. A majority of positively selected genes were related to metabolic processes, suggesting that digestive and metabolic system evolution expanded the diversity of yellow goosefish prey. Our study provides a valuable genetic resource for understanding the mechanisms underlying the unique features of the yellow goosefish and for investigating anglerfish evolution.

The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish.

Chondrichthyan (cartilaginous fish) occupies a key phylogenetic position and is important for investigating evolutionary processes of vertebrates. However, limited whole genomes impede our in-depth knowledge of important issues such as chromosome evolution and immunity. Here, we report the chromosome-level genome of white-spotted bamboo shark. Combing it with other shark genomes, we reconstructed 16 ancestral chromosomes of bamboo shark and illustrate a dynamic chromosome rearrangement process. We found that genes on 13 fast-evolving chromosomes can be enriched in immune-related pathways. And two chromosomes contain important genes that can be used to develop single-chain antibodies, which were shown to have high affinity to human disease markers by using enzyme-linked immunosorbent assay. We also found three bone formation-related genes were lost due to chromosome rearrangements. Our study highlights the importance of chromosome rearrangements, providing resources for understanding of cartilaginous fish diversification and potential application of single-chain antibodies.

The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis.

The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ∼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by ∼65.88% (∼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains ∼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution.

Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.

The genetic architecture of floral traits in the woody plant Prunus mume.

Mei (Prunus mume) is an ornamental woody plant that has been domesticated in East Asia for thousands of years. High diversity in floral traits, along with its recent genome sequence, makes mei an ideal model system for studying the evolution of woody plants. Here, we investigate the genetic architecture of floral traits in mei and its domestication history by sampling and resequencing a total of 351 samples including 348 mei accessions and three other Prunus species at an average sequencing depth of 19.3×. Highly-admixed population structure and introgression from Prunus species are identified in mei accessions. Through a genome-wide association study (GWAS), we identify significant quantitative traits locus (QTLs) and genomic regions where several genes, such as MYB108, are positively associated with petal color, stigma color, calyx color, and bud color. Results from this study shed light on the genetic basis of domestication in flowering plants, particularly woody plants.

Effects of MgSO4 and magnesium transporters on 6-hydroxydopamine-induced SH-SY5Y cells.

AIMS: The magnesium ion (Mg2+) fulfils several important functions for living organisms. We investigated whether there is a protective effect of MgSO4 on 6-OHDA-induced neurotoxicity in SH-SY5Y cells, and gained insight into the effects of cellular mRNA and protein expression of the magnesium transporters SLC41A1, NIPA1, MagT1 and CNNM2 on 6-OHDA-induced neurotoxicity. MAIN METHODS: The effect of MgSO4 on cell viability in 6-OHDA-treated SH-SY5Y cells was measured using a CCK-8 kit. The mRNA and protein expression of SLC41A1, NIPA1, MagT1, and CNNM2 were detected using reverse transcription-qPCR and Western blot. KEY FINDINGS: The results showed that SH-SY5Y cells treated with 25-50µM 6-OHDA for 24h significantly decreased cell viability, while if pre-incubated with 0.125-1mM MgSO4 for 1h before adding 6-OHDA it partially prevented the cell damage. There was a significant decrease in cellular mRNA and protein expression of SLC41A1, NIPA1, MagT1 and CNNM2 in 6-OHDA treated SH-SY5Y cells, and MgSO4 can reverse its decline. SIGNIFICANCE: Our results suggest that MgSO4 may protect SH-SY5Y cells against 6-OHDA-induced cell injury and that gene expression of SLC41A1, NIPA1, MagT1, and CNNM2 might be involved in dopaminergic neurons.