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Bananas (Musaspp.) are one of the most important tropical fruits and staple food, which are of great significance to human societies. Plantain and Silk are two important banana subgroups, which are both triploid hybrids (AAB) between the wild diploidMusa acuminataandM. balbisiana. In this study, we reported the first haplotype-resolved genome assembly of Plantain and Silk bananas with genome size of approximately 1.4 Gb. We discovered widespread asymmetric evolution in the subgenomes of Plantain and Silk, which could be linked to frequent homologous exchanges (HEs) events. This is the first study to uncover the genetic makeup of triploid banana and verify that subgenome B harbors a rich source of resistance genes. Of the 88,078 and 94,988 annotated genes in Plantain and Silk, only 58.5% and 59.4% were present in all three subgenomes, with >50% genes containing differently expressed alleles in different haplotypes. We also found that Plantain is more resistant to banana Fusarium wilt, exhibiting a much faster defense response after pathogenic fungi infection. Many differentially expressed genes in abscisic acid, ethylene, jasmonic acid and salicylic acid pathways were identified in Plantain. Our analysis revealed that MpMYB36 promotes the biosynthesis of secondary cell wall and deposition of lignin by directly binding to the promoter of MpPAL and MpHCT, which allows Plantain to inhibit the penetration of early infection. Moreover, the insertion of the key carotenoid synthesis gene (CRTISO) may be the potential genetic basis for the richness of carotenoids in Plantain. Our study provides an unprecedented genomic basis for basic research and the development of elite germplasm in cultivated bananas.

Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.

Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs. Many studies have revealed translational regulation in plants in response to various environmental stimuli. However, there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues, especially those of rice, a main staple crop that feeds nearly half of the world's population. Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice, Shanyou 63 (SY63), and its parental varieties Zhenshan 97 and Minghui 63. The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels. We identified 3392 upstream open reading frames (uORFs), and the uORF-containing genes were enriched in transcription factors. Only 668 of 13 492 long non-coding RNAs could be translated into peptides. Finally, we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency. Overall, these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.

Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs. Many studies have revealed the translational regulation in plants in response to various environmental stimuli. However, there has been no comprehensive landscape of translational regulation and allele-specific translation efficiency in multiple tissues of plants, especially in rice, a main staple crop feeding nearly half of the world population. Here, we used RNA-seq and Ribo-seq data to analyze the transcriptome and translatome of an elite hybrid rice SY63 and its parental varieties ZS97 and MH63. The results revealed that gene expression patterns varied more significantly between tissues than between varieties at both transcriptional and translational levels. Besides, we identified 3,392 upstream open reading frames (uORFs), and most of the uORF-containing genes were enriched for transcription factors. Only 668 long non-coding RNAs could be translated into peptides. Finally, we discovered numerous genes with allele-specific translation efficiency in SY63, and further demonstrated that some cis-regulatory elements (secondary structures of mRNAs and the binding of miRNAs) may contribute to allelic divergence in translation efficiency. Overall, our findings may improve the understanding of translational regulation in rice and provide information for the molecular basis of breading research.

The calmodulin binding transcription activator (CAMTA) is a transcription factor that is widely present in eukaryotes with conserved structure. It contributes to the response to biotic and abiotic stresses and promotes the growth and development of plants. Although previous studies have investigated the number and function of CAMTAs in some species, there is still a lack of comprehensive understanding of the evolutionary process, phylogenetic relationship, expression patterns, and functions of CAMTAs in plants. Here we identified 465 CMATA genes from 112 plants and systematically studied the origin of CAMTA family, gene expansion, functional differentiation, gene structure, and conservative motif distribution. Based on these analyses, we presented the evidence that CAMTA family was originated from chlorophyta, and we speculated that CAMTA might experience obvious structure variation during its early evolution, and that the number of CAMTA genes might gradually increase in higher plants. To reveal potential functions of CAMTA genes, we analyzed the expression patterns of 12 representative species and found significant species specificity, tissue specificity, and developmental stage specificity of CAMTAs. The results also indicated that the CAMTA genes might promote the maturation and senescence. The expression levels and regulatory networks of CAMTAs revealed that CAMTAs could enhance cold tolerance of rice by regulating carbohydrate metabolism-related genes to accumulate carbohydrates or by modulating target genes together with other transcription factors. Our study provides an insight into the molecular evolution of CAMTA family and lays a foundation for further study of related biological functions.

