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Abstract Plagiognathops microlepis is an economic freshwater fish in the subfamily Xenocyprinae of Cyprinidae. It is widely distributed in the freshwater ecosystem of China, with moderate economic value and broad development prospects. However, the lack of genomic resources has limited our understanding on the genetic basis, phylogenetic status and adaptive evolution strategies of this fish. Here, we assembled a chromosome-level reference genome of P. microlepis by integrating Pacbio HiFi long-reads, Illumina short-reads and Hi-C sequencing data. The size of this genome is 1004.34 Mb with a contig N50 of 38.80 Mb. Using Hi-C sequencing data, 99.59% of the assembled sequences were further anchored to 24 chromosomes. A total of 578.91 Mb repeat sequences and 28,337 protein-coding genes were predicted in the current genome, of which, 26,929 genes were functionally annotated. This genome provides valuable information for investigating the phylogeny and evolutionary history of cyprinid fishes, as well as the genetic basis of adaptive strategies and special traits in P. microlepis.

Abstract Plants with the C4 photosynthesis pathway typically respond to climate change differently from more common C3-type plants, due to their distinct anatomical and biochemical characteristics. These different responses are expected to drive changes in global C4 and C3 vegetation distributions. However, current C4 vegetation distribution models may not predict this response as they do not capture multiple interacting factors and often lack observational constraints. Here, we used global observations of plant photosynthetic pathways, satellite remote sensing, and photosynthetic optimality theory to produce an observation-constrained global map of C4 vegetation. We find that global C4 vegetation coverage decreased from 17.7% to 17.1% of the land surface during 2001 to 2019. This was the net result of a reduction in C4 natural grass cover due to elevated CO2 favoring C3-type photosynthesis, and an increase in C4 crop cover, mainly from corn (maize) expansion. Using an emergent constraint approach, we estimated that C4 vegetation contributed 19.5% of global photosynthetic carbon assimilation, a value within the range of previous estimates (18–23%) but higher than the ensemble mean of dynamic global vegetation models (14 ± 13%; mean ± one standard deviation). Our study sheds insight on the critical and underappreciated role of C4 plants in the contemporary global carbon cycle.

Abstract Changes in the interannual variability (IAV) of vegetation greenness and carbon sequestration are key indicators of the stability and climate sensitivities of terrestrial ecosystems. Recent studies have examined the changes in the vegetation IAV using atmospheric CO2 observations and dynamic global vegetation models (DGVMs), however, reported different and even contradictory IAV trends. Here, we investigate the changes in the IAV of vegetation greenness, quantified as coefficient of variability (CV), over the past few decades based on multiple satellite remote sensing products and DGVMs. Our results suggested that, on half of the global vegetated surface (mostly in the tropics), the CV trends detected by different satellite remote sensing products are conflicting. We found that 22.20% and 28.20% of the global vegetated surface (mostly in the non‐tropical land surface) show significant positive and negative CV trends (p ≤ 0.1), respectively. Regions with higher air temperature and greater aridity tend to have increasing CV trends, whereas greater vegetation greening trend and higher nitrogen deposition lead to smaller CV trends. DGVMs generally cannot capture the CV trends obtained from satellite remote sensing products, while the inconsistency among satellite remote sensing products is likely caused by their process algorithms rather than the sensors utilized. Our study closely examines the changes in the IAV of global vegetation greenness, and highlights substantial uncertainty when using satellite remote sensing to study the response of terrestrial ecosystems to climate change.

Abstract Increasing drought frequency and severity in a warming climate threaten forest ecosystems with widespread tree deaths. Canopy structure is important in regulating tree mortality during drought, but how it functions remains controversial. Here, we show that the interplay between tree size and forest structure explains drought-induced tree mortality during the 2012-2016 California drought. Through an analysis of over one million trees, we find that tree mortality rate follows a “negative-positive-negative” piecewise relationship with tree height, and maintains a consistent negative relationship with neighborhood canopy structure (a measure of tree competition). Trees overshadowed by tall neighboring trees experienced lower mortality, likely due to reduced exposure to solar radiation load and lower water demand from evapotranspiration. Our findings demonstrate the significance of neighborhood canopy structure in influencing tree mortality and suggest that re-establishing heterogeneity in canopy structure could improve drought resiliency. Our study also indicates the potential of advances in remote-sensing technologies for silvicultural design, supporting the transition to multi-benefit forest management.

