Amelioration of intestinal barrier function and reduction of blood lead level in adult women with recurrent spontaneous abortion by a novel product of dietary fiber mixture, Holofood.

BACKGROUND: The elevated circulating toxins secondary to the impairment of intestinal barrier integrity commonly elicit a chronic inflammatory response and finally contribute to multiple diseases. These toxins, including bacterial by-products and heavy metals, are the potent risk factors for the development of recurrent spontaneous abortion (RSA). Preclinical evidence suggests that several dietary fibers can restore intestinal barrier function and decrease the accumulation of heavy metals. However, it is uncertain whether treatment with a newly developed blend of dietary fibers product (Holofood) benefits patients with RSA. METHODS: In this trial, we enrolled 70 adult women with RSA, who were randomly assigned into the experiment group and the control group in a 2:1 ratio. Upon the basis of conventional therapy, subjects in the experiment group (n = 48) received 8 weeks oral administration with Holofood three times daily at a dose of 10 g each time. Subjects without Holofood consumption were set as the control (n = 22). Blood samples were collected for the determinations of metabolic parameters, heavy mental lead, and the indices related to intestinal barrier integrity (D-lactate, bacterial endotoxin, and diamine oxidase activity). RESULTS: The reduction amplitude in blood lead from baseline to week 8 was 40.50 ± 54.28 (µg/L) in the experiment group as compared with 13.35 ± 36.81 (µg/L) in the control group (P = 0.037). The decreased level of serum D-lactate from baseline to week 8 was 5.58 ± 6.09 (mg/L) in the experiment group as compared with - 2.38 ± 8.90 (mg/L, P < 0.0001) in the control group. The change in serum DAO activity from baseline to week 8 was 3.26 ± 2.23 (U/L) in the experiment group as compared with - 1.24 ± 2.22 (U/L, P < 0.0001) in the control group. Participants who received Holofood had a greater decline in blood endotoxin from baseline to week 8 than those in the control group. Moreover, by comparing with the self-baseline, Holofood consumption significantly decreased the blood levels of lead, D-lactate, bacterial endotoxin, and DAO activity. CONCLUSION: Our results suggest that Holofood affords a clinically relevant improvements in blood lead level and intestinal barrier dysfunction in patients with RSA.

A novel TF molecular switch-mechanism found in two contrasting ecotypes of a psammophyte, Agriophyllum squarrosum, in regulating transcriptional drought memory.

BACKGROUND: Prior drought stress may change plants response patterns and subsequently increase their tolerance to the same condition, which can be referred to as "drought memory" and proved essential for plants well-being. However, the mechanism of transcriptional drought memory in psammophytes remains unclear. Agriophyllum squarrosum, a pioneer species on mobile dunes, is widely spread in Northern China's vast desert areas with outstanding ability of water use efficiency. Here we conducted dehydration-rehydration treatment on A. squarrosum semi-arid land ecotype AEX and arid land ecotype WW to dissect the drought memory mechanism of A. squarrosum, and to determine the discrepancy in drought memory of two contrasting ecotypes that had long adapted to water heterogeneity. RESULT: Physiological traits monitoring unveiled the stronger ability and longer duration in drought memory of WW than that of AEX. A total of 1,642 and 1,339 drought memory genes (DMGs) were identified in ecotype AEX and WW, respectively. Furthermore, shared DMGs among A. squarrosum and the previously studied species depicted that drought memory commonalities in higher plants embraced pathways like primary and secondary metabolisms; while drought memory characteristics in A. squarrosum were mainly related to response to heat, high light intensity, hydrogen peroxide, and dehydration, which might be due to local adaptation to desert circumstances. Heat shock proteins (HSPs) occupied the center of the protein-protein interaction (PPI) network in drought memory transcription factors (TF), thus playing a key regulatory role in A. squarrosum drought memory. Co-expression analysis of drought memory TFs and DMGs uncovered a novel regulating module, whereby pairs of TFs might function as molecular switches in regulating DMG transforming between high and low expression levels, thus promoting drought memory reset. CONCLUSION: Based on the co-expression analysis, protein-protein interaction prediction, and drought memory metabolic network construction, a novel regulatory module of transcriptional drought memory in A. squarrosum was hypothesized here, whereby recurrent drought signal is activated by primary TF switches, then amplified by secondary amplifiers, and thus regulates downstream complicated metabolic networks. The present research provided valuable molecular resources on plants' stress-resistance basis and shed light on drought memory in A. squarrosum.