Networks are powerful tools to uncover functional roles of genes in phenotypic variation at a system-wide scale. Here, we constructed a maize network map that contains the genomic, transcriptomic, translatomic and proteomic networks across maize development. This map comprises over 2.8 million edges in more than 1,400 functional subnetworks, demonstrating an extensive network divergence of duplicated genes. We applied this map to identify factors regulating flowering time and identified 2,651 genes enriched in eight subnetworks. We validated the functions of 20 genes, including 18 with previously unknown connections to flowering time in maize. Furthermore, we uncovered a flowering pathway involving histone modification. The multi-omics integrative network map illustrates the principles of how molecular networks connect different types of genes and potential pathways to map a genome-wide functional landscape in maize, which should be applicable in a wide range of species.

Additional file 3: Table S1. Data of RNA-seq in this study. Table S2. Tissue distribution of ncRNAs. Table S3. Replicate distribution of circRNAs. Table S4. Software distribution of high-confidence circRNAs. Table S5. Primers list of 27 validated circRNAs. Table S6. Alternative splicing of circRNAs. Table S7. Genomic distribution of circRNAs. Table S8. Genomic distribution of lncRNAs. Table S9. Conservation of lncRNAs and circRNAs in MH63 with other species. Table S10. The proportion of number/length attributable to different TE superfamilies of TE-related lncRNAs/circRNAs.

Additional file 2: Figure S1. Workflow and characteristics of lncRNAs and circRNAs in rice. Figure S2. qPCR of 27 circRNAs from young leaf of MH63. Figure S3. DNA methylation of P-circRNAs and lncRNA loci in ZS97. Figure S4. Comprehensive epigenome map of lncRNA and P-circRNA in different varieties. Figure S5. Tissue specificity of lncRNAs and circRNAs in MH63. Figure S6. Gene ontology analysis of the target genes in MH63. Figure S7. Luciferase reporter assays of lncRNAs in 297 T cells. Figure S8. CeRNA network of DECs and DELs of panicle in MH63. Figure S9. CeRNA network of DECs and DELs of seedling in MH63. Figure S10. CeRNA network of DECs and DELs of root in MH63.

Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome completed almost two decades ago. However, all sequenced genomes to date contain gaps and missing sequences. Here, we report, for the first time, the assembly and analyses of two gap-free reference genome sequences of the eliteO. sativa xian/indicarice varieties ‘Zhenshan 97 (ZS97)’ and ‘Minghui 63 (MH63)’ that are being used as a model system to study heterosis. Gap-free reference genomes also provide global insights into the structure and function of centromeres. All rice centromeric regions share conserved centromere-specific satellite motifs but with different copy numbers and structures. Importantly, we demonstrate that >1,500 genes are located in centromere regions, of which ~15.6% are actively transcribed. The generation and release of both the ZS97 and MH63 gap-free genomes lays a solid foundation for the comprehensive study of genome structure and function in plants and breed climate resilient varieties for the 21stcentury.

Interactomes are powerful tools for encoding and decoding complex life systems. Here, we generated a maize interactome map that integrates genomic interactions, transcriptomic co-expression networks, translatomic co-expression networks, and protein–protein interactions throughout the maize lifecycle. This map, containing over 9 million interactions in more than 5,000 functional modules, reveals extensive functional divergence for duplicate genes and a progressive increase in regulatory divergence between the two maize subgenomes during the flow of genetic information. This network enables dissecting and validating gene functions, re-constructing regulatory pathways, and deciphering molecular mechanisms underlying complex traits combining big data mining technique-machine learning. By applying this map to flowering-time, we identified 1,843 high-confidence genes enriched in eight molecular pathways that are related to flowering time. The function of 30 (out of 58 tested) genes, including 27 novel genes, was verified by loss-of-function mutagenesis. Furthermore, a new pathway involving histone modification was identified and confirmed to regulate flowering time. The interactome map illustrates how coherent sets of molecular interactions connect different types of functional elements and pathway modules to map a genome-wide functional wiring landscape of maize, which will be applicable in a wide range of species.

Interactomes are powerful tools for encoding and decoding complex life systems. Here, we generated a maize interactome map that integrates genomic interactions, transcriptomic co-expression networks, translatomic co-expression networks, and protein–protein interactions throughout the maize lifecycle. This map, containing over 9 million interactions in more than 5,000 functional modules, reveals extensive functional divergence for duplicate genes and a progressive increase in regulatory divergence between the two maize subgenomes during the flow of genetic information. This network enables dissecting and validating gene functions, re-constructing regulatory pathways, and deciphering molecular mechanisms underlying complex traits combining big data mining technique-machine learning. By applying this map to flowering-time, we identified 1,843 high-confidence genes enriched in eight molecular pathways that are related to flowering time. The function of 30 (out of 58 tested) genes, including 27 novel genes, was verified by loss-of-function mutagenesis. Furthermore, a new pathway involving histone modification was identified and confirmed to regulate flowering time. The interactome map illustrates how coherent sets of molecular interactions connect different types of functional elements and pathway modules to map a genome-wide functional wiring landscape, which will be applicable in a wide range of species.