The common carp (Cyprinus carpio) is one of the most important aquaculture species in China, known for its remarkable adaptability and nutritional profile. However, the specific molecular response mechanisms regulating the nutritional deposition of carp remain inadequately elucidated. This study conducted a comprehensive analysis of muscle nutritional content and transcriptome data from liver and muscle tissues of three distinct carp varieties. The aim was to elucidate the key genes and signaling pathways that regulate muscle nutritional composition in carp. The findings revealed that FFRC carp (FFRC) exhibited significantly higher levels of crude fat, total n-3 polyunsaturated fatty acids, and total n-6 polyunsaturated fatty acids in muscle tissue compared to Ying carp (YC) and Huanghe carp (HC) (p < 0.05). Transcriptomic analyses correlated these elevated levels with a marked upregulation of genes involved in the activation and transportation of fatty acid (fabp7, acsl5, acsbg2) as well as biosynthesis and elongation of long-chain unsaturated fatty acids (elovl2, fads2) within the liver. Furthermore, the flavor amino acid, essential amino acids, and crude protein content in the muscle of HC were significantly higher than in FFRC and YC (p < 0.05). Transcriptomic analyses indicated that this was associated with significant changes in the expression of genes related to amino acid metabolism (asns, alt, ldha, glul, setd, prodh, l3hypdh, hoga1) within their muscle tissue. This research provides a theoretical foundation for the precise modulation of the muscle nutritional composition in carp.

Bone morphogenetic protein 6 (BMP-6) is a constituent of the TGF-β superfamily, known for its ability to stimulate bone and cartilage formation. The investigation of bmp6’s involvement in the formation of intermuscular bones in fish has garnered significant attention in recent years. The rib cage is an important skeletal structure that plays a protective function for internal organs in fish. However, there has been limited research conducted on the effects of the bmp6 gene on rib development. Silver carp is one of four major fish in China, favoured for its affordability and tender muscle. Nevertheless, the presence of numerous intermuscular bones in silver carp significantly hinders the advancement of its palatability and suitability for processing. This study showcases the effective utilisation of CRISPR/Cas9 technology for the purpose of disrupting the bmp6 gene in silver carp, leading to the creation of chimeras in the P0 generation, marking the first instance of such an achievement. The chimeras exhibited complete viability, normal appearance, and partial intermuscular bones loss, with approximately 30% of them displaying rib bifurcation or bending. Subsequently, a transcriptome analysis on ribs of P0 chimeras and wild-type silver carp was conducted, leading to the identification of 934 genes exhibiting differential expression, of which 483 were found to be up-regulated and 451 were found to be down-regulated. The results of the KEGG analysis revealed that the “NF-kappa B signalling pathway”, “Hippo signalling pathway”, “osteoclast differentiation”, and “haematopoietic cell lineage” exhibited enrichment and displayed a significant correlation with bone development. The up-regulated genes such as tnfα, fos, and ctgf in pathways may facilitate the proliferation and differentiation of osteoclasts, whereas the down-regulation of genes such as tgfb2 and tgfbr1 in pathways may hinder the formation and specialisation of osteoblasts, ultimately resulting in rib abnormalities. This study presents novel findings on the impact of bmp6 gene deletion on the rib development of silver carp, while simultaneously investigating the previously unexplored molecular mechanisms underlying rib defects in fish.

In this study, we investigated the body characteristics, carotenoid composition, and nutritional quality of Eriocheir sinensis with different hepatopancreas redness (a*). We distributed the crabs into two groups based on the hepatopancreas a* values and compared their body characteristics, chroma, carotenoid composition, and protein, lipid, total sugar, amino acid, and fatty acid content via paired t-test. The results revealed that the relationships between hepatopancreas a* values and crab quality are sex specific. In female crabs, the differences in nutritional characteristics were evident mainly in the hepatopancreases and ovaries. In the redder hepatopancreases, the content of zeaxanthin and β-carotene increased, and the levels of C22:6n3 and C20:5n3 decreased (p < 0.05). In the ovaries, the content of astaxanthin, canthaxanthin, β-carotene, umami, and sweet amino acids were lower in the redder hepatopancreas crabs (p < 0.05). In male crabs, there were positive relationships between hepatopancreas a* and amino acid and fatty acid content. The content of leucine, arginine, and total umami amino acids in muscles and of unsaturated fatty acids and n-6 polyunsaturated fatty acids in hepatopancreases and testicles increased with increasing hepatopancreas a* values (p < 0.05). Therefore, the redder the hepatopancreas, the higher the nutritional quality of male crabs.