Parvimonas micra activates the Ras/ERK/c-Fos pathway by upregulating miR-218-5p to promote colorectal cancer progression.

BACKGROUND: Colorectal cancer (CRC) is the third most common cancer in the world, and a strong relationship exists between CRC and gut microbiota, which affects the occurrence, development, and metastasis of cancer. Bioinformatics-based analyses revealed that the abundance of Parvimonas micra (P. micra) in the feces of patients with cancer is significantly higher than that in healthy people. Therefore, an important relationship may exist between P. micra and CRC. METHODS: We first confirmed that P. micra can promote the proliferation of cell lines through cell experiments and mouse models. Then we selected the signaling pathways and content of exosomes to promote the development of CRC by transcriptomics and microRNA sequencing. Finally, we confirmed that P. micra promoted CRC development through miR-218-5p/Ras/ERK/c-Fos pathway through the in vivo and in vitro experiments. RESULTS: First, it was confirmed by in vitro and in vivo experiments that P. micra can promote the development of CRC. Transcriptome analysis after the coincubation of bacteria and cells revealed that P. micra promoted cell proliferation by activating the Ras/ERK/c-Fos pathway. Furthermore, microRNA sequencing analysis of the cells and exosomes showed that miR-218-5p and protein tyrosine phosphatase receptor R (PTPRR) were the key factors involved in activating the Ras/ERK/c-Fos pathway, and the miR-218-5p inhibitor was used to confirm the role of microRNA in xenograft mice. CONCLUSION: This experiment confirmed that P. micra promoted the development of CRC by upregulating miR-218-5p expression in cells and exosomes, inhibiting PTPRR expression, and ultimately activating the Ras/ERK/c-Fos signaling pathway.

A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing.

Whole-genome genotyping methods are important for breeding. However, it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species. In our study, we accidently discovered that in adapter ligation-mediated PCR, the amplification by primer-template mismatched annealing (PTMA) along the genome could generate thousands of stable PCR products. Based on this observation, we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing (FBI-seq) using one specific primer, in which foreground genotyping is performed by primer-template perfect annealing (PTPA), while background genotyping employs PTMA. Unlike DNA arrays, multiple PCR, or genome target enrichments, FBI-seq requires little preliminary work for primer design and synthesis, and it is easily adaptable to different foreground genes and species. FBI-seq therefore provides a prolific, robust, and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the post-genomics era.

The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation.

Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genome of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

Corrigendum: Integrated metabolomics and transcriptomics insights on flavonoid biosynthesis of a medicinal functional forage, Agriophyllum squarrosum (L.), based on a common garden trial covering six ecotypes.

[This corrects the article DOI: 10.3389/fpls.2022.985572.].

A comprehensive dynamic immune acetylproteomics profiling induced by Puccinia polysora in maize.

Lysine-ε-acetylation (Kac) is a reversible post-translational modification that plays important roles during plant-pathogen interactions. Some pathogens can deliver secreted effectors encoding acetyltransferases or deacetylases into host cell to directly modify acetylation of host proteins. However, the function of these acetylated host proteins in plant-pathogen defense remains to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein abundance and lysine acetylation changes in maize infected with Puccinia polysora (P. polysora) at 0 h, 12 h, 24 h, 48 h and 72 h. A total of 7412 Kac sites from 4697 proteins were identified, and 1732 Kac sites from 1006 proteins were quantified. Analyzed the features of lysine acetylation, we found that Kac is ubiquitous in cellular compartments and preferentially targets lysine residues in the -F/W/Y-X-X-K (ac)-N/S/T/P/Y/G- motif of the protein, this Kac motif contained proteins enriched in basic metabolism and defense-associated pathways during fungal infection. Further analysis of acetylproteomics data indicated that maize regulates cellular processes in response to P. polysora infection by altering Kac levels of histones and non-histones. In addition, acetylation of pathogen defense-related proteins presented converse patterns in signaling transduction, defense response, cell wall fortification, ROS scavenging, redox reaction and proteostasis. Our results provide informative resources for studying protein acetylation in plant-pathogen interactions, not only greatly extending the understanding on the roles of acetylation in vivo, but also providing a comprehensive dynamic pattern of Kac modifications in the process of plant immune response.

