Effects of co-application of biochar and nitrogen fertilizer on soil profile carbon and nitrogen stocks and their fractions in wheat field.

Applying biochar to nitrogen (N)-fertilized soils is recognized as an effective technique for enhancing soil carbon (C) accumulation and improving agroecosystem sustainability. However, the impact of co-application of biochar and N fertilizer on soil C and N stocks, as well as their fractions, within the 0-60 cm soil profile remains unclear. This study examined the soil C and N fractions as well as stocks in soil profiles, and the primary influencing factors in wheat field with different rates of biochar (0, 20 and 40 t ha; B0, B1 and B2) and N application (0, 180 and 360 kg N ha; N0, N1 and N2).

Disturbance history, neighborhood crowding and soil conditions jointly shape tree growth in temperate forests.

Understanding how different mechanisms act and interact in shaping communities and ecosystems is essential to better predict their future with global change. Disturbance legacy, abiotic conditions, and biotic interactions can simultaneously influence tree growth, but it remains unclear what are their relative contributions and whether they have additive or interactive effects. We examined the separate and joint effects of disturbance intensity, soil conditions, and neighborhood crowding on tree growth in 10 temperate forests in northeast China.

A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization.

The six species of lungfish possess both lungs and gills and are the closest extant relatives of tetrapods. Here, we report a single-cell transcriptome atlas of the West African lungfish (Protopterus annectens). This species manifests the most extreme form of terrestrialization, a life history strategy to survive dry periods that can last for years, characterized by dormancy and reversible adaptive changes of the gills and lungs.

CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network.

The genetic information coded in DNA leads to trait innovation via a gene regulatory network (GRN) in development. Here, we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network (CNEReg) to investigate the ruminant multi-chambered stomach innovation. We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep, and revealed 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs).

Tree growth response to soil nutrients and neighborhood crowding varies between mycorrhizal types in an old-growth temperate forest.

Forest dynamics are shaped by both abiotic and biotic factors. Trees associating with different types of mycorrhizal fungi differ in nutrient use and dominate in contrasting environments, but it remains unclear whether they exhibit differential growth responses to local abiotic and biotic gradients where they co-occur. We used 9-year tree census data in a 25-ha old-growth temperate forest in Northeast China to examine differences in tree growth response to soil nutrients and neighborhood crowding between tree species associating with arbuscular mycorrhizal (AM), ectomycorrhizal (EM), and dual-mycorrhizal (AEM) fungi.

GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life.

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes.

Adaptation of Soil Fungal Community Structure and Assembly to Long- Versus Short-Term Nitrogen Addition in a Tropical Forest.

Soil fungi play critical roles in ecosystem processes and are sensitive to global changes. Elevated atmospheric nitrogen (N) deposition has been well documented to impact on fungal diversity and community composition, but how the fungal community assembly responds to the duration effects of experimental N addition remains poorly understood. Here, we aimed to investigate the soil fungal community variations and assembly processes under short- (2 years) versus long-term (13 years) exogenous N addition (∼100 kg N ha yr) in a N-rich tropical forest of China.

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses.

Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation.

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. In this study, we developed a tissue-based proteome map using 34 major normal pig tissues. A total of 5841 unknown protein isoforms were identified and systematically characterized, including 2225 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome.

β-Cyanoalanine Synthase Regulates the Accumulation of β-ODAP via Interaction with Serine Acetyltransferase in .

β--Oxalyl-l-α,β-diaminopropionic acid (β-ODAP), found in at first, causes a neurological disease, lathyrism, when over ingested in an unbalanced diet. Our previous research suggested that β-ODAP biosynthesis is related to sulfur metabolism. In this study, β-cyanoalanine synthase (β-CAS) was confirmed to be responsible for β-ODAP biosynthesis via enzymatic analysis.

Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution.

G-quadruplex (G4) structures have been predicted in the genomes of many organisms and proven to play regulatory roles in diverse cellular activities. However, there is little information on the evolutionary history and distribution characteristics of G4s. Here, whole-genome characteristics of potential G4s were studied in 37 evolutionarily representative species.

