Paper mulberry(Broussonetia papyrifera)is a well-known woody tree historically used for Cai Lun papermaking,one of the four great inventions of ancient China.More recently,Paper mulberry has also been used as forage t...Paper mulberry(Broussonetia papyrifera)is a well-known woody tree historically used for Cai Lun papermaking,one of the four great inventions of ancient China.More recently,Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents.In this study,we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches,including Illumina and PacBio sequencing platform as well as Hi-C,optical,and genetic maps.The assembled Paper mulberry genome consists of 386.83 Mb,which is close to the estimated size,and 99.25%(383.93 Mb)of the assembly was assigned to 13 pseudochromosomes.Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families,respectively,accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry.Moreover,the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine,forage,papermaking,and barkcloth making.We also identified the rootassociated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation.Collectively,these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition.Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making,and as forage.These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide.展开更多
N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distri...N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive.Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars,Nipponbare (Nip;Japonica)and 93-11 (Indica).Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis.We found that 6mA levels are positively correlated with the expression of key stressrelated genes,which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover,we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.展开更多
Chain architecture effect on static and dynamic properties of unentangled polymers is explored by molecular dynamics simulation and Rouse mode analysis based on graph theory.For open chains,although they generally obe...Chain architecture effect on static and dynamic properties of unentangled polymers is explored by molecular dynamics simulation and Rouse mode analysis based on graph theory.For open chains,although they generally obey ideal scaling in chain dimensions,local structure exhibits nonideal behavior due to the incomplete excluded volume(EV)screening,the reduced mean square internal distance(MSID)can be well described by Wittmer'theory for linear chains and the resulting chain swelling is architecture dependent,i.e.,the more branches a bit stronger swelling.For rings,unlike open chains they are compact in term of global sizes.Due to EV effect and nonconcatenated constraints their local structure exhibits a quite different non-Gaussian behavior from open chains,i.e.,reduced MSID curves do not collapse to a single master curve and fail to converge to a chain-length-independent constant,which makes the direct application of Wittmer's theory to rings quite questionable.Deviation from ideality is further evidenced by limited applicability of Rouse prediction to mode amplitude and relaxation time at high modes as well as the non-constant and mode-dependent scaled Rouse mode amplitudes,while the latter is architecture-dependent and even molecular weight dependent for rings.The chain relaxation time is architecture-dependent,but the same scaling dependence on chain dimensions does hold for all studied architectures.Despite mode orthogonality at static state,the role of cross-correlation in orientation relaxation increases with time and the time-dependent coupling parameter rises faster for rings than open chains even at short time scales it is lower for rings.展开更多
基金the National Natural Science Foundation of China(31770360,31870247)the Poverty Relief Project of the Chinese Academy of Sciences(KFJ-FP-24)the Huimin Technology Demonstration Project of the Natio nal Modem Agricultural Science and Technology Achievements City(Z151100001015008).
文摘Paper mulberry(Broussonetia papyrifera)is a well-known woody tree historically used for Cai Lun papermaking,one of the four great inventions of ancient China.More recently,Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents.In this study,we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches,including Illumina and PacBio sequencing platform as well as Hi-C,optical,and genetic maps.The assembled Paper mulberry genome consists of 386.83 Mb,which is close to the estimated size,and 99.25%(383.93 Mb)of the assembly was assigned to 13 pseudochromosomes.Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families,respectively,accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry.Moreover,the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine,forage,papermaking,and barkcloth making.We also identified the rootassociated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation.Collectively,these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition.Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making,and as forage.These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide.
基金The Ministry of Science and Technology of the People's Republic of China (2016YFD0101001)to X.G.,National Natural Science Foundation of China (31871606,31671670)to X.G.,Recruitment program of Global Youth Expert of China to X.G.,and Fundamental Research funds for Central Non-profit Scientific Institution (1610392017001)to X.G.
文摘N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive.Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars,Nipponbare (Nip;Japonica)and 93-11 (Indica).Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis.We found that 6mA levels are positively correlated with the expression of key stressrelated genes,which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover,we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.
基金supported by the National Natural Science Foundation of China(Nos.21790343,21574142,21174154)the National Key Research and Development Program of China(No.2016YFB1100800).
文摘Chain architecture effect on static and dynamic properties of unentangled polymers is explored by molecular dynamics simulation and Rouse mode analysis based on graph theory.For open chains,although they generally obey ideal scaling in chain dimensions,local structure exhibits nonideal behavior due to the incomplete excluded volume(EV)screening,the reduced mean square internal distance(MSID)can be well described by Wittmer'theory for linear chains and the resulting chain swelling is architecture dependent,i.e.,the more branches a bit stronger swelling.For rings,unlike open chains they are compact in term of global sizes.Due to EV effect and nonconcatenated constraints their local structure exhibits a quite different non-Gaussian behavior from open chains,i.e.,reduced MSID curves do not collapse to a single master curve and fail to converge to a chain-length-independent constant,which makes the direct application of Wittmer's theory to rings quite questionable.Deviation from ideality is further evidenced by limited applicability of Rouse prediction to mode amplitude and relaxation time at high modes as well as the non-constant and mode-dependent scaled Rouse mode amplitudes,while the latter is architecture-dependent and even molecular weight dependent for rings.The chain relaxation time is architecture-dependent,but the same scaling dependence on chain dimensions does hold for all studied architectures.Despite mode orthogonality at static state,the role of cross-correlation in orientation relaxation increases with time and the time-dependent coupling parameter rises faster for rings than open chains even at short time scales it is lower for rings.