Integrated metabolomics and transcriptomics insights on flavonoid biosynthesis of a medicinal functional forage, Agriophyllum squarrosum (L.), based on a common garden trial covering six ecotypes.

Agriophyllum squarrosum (L.) Moq., well known as sandrice, is an important wild forage in sandy areas and a promising edible and medicinal resource plant with great domestication potential. Previous studies showed flavonoids are one of the most abundant medicinal ingredients in sandrice, whereby isorhamnetin and isorhamnetin-3-glycoside were the top two flavonols with multiple health benefits. However, the molecular regulatory mechanisms of flavonoids in sandrice remain largely unclear. Based on a common garden trial, in this study, an integrated transcriptomic and flavonoids-targeted metabolomic analysis was performed on the vegetative and reproductive periods of six sandrice ecotypes, whose original habitats covered a variety of environmental factor gradients. Multiple linear stepwise regression analysis unveiled that flavonoid accumulation in sandrice was positively correlated with temperature and UVB and negatively affected by precipitation and sunshine duration, respectively. Weighted co-expression network analysis (WGCNA) indicated the bHLH and MYB transcription factor (TF) families might play key roles in sandrice flavonoid biosynthesis regulation. A total of 22,778 differentially expressed genes (DEGs) were identified between ecotype DL and ecotype AEX, the two extremes in most environmental factors, whereby 85 DEGs could be related to known flavonoid biosynthesis pathway. A sandrice flavonoid biosynthesis network embracing the detected 23 flavonoids in this research was constructed. Gene families Plant flavonoid O-methyltransferase (AsPFOMT) and UDP-glucuronosyltransferase (AsUGT78D2) were identified and characterized on the transcriptional level and believed to be synthases of isorhamnetin and isorhamnetin-3-glycoside in sandrice, respectively. A trade-off between biosynthesis of rutin and isorhamnetin was found in the DL ecotype, which might be due to the metabolic flux redirection when facing environmental changes. This research provides valuable information for understanding flavonoid biosynthesis in sandrice at the molecular level and laid the foundation for precise development and utilization of this functional resource forage.

Genetic and transcriptomic dissection of an artificially induced paired spikelets mutant of wheat (Triticum aestivum L.).

KEY MESSAGE: Morphological, genetic and transcriptomic characterizations of an EMS-induced wheat paired spikelets (PS) mutant were performed. A novel qualitative locus WPS1 on chromosome 1D was identified. Grain yield of wheat is significantly associated with inflorescence or spike architecture. However, few genes related to wheat spike development have been identified and their underlying mechanisms are largely unknown. In this study, we characterized an ethyl methanesulfonate (EMS)-induced wheat mutant, wheat paired spikelets 1 (wps1). Unlike a single spikelet that usually develops at each node of rachis, a secondary spikelet appeared below the primary spikelet at most of the rachis nodes of wps1. The microscope observation showed that the secondary spikelet initiated later than the primary spikelet. Genetic analysis suggested that the PS of wps1 is controlled by a single dominant nuclear gene, designated WHEAT PAIRED SPIKELETS 1 (WPS1). Further RNA-seq based bulked segregant analysis and molecular marker mapping localized WPS1 in an interval of 208.18-220.92 Mb on the chromosome arm 1DL, which is different to known genes related to spike development in wheat. By using wheat omics data, TraesCS1D02G155200 encoding a HD-ZIP III transcription factor was considered as a strong candidate gene for WPS1. Transcriptomic analysis indicated that PS formation in wps1 is associated with auxin-related pathways and may be regulated by networks involving TB1, Ppd1, FT1, VRN1, etc. This study laid the solid foundation for further validation of the causal gene of WPS1 and explored its regulatory mechanism in PS formation and inflorescence development, which may benefit to kernel yield improvement of wheat based on optimization or design of spike architecture in the future.

