Explore the vast range of titles available.

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. Mei ( Prunus mume ) is a woody tree that produces ornamental blossoms which symbolize spring in East Asia. Here, Zhang et al. resequence wild and domesticated mei to reveal considerable admixture and introgression from other Prunus species and identify loci associated with floral traits.

Cartilaginous fishes (e.g., sharks, rays, and skates) cannot see blue or violet light, potentially because they lack the shortwave-sensitive cone opsin gene ( sws ). Widespread gene loss can occur during evolution, but the evolutionary mechanisms underlying sws loss remains unclear. Here, we construct whole-genome assemblies of Okamejei kenojei (skate) and Prionace glauca (blue shark). We then analyze the distribution characteristics and intragroup differences of opsin-related genes in cartilaginous fishes. Using a zebrafish model with sws deleted we infer that in the presence of SWS1 and SWS2, blue and violet light respectively, can induce cell aging. This is followed by photoreceptor layer thinning, demonstrating, sws loss aids in preventing shortwave light damage to the eye. In the retinas of numerous cartilaginous fishes, the tapetum lucidum strongly reflects light. Therefore, in cartilaginous fish, the existence of tapetum lucidum in the retina and loss of sws may be interdependent; in other words, this adaptive gene loss may increase cartilaginous fish fitness. Cartilaginous fishes lost the short-wave-sensitive ( sws ) opsin genes at some point in their evolutionary history. Here, the authors present genome assemblies of Okamejei kenojei (skate) and Prionace glauca (blue shark) that confirm sws loss, together with experimental evidence that sws loss reduces shortwave light damage to the eye.

Northeast China boasts abundant resources of cold mountain grapes. This study focused on three varieties of cold mountain grape brandy, Beibing Hong (BBH), Shuanghong (SH), and Zuoshanyi (ZSY), with varying ageing periods to investigate changes in their physicochemical properties, nutrients, and aroma compounds. Results showed that alcohol content and pH gradually decreased with ageing, while total acidity (including inorganic acids) increased. Specific organic acids declined over time, whereas polyphenolic compounds increased with longer ageing. Furthermore, the total quantity of aroma substances in all three brandies was positively correlated with ageing duration, with 18-month-aged BBH brandy exhibiting the highest content and the richest aromatic variety. Clustering analysis via heat maps revealed that brandies aged 12 and 18 months grouped together, showing that ageing time correlated positively with most esters and alcohols and negatively with acids. No significant variations were observed in the contents of terpenes, aldehydes and ketones among the three brandy varieties.

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.

Background and aimsDead leaves may remain standing all winter before entering the soil as litter in subtropical forests. However, little is known about the standing decomposition of dead leaves and how this might influence subsequent litter decomposition in the soil.MethodsWe conducted an investigation of the standing decomposition of dead leaves in winter in a subtropical forest. In the following summer, we conducted a decomposition experiment of pre-standing litter (dead leaves picked immediately after leaf death) and post-standing litter (dead leaves picked after winter) in the soil using the litterbag method, further exploring the influences of the standing process on subsequent litter decomposition in the soil.ResultsAfter 159 days of standing decomposition, up to 43% of leaf mass was lost, with lignin and cellulose degraded by 30% and 35%, respectively. After 163 days of decomposition in the soil, the mass losses of pre-standing and post-standing litter were 31% and 52%, respectively. The decomposition rate (k) of post-standing litter was 2 times that of pre-standing litter. Restrained by the low photodegradability of litter in the later stage of decomposition, standing decomposition still conformed to the exponential decomposition model.ConclusionThe standing decomposition of dead leaves in winter is driven predominantly by the abiotic process of photodegradation with leaching, resulting in substantial carbon loss in the standing phase and a doubling of the subsequent litter decomposition rate in soil, thus profoundly influencing the carbon process of subtropical forest ecosystems.

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.