Background: Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) can play important roles in many biological processes. However, no study of the influence of epigenetics factors or the 3D structure of the genome in their regulation is available in plants. Results: In the current analysis, we identified a total of 15,122 lncRNAs and 7,902 circRNAs in three tissues (root, leaf and panicle) of the rice varieties Minghui 63, Zhenshan 97 and their hybrid Shanyou 63. Above 73% of the lncRNAs and parental genes of circRNAs (P-circRNA) are shared among Oryza sativa with high expression specificity. Compared with protein-coding genes, lncRNAs have higher methylation levels. CircRNAs tend to locate in the middle of genes with high CG and CHG methylation. The activated lncRNAs and P-circRNA are mainly transcribed from demethylated regions containing CHH methylation. In addition, ~53% lncRNAs and ~15% P-circRNA are associated with transposable elements, especially miniature inverted-repeat transposable elements and RC/helitron. We didn’t find correlation between the expression of lncRNAs and histone modifications; however, the binding strength and interaction of RNAPII significantly affects lncRNA expression. In contrast, parental genes of circRNAs tend to combine active histone modifications. Finally, lncRNAs and circRNAs acting as competing-endogenous RNAs have the potential to regulate the expression of genes with important roles in the growth and development of rice. Conclusions: Together, our results provide insights into the epigenetic and regulatory mechanisms of lncRNAs and circRNAs in rice and open the door to increase our understanding of ncRNAs in plants.

Additional file 16. Review history.

Additional file 2: Fig S2. α-Diversity analysis (Shannon index) among the GX.DG, GX.SG, HB, and NC groups. Experimental description references to Fig. 2.

Additional file 9: Fig S8. Copy numbers of B. pseudolongum and B. animalis in feces. (A) Survival rate of mice infected with a LD50 dose of GX virus (n=20) or equivoluminal PBS (NC group, n=10). (B and C) On day 2 and 10 post-infection, fecal samples were collected, and the DNA was extracted respectively. After 15 days infection, the pre-extracted DNA of fecal samples were divided into two groups based on whether the corresponding mice died or survived from the infection. Then, qRT-PCR was performed to detect the copy numbers of B. pseudolongum(B) and B. animalis(C). The data are presented as the mean ± SD. Statistics for the copy number was two-way ANOVA. *P

Additional file 8: Fig S7. LDA effect size (LEfSe) comparison of gut microbes at species level in the GX.SG and GX.DG groups. Experimental description references to Fig. 3. (A–E) LEfSe analysis of gut microbes collected on days 5 (A), 8 (B), 9 (C), 10 (D), and 11 (E) post-infection.

Additional file 5: Fig S5. Classification of bacterial genera based on their variation trends in the four mouse groups. Experimental description references to Fig. 2. (A) Bacteria whose abundance increased only in the GX.DG group. (B) Bacteria whose abundance first increased and then decreased only in the GX.DG group. (C) Bacteria whose abundance increased in both the GX.DG and GX.SG groups. (D) Bacteria whose abundance decreased only in the GX.DG group. (E) Bacteria whose abundance increased in the GX.DG, GX.SG, and HB groups, with the greatest increase in the HB group.

Additional file 4: Fig S4. Bacterial phyla showing significant differences in abundance, other than those shown in Fig. 2c. Experimental description references to Fig. 2. The data are presented as the relative abundance of specific microbiota at the phylum level in indicated groups and were analyzed by Wilcoxon-Mann-Whitney test, at *P

Additional file 6 Fig S6. Rarefaction curves. The rarefaction analysis involved random sampling with replacement and estimation of the total number of genes that were identified in the samples. The values represent that the curve in all group is near smooth when the sample number are great enough with few new genes detected.

Additional file 3: Fig S3. Principal coordinate analysis (PCoA) of the weighted UniFrac distances among the GX.DG, GX.SG, HB, and NC groups at four infection stages. Experimental description references to Fig. 2. Sample clustering at stage 4 (days 9-15) revealed differences between the GX.DG group and the other three groups.

