Rye(Secale cereale)is an important crop with multiple uses and a valuable genetic resource for wheat breeding.However,due to its complex genome and outcrossing nature,the origin of cultivated rye remains elusive.The g...Rye(Secale cereale)is an important crop with multiple uses and a valuable genetic resource for wheat breeding.However,due to its complex genome and outcrossing nature,the origin of cultivated rye remains elusive.The geneticist N.I.Vavilov proposed that cultivated rye had been domesticated from weedy rye,rather than directly from wild species like other crops.Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds.To this end,in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild,weedy,and cultivated rye,and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans.We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits,including shattering,grain yield,and disease resistance.Furthermore,we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye.Taken together,our findings unravel the domestication history of cultivated rye,suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale,and provide an important resource for future rye and wheat breeding.展开更多
Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants.Five years ago,we developed a comprehensive plant circRNA database(PlantcircBase),w...Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants.Five years ago,we developed a comprehensive plant circRNA database(PlantcircBase),which has attracted much attention from the plant circRNA community.Here,we report an updated PlantcircBase(v.7.0),which contains 171,118 circRNAs from 21 plant species.Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing(RNAseq)datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study.A plant multiple conservation score(PMCS),based on the conservation of both sequence and expression profiles,was calculated for each circRNA to quantify and compare the conservation of all circRNAs.A new parameter,plant circRNA confidence level(PCCL),is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA.All this information and other details of circRNAs can be browsed,searched,and downloaded from PlantcircBase 7.0,which also provides online bioinformatics tools for visualization and sequence alignment.PlantcircBase 7.0 is publicly and freely accessible at http://ibi.zju.edu.cn/plantcircbase/.展开更多
Dear Editor,Many functional characteristics of plant tissue attribute to highly specialized cells in the tissue.Dissecting cell types and profiling the transcriptome and proteome of individual cell types of plant tiss...Dear Editor,Many functional characteristics of plant tissue attribute to highly specialized cells in the tissue.Dissecting cell types and profiling the transcriptome and proteome of individual cell types of plant tissues are important for understanding cellular activities underlying plant development and stress adaptation(Shaw et al.,2021).Single-cell RNA sequencing(scRNA-seq)provides such a tool for studying the transcriptional activities of individual cell types at single-cell resolution in any given organism(Rich-Griffin et al.,2020).展开更多
基金This work was supported by the National Natural Science Foundation(grant 9143511)Department of Science and Technology of Zhejiang Province(grant 2020C02002)+1 种基金the Zhejiang Natural Science Foundation(grant LZ17C130001)the Jiangsu Collaborative Innovation Center for Modern Crop Production,and the 111 Project(grant B17039)to L.F.
文摘Rye(Secale cereale)is an important crop with multiple uses and a valuable genetic resource for wheat breeding.However,due to its complex genome and outcrossing nature,the origin of cultivated rye remains elusive.The geneticist N.I.Vavilov proposed that cultivated rye had been domesticated from weedy rye,rather than directly from wild species like other crops.Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds.To this end,in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild,weedy,and cultivated rye,and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans.We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits,including shattering,grain yield,and disease resistance.Furthermore,we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye.Taken together,our findings unravel the domestication history of cultivated rye,suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale,and provide an important resource for future rye and wheat breeding.
基金supported by the National Natural Science Foundation of China(32101729,31871589,and 91740108)the National Postdoctoral Program for Innovative Talents(BX20200301).
文摘Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants.Five years ago,we developed a comprehensive plant circRNA database(PlantcircBase),which has attracted much attention from the plant circRNA community.Here,we report an updated PlantcircBase(v.7.0),which contains 171,118 circRNAs from 21 plant species.Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing(RNAseq)datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study.A plant multiple conservation score(PMCS),based on the conservation of both sequence and expression profiles,was calculated for each circRNA to quantify and compare the conservation of all circRNAs.A new parameter,plant circRNA confidence level(PCCL),is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA.All this information and other details of circRNAs can be browsed,searched,and downloaded from PlantcircBase 7.0,which also provides online bioinformatics tools for visualization and sequence alignment.PlantcircBase 7.0 is publicly and freely accessible at http://ibi.zju.edu.cn/plantcircbase/.
基金supported by the China Postdoctoral Science Foundation(2019M662066)the National Postdoctoral Program for Innovative Talents(BX20200301)+1 种基金the National Natural Science Foundation of China(91740108)the Jiangsu Collaborative Innovation Center for Modern Crop.
文摘Dear Editor,Many functional characteristics of plant tissue attribute to highly specialized cells in the tissue.Dissecting cell types and profiling the transcriptome and proteome of individual cell types of plant tissues are important for understanding cellular activities underlying plant development and stress adaptation(Shaw et al.,2021).Single-cell RNA sequencing(scRNA-seq)provides such a tool for studying the transcriptional activities of individual cell types at single-cell resolution in any given organism(Rich-Griffin et al.,2020).