Objective: To study the therapeutic effect and mechanism of Suanzaoren Decoction on mice with depression. Methods: A model of depression was prepared by chronic unpredictable stimulation and reserpine induction. Behavioral tests, determination of norepinephrine and dopamine were performed. Results: The behavioral indicators of the model group were reduced, and the expression of norepinephrine and dopamine was decreased. Conclusion: Suanzaoren Decoction has an effect on the increase of serum norepinephrine and dopamine content, indicating that the jujube seed Soup has a certain effect on depression.

There is ample evidence of the loss of the shortwave visual protein gene in cartilaginous fish. However, the underlying logic and mechanisms by which organisms need to adapt to the environment behind the opsin loss are still unclear. Here, we report the assembly structure of the whole genome of Okamejei kenojei and Prionace glauca, identify TcMar difference between skates/rays and sharks/chimaeras, and analyze the distribution characteristics and intra group differentiation of opsin-related genes in cartilaginous fish. By establishing a zebrafish model with short wave opsin gene deletion, we find blue or violet light via short-wave sensitive opsins SWS1 or SWS2 can cause the photoreceptor layer thinning (the biomarker for age-related macular degeneration in human eye) through enactive the cell aging. The loss of sws is helpful for alleviating the short-wave light damage on the eye. Since the tapetum lucidum in the eye is found broad existence in various cartilaginous fish, a logical hypothesis was creatively proposed that the existence of tapetum lucidum on the retina of cartilaginous fish is interdependent with the loss of shortwave visual protein gene, providing a new perspective and explanatory path for further understanding of the evolution of visual genes in cartilaginous fish.

Invertebrates, animals (metazoans) without backbones, encompass ∼97% of all animal yet remains understudied. They have provided insights into molecular mechanisms underlying fundamentally identical mechanisms in phylogenetically diverse animals, including vertebrates. Marine invertebrates have long fascinated researchers due to their abundance, diversity, adaptations, and impact on ecosystems and human economies. Here, we report a compendium and appraisal of 190 marine invertebrate genomes spanning 21 phyla, 43 classes, 92 orders, and 134 families. We identify a high proportion and long unit size of tandem repeats, likely contributing to reported difficulties in invertebrate genome assembly. A well-supported phylogenetic tree of marine invertebrates from 974 single-copy orthologous genes resolved topological controversies. We show that Ctenophora is at the basal phylum and Porifera is the sister group of Parahoxozoa; that Xenacoelomorpha is within Bilateria and is the sister group to Protostomia, rejecting three out of four hypotheses in the field; and that Bryozoa is at the basal position of Lophotrochozoa, not grouped into Lophophorata. We also present insights into the genetic underpinnings of metazoans from Hox genes, innate immune gene families, and nervous system gene families. Our marine invertebrate genome compendium provides a unified foundation for studies on their evolution and effects on ecological systems and human life.

Abstract The monocot family Melanthiaceae with varying genome sizes in a range of 230-fold is an ideal model to study the genome size fluctuation in plants. Its family member Paris genus demonstrates an evolutionary trend of bearing huge genomes characterized by an average c-value of 49.22 pg. Here, we report a 70.18 Gb genome assembly out of the 82.55 Gb genome of Paris polyphylla var. yunnanensis (PPY), which represents the biggest sequenced genome to date. We annotate 69.53% repetitive sequences in this genome and 62.50% of which are long-terminal repeat (LTR) transposable elements. Further evolution analysis indicates that the giant genome likely results from the joint effect of common and species-specific expansion of different LTR superfamilies, which might contribute to the environment adaptation after speciation. Moreover, we identify the candidate pathway genes for the biogenesis of polyphyllins, the PPY-specific medicinal saponins, by complementary approaches including genome mining, comprehensive analysis of 31 next-generation RNA-seq data and 55.23 Gb single-molecule circular consensus sequencing (CCS) RNA-seq reads, and correlation of the transcriptome and phytochemical data of five different tissues at four growth stages. This study not only provides significant insights into plant genome size evolution, but also paves the way for the following polyphyllin synthetic biology. Competing Interest Statement The authors have declared no competing interest.