Changes in vegetation responses to precipitation may be hydroclimate dependent. Here the authors reveal contrasting trends of vegetation sensitivity to precipitation in drylands vs. wetter ecosystems over the last 4 decades and identify increased CO2 as a major contributing factor.

Silver carp (Hypophthalmichthys molitrix) is a widely distributed food resource and phytoplankton predator in China, which has been used to control algal blooms. Silver carp is quite resistant to microcystins (MCs), which are typical hepatotoxins generated by toxic algae. ATP-Binding Cassette, Subfamily C (ABCC) transporter are critical detoxification genes that could export toxic substances out of the cell, and with regard to ABCC transporters in H. molitrix, current studies are limited. In order to investigate the roles of ABCC genes in excretion of MCs, the full-length transcriptome of silver carp was analyzed to screen a total of nine ABCC transporter genes, which were expressed ubiquitously in silver carp tissues, especially in the liver. Furthermore, microcystin-LR (MC-LR) intraperitoneal injection was performed, and the results showed that, except abcc2, abcc10 and abcc12, the expression of other ABCC genes increased rapidly within 1 h and then began to decline after 6 h. Among these five genes, abcc3 and abcc9 exhibited the most pronounced response, indicating that these two were the most preeminent detoxification genes of microcystin in ABCC genes family in silver carp. Meanwhile, the activities of glutathione-S-transferase (GST) were increased significantly, while the content of glutathione (GSH) demonstrated a dramatic decrease, implying that GST catalyzed binding of GSH and MC-LR, and then excreted through ABCC transporters. The findings of this study will be useful in further investigating the fundamental characteristics of silver carp and provide new insights into the potential function of ABCC genes in the detoxication of MC-LR.

The apparent temperature sensitivity of atmospheric CO2 growth rate has increased markedly over the past six decades, however, the increase remains unexplained. Here we show that tropical extreme droughts amplified the interannual variability in atmospheric CO2 growth rate and drove the sensitivity change.

Using global flux tower observations, the authors show that atmospheric dryness always reduces photosynthesis, whereas soil dryness can increase photosynthesis if soil water stores are sufficient.

The fraction of leaf nitrogen allocated to RuBisCO indicates differing nitrogen use strategies of plants and varies considerably. Here the authors show that this variation is largely driven by leaf thickness and phosphorus content with light intensity, atmospheric dryness and soil pH also having considerable influence.

The objective of this study was to investigate the PPBRs of EF and CF in the plasma of yellow catfish, grass carp, and largemouth bass at different temperatures with different concentrations. A fast and simple ultrafiltration method was used to determine the PPBRs of EF and CF. Results showed that PPBRs of EF decreased from 37.71% to 9.66%, from 46.10% to 13.52%, and from 43.90% to 4.36% in the plasma of yellow catfish with the increase of concentration from 15 to 25 °C. The same trends of PPBRs of EF were presented in the plasma of grass carp and largemouth bass. In comparison to the data at the same concentration of EF at disparate temperatures, the PPBRs of EF at a concentration of 1 µg/mL increased from 37.71% to 46.10% and then decreased to 43.90% in the plasma of yellow catfish with elevated temperature from 15 to 25 °C. There is no obvious regularity with the rise of temperature, and the same phenomenon also were found in other concentrations and species. Meanwhile, the PPBRs of CF also decreased in the three species with the rise in concentration. Under the consistent concentration, the temperature-dependent regularities were not found in the PPBRs of CF. Overall, the increased concentration reduced the PPBRs of EF and CF in the plasma of three fish species, and the alteration in temperature only has a certain effect on the PPBRs of EF and CF.