Copranaerobaculum intestinale gen. nov., sp. nov., a novel anaerobic bacterium isolated from human faeces.

A novel obligate anaerobic organism, designated DONG20-135T, was isolated from human faeces collected in Beijing, PR China. Cells were Gram-stain-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 25‒45 °C (optimum, 30‒35 °C), a pH range of 6-9 (optimum, pH 8) and in the presence of 0‒3.5 % (w/v) NaCl (optimum, 0.5‒1.5 %). The major fatty acids were C16 : 0, C18 : 1 ω9c and C10 : 0, the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, four glycolipids, six aminolipids, three aminophospholipids and four unidentified lipids. No respiratory quinones were detected. The cell-wall peptidoglycan of the strain was A1γ type, containing meso-diaminopimelic acid. The 16S rRNA gene sequences shared a lower identity (<92.7 % similarity) with the described species. The phylogenetic tree based on 16S rRNA gene sequences and the protein-concatamer tree showed that strain DONG20-135T formed a distinct lineage within the family Erysipelotrichaceae. The genomic DNA G + C content was 42.2 mol%. Based on the results of phenotypic, chemotaxonomic and genomic analyses, strain DONG20-135T represents a novel genus of the family Erysipelotrichaceae, for which the name Copranaerobaculum intestinale gen. nov., sp. nov. is proposed (=KCTC 15868T=CGMCC 1.17357T).

Metagenomics analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues.

Introduction. Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized.Hypothesis/Gap Statement. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth.Aim. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing.Methodology. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing.Results. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. Myroides odoratimimus and Cellulophaga baltica could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities.Conclusion. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.

The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize.

Southern corn rust (SCR), caused by the fungal pathogen Puccinia polysora, is a major threat to maize production worldwide. Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR. Here, we report the molecular cloning and characterization of RppC, which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus. Furthermore, we identified the corresponding avirulence effector, AvrRppC, which is secreted by P. polysora and triggers RppC-mediated resistance. Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance, indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production. Currently, RppC is the most frequently deployed SCR resistance gene in China, and a better understanding of its mode of action is critical for extending its durability.

High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan.

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding. Tian-you-hua-zhan has been a leading hybrid in China over the past decade. Here, de novo genome assembly strategy optimization for the rice indica lines Huazhan (HZ) and Tianfeng (TF), including sequencing platforms, assembly pipelines and sequence depth, was carried out. The PacBio and Nanopore platforms for long-read sequencing were utilized, with the Canu, wtdbg2, SMARTdenovo, Flye, Canu-wtdbg2, Canu-SMARTdenovo and Canu-Flye assemblers. The combination of PacBio and Canu was optimal, considering the contig N50 length, contig number, assembled genome size and polishing process. The assembled contigs were scaffolded with Hi-C data, resulting in two "golden quality" rice reference genomes, and evaluated using the scaffold N50, BUSCO, and LTR assembly index. Furthermore, 42,625 and 41,815 non-transposable element genes were annotated for HZ and TF, respectively. Based on our assembly of HZ and TF, as well as Zhenshan97, Minghui63, Shuhui498 and 9311, comprehensive variations were identified using Nipponbare as a reference. The de novo assembly strategy for rice we optimized and the "golden quality" rice genomes we produced for HZ and TF will benefit rice genomics and breeding research, especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.

Genetic dissection of maize plant architecture using a novel nested association mapping population.

The leaf angle (LA), plant height (PH), and ear height (EH) are key plant architectural traits influencing maize (Zea mays L.) yield. However, their genetic determinants have not yet been well-characterized. Here, we developed a maize advanced backcross-nested association mapping population in Henan Agricultural University (HNAU-NAM1) comprised of 1,625 BC1 F4 /BC2 F4 lines. These were obtained by crossing a diverse set of 12 representative inbred lines with the common GEMS41 line, which were then genotyped using the MaizeSNP9.4K array. Genetic diversity and phenotypic distribution analyses showed considerable levels of genetic variation. We obtained 18-88 quantitative trait loci (QTLs) associated with LA, PH, and EH by using three complementary mapping methods, named as separate linkage mapping, joint linkage mapping, and genome-wide association studies. Our analyses enabled the identification of ten QTL hot-spot regions associated with the three traits, which were distributed on nine different chromosomes. We further selected 13 major QTLs that were simultaneously detected by three methods and deduced the candidate genes, of which eight were not reported before. The newly constructed HNAU-NAM1 population in this study will further broaden our insights into understanding of genetic regulation of plant architecture, thus will help to improve maize yield and provide an invaluable resource for maize functional genomics and breeding research.