High-continuity genome assembly of the jellyfish .

The Atlantic sea nettle ( ) has an important evolutionary position due to its high ecological value. However, due to limited sequencing technologies and complex jellyfish genomic sequences, the current genome assembly is highly fragmented. Here, we used the most advanced high-throughput chromosome conformation capture (Hi-C) technology to obtain high-coverage sequencing data of the genome.

Improved Assembly of the Achlorophyllous Orchid .

Achlorophyllous plants are full mycoheterotrophic plants with no chlorophyll and they obtain their nutrients from soil fungi. is a perennial, achlorophyllous orchid that displays distinctive evolutionary strategy of adaptation to the non-photosynthetic lifestyle. Here in this study, the genome of was assembled to 1.

Draft Genome of the European Mouflon ().

Mouflon () with its huge and beautiful horns is considered as one of the ancestors of domesticated sheep. The European mouflon () is in the Asiatic mouflon () clade. In order to provide novel genome information for mouflon, moreover promote genetic analysis of genus both domestic and wild, we propose to sequence the mouflon genome.

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore.

Background: The availability of reference genomes has revolutionized the study of biology. Multiple competing technologies have been developed to improve the quality and robustness of genome assemblies during the past decade. The 2 widely used long-read sequencing providers-Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)-have recently updated their platforms: PacBio enables high-throughput HiFi reads with base-level resolution of >99%, and ONT generated reads as long as 2 Mb.

An Indo-Pacific Humpback Dolphin Genome Reveals Insights into Chromosome Evolution and the Demography of a Vulnerable Species.

The Indo-Pacific humpback dolphin () is a small inshore species of odontocete cetacean listed as Vulnerable on the IUCN Red List. Here, we report on the evolution of . chromosomes from its cetruminant ancestor and elucidate the evolutionary history and population genetics of two neighboring .

Chromosome-level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs.

The blue king crab, Paralithodes platypus, which belongs to the family Lithodidae, is a commercially and ecologically important species. However, a high-quality reference genome for the king crab has not yet been reported. Here, we assembled the first chromosome-level blue king crab genome, which contains 104 chromosomes and an N50 length of 51.

An early gall-inducing parasitic wasp adversely affects the fitness of its host Ficus tree but not the pollinator.

The fig tree-fig pollinator mutualism is one of the most tightly knit symbiotic systems. The research on the ecology of non-pollinators which exploit the mutualism without providing services to the host is very limited and conclusions about the role they play in the maintenance of this mutualism are full of contradictions. The non-pollinating fig wasps species are highly diverse in their feeding habit and ecological function, which may result in different consequences on the mutualism.

Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K).

Background: With more than 30,000 species, fish-including bony, jawless, and cartilaginous fish-are the largest vertebrate group, and include some of the earliest vertebrates. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish.

Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis.

Significantly increasing crop yield is a major and worldwide challenge for food supply and security. It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide. Yet, the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery.

The origin of domestication genes in goats.

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the gene, which encodes a gastrointestinally secreted mucin.

High-Quality Genome Assembly of Provides Insights Into the Adaptive Evolution of Jellyfish.

Jellyfish, such as , hold an important evolutionary position and have great ecological value. However, limited genomic resources are currently available for studying their basic genetic and development processes. Here, we assembled the first high-quality reference genome of , and successfully annotated 21,606 protein-coding genes.

De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps.

Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps.

Electrospray-Printed Three-Tiered Composite Membranes with Enhanced Mass Transfer Coefficients for Phenol Removal in an Aqueous-Aqueous Membrane Extractive Process.

The aqueous-aqueous membrane extractive process is an ideal approach to remove recalcitrant organics from highly saline and harsh wastewater. However, it is still challenging to develop highly efficient membranes for the extractive process. In this work, three-tiered polydimethylsiloxane (PDMS)/polyvinylidene fluoride (PVDF) nanofiber/nonwoven fabric composite membranes were prepared by electrospinning and electrospray printing for the first time.

Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene.

Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C.