The silver carp (Hypophthalmichthys molitrix) is an economically, as well as environmentally, important fish that harbors low environmental hypoxia tolerance and frequently contributes to a loss of aquaculture productivity. The gill is the first tissue attacked by hypoxia; however, the response of the gills of H. molitrix to hypoxia stress at the tissue, cellular, and molecular levels has not been clearly established. The influence of hypoxia on histological features along with gene expression in silver carp gills were explored in this research. The hematoxylin and eosin-stained sections and electron microscopy examinations of gills indicated that the gill lamellae were seriously twisted, gill filaments were dehisced, and the swelling and shedding of epithelial cell layer in the gill tissue were intensified along with the degree of hypoxia. In the hypoxia, semi-asphyxia, and asphyxia groups, the gill transcriptomic assessment of shifts in key genes, as well as modulatory networks in response to hypoxic conditions revealed 587, 725, and 748 differentially expressed genes, respectively. These genes are abundant in immune response signaling cascades (e.g., complement and coagulation cascades, Nucleotide-binding and oligomerization domain (NOD)-like receptor signaling cascade, and differentiation of Th1 along with Th2 cells) and oxygen transport [e.g., MAPK, PI3K-Akt, and hypoxia-inducible factor 1 (HIF-1) signaling cascades]. Genes linked to immune response (e.g., c2, c3, c6, klf4, cxcr4, cd45, and cd40) and oxygen transport (e.g., egln1, egln3, epo, ldh, and vegfa) were additionally identified. According to our findings, the silver carp may be using “HIF-1” to obtain additional oxygen during hypoxia. These findings illustrate that hypoxia stress might damage gill tissue, trigger an immunological response, and activate HIF-1 signaling to increase oxygen availability under hypoxic situations. The findings of this work will help scientists better understand the molecular mechanisms driving hypoxia responses in hypoxia-sensitive fish and speed up the development of hypoxia-resistant varieties.

Abstract Large uncertainties in North American terrestrial carbon fluxes hinder regional climate projections. Terrestrial biosphere models (TBMs), the essential tools for understanding continental‐scale carbon cycle, diverge on whether temperate forests or croplands dominate carbon uptake in North America. Evidence from novel photosynthetic proxies, such as those based on chlorophyll fluorescence, has cast doubt on the “weak cropland, strong forest” carbon uptake patterns simulated by most TBMs. However, no systematic evaluation of TBMs has yet been attempted to pin down space‐time patterns that are most consistent with regional CO2 observational constraints. Here, we leverage atmospheric CO2 observations and satellite‐observed photosynthetic proxies to understand emergent space‐time patterns in North American carbon fluxes from a large suite of TBMs and data‐driven models. To do so, we evaluate how well the atmospheric signals resulting from carbon flux estimates reproduce the space‐time variability in atmospheric CO2, as is observed by a network of continuous‐monitoring towers over North America. Models with gross or net carbon fluxes that are consistent with the observed CO2 variability share a salient feature of growing‐season carbon uptake in Midwest US croplands. Conversely, the remaining models place most growing‐season uptake in boreal or temperate forests. Differences in model explanatory power depend mainly on the simulated annual cycles of cropland uptake—especially, the timing of peak uptake—rather than the distribution of annual mean fluxes across biomes. Our results suggest that improved model representation of cropland phenology is crucial to robust, policy‐relevant estimation of North American carbon exchange.

The Chinese soft-shelled turtle Pelodiscus sinensis shows obvious sexual dimorphism. The economic and nutrition value of male individuals are significantly higher than those of female individuals. Pseudo-females which are base to all-male breeding have been obtained by estrogen induction, while the gene function and molecular mechanism of sex reversal remain unclear in P. sinensis. Here, comparative transcriptome analyses of female, male, and pseudo-female gonads were performed, and 14,430 genes differentially expressed were identified in the pairwise comparison of three groups. GO and KEGG analyses were performed on the differentially expressed genes (DEGs), which mainly concentrated on steroid hormone synthesis. Furthermore, the results of gonadal transcriptome analysis revealed that 10 sex-related sox genes were differentially expressed in males vs. female, male vs. pseudo-female, and female vs. pseudo-female. Through the differential expression analysis of these 10 sox genes in mature gonads, six sox genes related to sex reversal were further screened. The molecular mechanism of the six sox genes in the embryo were analyzed during sex reversal after E2 treatment. In mature gonads, some sox family genes, such as sox9sox12, and sox30 were highly expressed in the testis, while sox1, sox3, sox6, sox11, and sox17 were lowly expressed. In the male embryos, exogenous estrogen can activate the expression of sox3 and inhibit the expression of sox8, sox9, and sox11. In summary, sox3 may have a role in the process of sex reversal from male to pseudo-female, when sox8 and sox9 are inhibited. Sox family genes affect both female and male pathways in the process of sex reversal, which provides a new insight for the all-male breeding of the Chinese soft-shelled turtle.