[Isolation and identification of cholesterol-degrading intestinal bacteria by culturomics and evaluation of their functions].

High cholesterol is one of the important factors inducing cardiovascular and cerebrovascular diseases. Drug therapy is the main method for reducing cholesterol, but has the disadvantages such as high cost and side effects. Studies have shown that intestinal bacteria play important roles in cholesterol metabolism. However, there are few reports on the screening and functional evaluation of cholesterol-lowering intestinal bacteria. In this study, 36 bile-tolerant bacteria were screened from healthy people stool through culturomics using bovine bile acid or artificial mixed bile acids as substrates. Taking Lactobacillus rhamnosus GG (LGG) as a positive control, three bile acid concentration groups (0 g/L, 0.3 g/L, 3 g/L) were set up to evaluate the cholesterol-lowering ability of bile-tolerant bacteria in vitro. Ten bacteria (including Proteus mirabilis, Providencia stuartii, Proteus vulgaris et al) were identified as the dominant cholesterol-lowering bacteria. Six of the above bacteria, Proteus mirabilis, Providencia stuartii, Proteus vulgaris, Proteus penneri, Wohlfahrtiimonas chitiniclastica, Providencia rettger, were evaluated for their ability to reduce triglycerides in vitro and tolerance to artificial gastric juice. Comparing with strain LGG, the six bacteria showed better triglyceride-lowering ability in vitro. With the decrease of pH value of artificial gastric juice and the increase of treatment time, the survival rate of six bacteria decreased. The above screening experiments and functional evaluation provide a basis for further development of potential cholesterol-lowering bacterial products.

Variations in Flavonoid Metabolites Along Altitudinal Gradient in a Desert Medicinal Plant Agriophyllum squarrosum.

Agriophyllum squarrosum (L.) Moq., a pioneer plant endemic to the temperate deserts of Asia, could be domesticated into an ideal crop with outstanding ecological and medicinal characteristics. A previous study showed differential flavonoid accumulation between two in situ altitudinal ecotypes. To verify whether this accumulation was determined by environmental or genetic factors, we conducted flavonoid-targeted metabolic profiling among 14 populations of A. squarrosum collected from regions with different altitudes based on a common garden experiment. Results showed that the most abundant flavonoid in A. squarrosum was isorhamnetin (48.40%, 557.45 µg/g), followed by quercetin (13.04%, 150.15 µg/g), tricin (11.17%, 128.70 µg/g), isoquercitrin (7.59%, 87.42 µg/g), isovitexin (7.20%, 82.94 µg/g), and rutin (7.00%, 80.62 µg/g). However, based on a common garden at middle-altitude environment, almost none of the flavonoids was enriched in the high-altitude populations, and even some flavonoids, such as quercetin, tricin, and rutin, were significantly enriched in low-altitude populations. This phenomenon indicated that the accumulation of flavonoids was not a result of local adaptation to high altitude. Furthermore, association analysis with in situ environmental variables showed that the contents of quercetin, tricin, and rutin were strongly positively correlated with latitude, longitude, and precipitation gradients and negatively correlated with temperature gradients. Thus, we could conclude that the accumulations of flavonoids in A. squarrosum were more likely as a result of local adaption to environmental heterogeneity combined with precipitation and temperature other than high altitude. This study not only provides an example to understand the molecular ecological basis of pharmacognosy, but also supplies methodologies for developing a new industrial crop with ecological and agricultural importance.

Organic acid metabolites involved in local adaptation to altitudinal gradient in Agriophyllum squarrosum, a desert medicinal plant.