Background Influenza is a severe respiratory illness that continually threatens global health. It has been widely known that gut microbiota modulates the host response to protect against influenza infection, but mechanistic details remain largely unknown. Here, we took advantage of the phenomenon of lethal dose 50 (LD50) and metagenomic sequencing analysis to identify specific anti-influenza gut microbes and analyze the underlying mechanism. Results Transferring fecal microbes from mice that survive virulent influenza H7N9 infection into antibiotic-treated mice confers resistance to infection. Some gut microbes exhibit differential features to lethal influenza infection depending on the infection outcome. Bifidobacterium pseudolongum and Bifidobacterium animalis levels are significantly elevated in surviving mice when compared to dead or mock-infected mice. Oral administration of B. animalis alone or the combination of both significantly reduces the severity of H7N9 infection in both antibiotic-treated and germ-free mice. Functional metagenomic analysis suggests that B. animalis mediates the anti-influenza effect via several specific metabolic molecules. In vivo tests confirm valine and coenzyme A produce an anti-influenza effect. Conclusions These findings show that the severity of influenza infection is closely related to the heterogeneous responses of the gut microbiota. We demonstrate the anti-influenza effect of B. animalis, and also find that the gut population of endogenous B. animalis can expand to enhance host influenza resistance when lethal influenza infection occurs, representing a novel interaction between host and gut microbiota. Further, our data suggest the potential utility of Bifidobacterium in the prevention and as a prognostic predictor of influenza.

Hybrids are always a focus of botanical research and have a high practical value in agricultural production. To better understand allele regulation and differences in DNA methylation in hybrids, we developed a phasing pipeline for hybrid rice based on two parental genomes (PP2PG), which is applicable for Iso-Seq, RNA-Seq, and Bisulfite sequencing (BS-Seq). Using PP2PG, we analyzed differences in gene transcription, alternative splicing, and DNA methylation in an allele-specific manner between parents and progeny or different progeny alleles. The phasing of Iso-Seq data provided a great advantage in separating the whole gene structure and producing a significantly higher separation ratio than RNA-Seq. The interaction of hybrid alleles was studied by constructing an allele co-expression network that revealed the dominant allele effect in the network. The expression variation between parents and the parental alleles in progeny showed tissue- or environment-specific patterns, which implied a preference for trans-acting regulation under different conditions. In addition, by comparing allele-specific DNA methylation, we found that CG methylation was more likely to be inherited than CHG and CHH methylation, and its enrichment in genic regions was connected to gene structure. In addition to an effective phasing pipeline, we also identified differentiation in OsWAK38 gene structure that may have led to the expansion of allele functions in hybrids. In summary, we developed a phasing pipeline and provided valuable insights into alternative splicing, interaction networks, trans-acting regulation, and the inheritance of DNA methylation in hybrid rice., This study reports the development of an effective and accurate phasing pipeline (PP2PG) for multiple types of sequencing data (Iso-seq, RNA-seq, and BS-seq) and provides valuable insights into alternative splicing, interaction networks, trans-acting regulation, and the inheritance of DNA methylation in hybrid rice.

Figure S4. Manually confirmed DTM63 insertion sites. (A) Manually confirmed case of C. grandis. (B). Manually confirmed case of C. sinensis. (C) Manually confirmed case of C. clementina. (D) Manually confirmed case of C. ichngensis. Sequences in blue represent TSD and the “N” in red represent a copy full-length DTM63. The corresponding homologous regions were listed in Additional file 7: Table S3. (DOCX 584 kb)

Table S1. Information of conserved and non-conserved MITEs insertion between different genomic regions (DOCX 12 kb)

Table S2. Information of newly inserted MITEs in different genomic regions of three Citrus species. (DOCX 13 kb)

Table S3. Information of DTM63 insertion sites. (DOCX 14 kb)

Figure S2. The pipeline of LTR retrotransposons classification and annotation. (DOCX 475 kb)

Figure S3. Relative abundance of MITE families in Citrus species. (DOCX 1605 kb)

Figure S1. The pipeline of MITE classification and annotation. (DOCX 151 kb)

To investigate the possible effects on nervous system and health condition under the exposure to electromagnetic field.Take the resident around the power transmission line as the objects and were divided into 3 groups by the distance from the power transmission line 20 m, 100 m and 500 m, respectively. Some living conditions and health conditions were recorded by face-to-face the questionnaire survey, and Hematological indices of each groups were examined including IgG, IgM, leukocyte formulae, erythrocyte, hemoglobin and platelet.There was no significant difference in each group, according exposure of daily life, such as drinking and smoking (P0.05). Compared with the each distance groups, it was presented significant difference between the distance from the power transmission line and the incidence of headache or dizziness, insomnia and easy weary and so on (P0.05). In hematology aspect, with the horizontal distance from the power transmission line decreasing, PLT level of residents was reductive and the difference was statistically significant (P0.001), whereas leukocyte formulae, erythrocyte, hemoglobin, IgG and IgM had no significant difference among each group (P0.05).Closely exposure to electromagnetic field may induce headache and so on and decrease the level of PLT.