Hypoxia is one of the serious stresses in fish culture, which can lead to physical and morphological changes, and cause injury and even death to fish. Silver carp (Hypophthalmichthys molitrix) is an important economic fish and widely distributed in China. MicroRNA is a kind of endogenous non-coding single-stranded small RNA, which is involved in cell development, and immune response and gene expression regulation. In this study, silver carp were kept in the closed containers for hypoxia treatment by spontaneous oxygen consumption. The samples of heart, brain, liver and gill were collected, and the total RNAs extracted separately from the four tissues were mixed in equal amounts according to the concentration. Afterwards, the RNA pool was constructed for high-throughput sequencing, and based on the small RNA sequencing, the differentially expressed microRNAs were identified. Furthermore, their target gene prediction and enrichment analyses were carried out. The results showed that a total of 229 known miRNAs and 391 putative novel miRNAs were identified, which provided valuable resources for further study on the regulatory mechanism of miRNAs in silver carp under hypoxia stress. The authors verified 16 differentially expressed miRNAs by qRT-PCR, and the results were consistent with small RNA sequencing (sRNA-seq). The predicted target genes number of differentially expressed miRNAs was 25,146. GO and KEGG functional enrichment analysis showed that these target genes were mainly involved in the adaption of hypoxia stress in silver carp through biological regulation, catalytic activity and apoptosis. This study provides references for further study of interaction between miRNAs and target genes, and the basic data for the response mechanism under hypoxia stress in silver carp.

This study evaluates the performances of three global satellite datasets (Advanced Very High Resolution Radiometer (AVHRR), Moderate Resolution Imaging Spectroradiometer (MODIS) and Satellite pour l’ observation de la Terre (SPOT) of the Mongolian Plateau, where in situ observation is insufficient to assess vegetation dynamics on terrestrial systems. We give a comprehensive assessment of the historical changes in vegetation dynamics by using comparative and correlation methods on the three archives using two indices: the growing season’s Normalized Difference Vegetation Index (NDVI) and the Start of the Season Index (SOS). The main findings are: (1) MODIS and SPOT have generally better comparability and consistency in the spatial-temporal trends of NDVI and SOS than AVHRR in this area; (2) all the three archives exhibit better consistency in Inner Mongolia than in Mongolia; (3) integration data analysis of AVHRR (1982–1997) and SPOT (1998–2012) shows that the dynamics of vegetation growth has three distinct phases: enhanced before 1994; a flatter/slightly decreasing trend before 2001; and, then, a rapid recovery between 2001 and 2012 with remarkable spatial heterogeneity, with Inner Mongolia experiencing a significant greening in vegetation NDVI compared with no obvious changes in Mongolia; (4) the temporal average SOS showed no significant “earlier spring” onset during the past 31 years, on the middle and northern Mongolian Plateau.

Using estimated leaf unfolding data and two types of Normalized Difference Vegetation Index (NDVI and NDVI3g) data generated from the Advanced Very High Resolution Radiometer (AVHRR) in the deciduous broadleaf forest of northern China during 1986 to 2006, we analyzed spatial, temporal and spatiotemporal relationships and differences between ground-based growing season beginning (BGS) and NDVI (NDVI3g)-retrieved start of season (SOS and SOS3g), and compared effectiveness of NDVI and NDVI3g in monitoring BGS. Results show that the spatial series of SOS (SOS3g) correlates positively with the spatial series of BGS at all pixels in each year (P < 0.001). Meanwhile, the time series of SOS (SOS3g) correlates positively with the time series of BGS at more than 65% of all pixels during the study period (P < 0.05). Furthermore, when pooling SOS (SOS3g) time series and BGS time series from all pixels, a significant positive correlation (P < 0.001) was also detectable between the spatiotemporal series of SOS (SOS3g) and BGS. In addition, the spatial, temporal and spatiotemporal differences between SOS (SOS3g) and BGS are at acceptable levels overall. Generally speaking, SOS3g is more consistent and accurate than SOS in capturing BGS, which suggests that NDVI3g data might be more sensitive than NDVI data in monitoring vegetation leaf unfolding.