Agriophyllum squarrosum (L.) Moq., a pioneer plant endemic to the temperate deserts of Asia, could be domesticated into an ideal crop with outstanding ecological and medicinal characteristics. A previous study showed differential organic acid accumulation between two in situ altitudinal ecotypes. To verify whether this accumulation was determined by environmental or genetic factors, we conducted organic acid targeted metabolic profiling among 14 populations of A. squarrosum collected from regions with different altitudes based on a common garden experiment. Results showed that the most abundant organic acid in A. squarrosum was citric acid (96.03%, 2322.90 µg g-1). Association analysis with in situ environmental variables showed that salicylic acid content was positively correlated with altitudinal gradient. Considering the enrichment of salicylic acid and protocatechualdehyde in high-altitude populations based on the common garden experiment, and the high expression of their biosynthesis relative genes (i.e., PAL and C4H) in the in situ high-altitude ecotype, we propose that organic acid accumulation could be involved in local adaptation to high altitudes. This study not only addresses the molecular basis of local adaptation involving the accumulation of organic acids in the desert plant A. squarrosum but also provides a method to screen wild germplasms to mitigate the impact of global climate change.

The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution.

Gymnosperms are a unique lineage of plants that currently lack a high-quality reference genome due to their large genome size and high repetitive sequence content. Here, we report a nearly complete genome assembly for Ginkgo biloba with a genome size of 9.87 Gb, an N50 contig size of 1.58 Mb and an N50 scaffold size of 775 Mb. We were able to accurately annotate 27,832 protein-coding genes in total, superseding the inaccurate annotation of 41,840 genes in a previous draft genome assembly. We found that expansion of the G. biloba genome, accompanied by the notable extension of introns, was mainly caused by the insertion of long terminal repeats rather than the recent occurrence of whole-genome duplication events, in contrast to the findings of a previous report. We also identified candidate genes in the central pair, intraflagellar transport and dynein protein families that are associated with the formation of the spermatophore flagellum, which has been lost in all seed plants except ginkgo and cycads. The newly obtained Ginkgo genome provides new insights into the evolution of the gymnosperm genome.

Genomic Adaptive Evolution of Sand Rice (Agriophyllum squarrosum) and Its Implications for Desert Ecosystem Restoration.

Natural selection is a significant driver of population divergence and speciation of plants. Due to local adaptation to geographic regions with ecological gradients, plant populations harbored a wide range of adaptive genetic variation to enable them to survive the heterogeneous habitats. This is all the more necessary for desert plants, as they must tolerant more striking gradients of abiotic stresses. However, the genomic mechanism by which desert plants adapt to ecological heterogeneity remains unclear, which could help to guide the sustainability of desert ecosystems. Here, using restriction-site-associated DNA sequencing in 38 natural populations, we investigated the genomic divergence and environmental adaptation of sand rice, Agriophyllum squarrosum, an annual pioneer species that covers sand dunes in northern China. Population genetic structure analyses showed that sand rice could be divided into three geographically distinct lineages, namely, Northwest, Central, and East. Phylogeographic analyses revealed that the plant might originate locally in Bergen County and further differentiated into the East lineage and then the Central lineage. Ecological niche modeling found that different lineages occupied distinct ecological niches, suggesting that the ecological gradient would have triggered genomic differentiation among sand rice lineages. Ecological association study supported that the three SNPs under divergent selection were closely correlated with precipitation gradients, indicating that precipitation might be the most important stress trigger for lineage diversity in sand rice. These adaptive SNPs could be used to genotype suitable germplasms for the ecological restoration of specific desertified lands. Further analyses found that genetic structure could significantly overestimate the signals for balancing selection. Within the Central lineage, we still found that 175 SNPs could be subject to balancing selection, which could be the means by which sand rice maintains genetic diversity and adapts to multiple stresses across heterogeneous deserts and sandy lands. From a genomic point of view, this study highlighted the local and global adaptation patterns of a desert plant to extreme and heterogeneous habitats. Our data provide molecular guidance for the restoration of desertified lands in the arid and semi-arid regions of China and could facilitate the marker assistant breeding of this potential crop to mitigate climate change.