The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color studies.Here,we investigated the divergence be...The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color studies.Here,we investigated the divergence between two parental species with different f lower color widely used for azalea breeding.Gapless genome assembly was generated for the yellow-f lowered azalea,Rhododendron molle.Comparative genomics found recent proliferation of long terminal repeat retrotransposons(LTR-RTs),especially Gypsy,has resulted in a 125 Mb(19%)genome size increase in species-specific regions,and a significant amount of dispersed gene duplicates(13402)and pseudogenes(17437).Metabolomic assessment revealed that yellow f lower coloration is attributed to the dynamic changes of carotenoids/f lavonols biosynthesis and chlorophyll degradation.Time-ordered gene co-expression networks(TO-GCNs)and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct f lower pigmentation.B3 and ERF TFs were found dominating the gene regulation of carotenoids/f lavonols characterized pigmentation in R.molle,while WRKY,ERF,WD40,C2H2,and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-f lowered R simsii.This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.展开更多
Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a hap...Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.展开更多
Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be elucidated.Here,we...Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be elucidated.Here,we present a chromosome-scale genome assembly of tetraploid scarlet sage(Salvia splendens),one of the most diverse ornamental plants.We found evidence for three WGD events following an older WGD event shared by most eudicots(theγevent).A comprehensive,spatiotemporal,genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries,which could be associated with genomic rearrangements,transposable element proximity discrepancies,coding sequence variation,selection pressure,and transcription factor binding site differences.The observed differences between homoeologs may reflect the first step toward sub-and/or neofunctionalization.This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.展开更多
Anoplophora glabripennis(Asian longhorn beetle,ALB)and Anoplophora chinensis(Citrus longhorn beetle,CLB)are native forest pests in China;they have become important international quarantine pests.They are found using t...Anoplophora glabripennis(Asian longhorn beetle,ALB)and Anoplophora chinensis(Citrus longhorn beetle,CLB)are native forest pests in China;they have become important international quarantine pests.They are found using the same Salix aureopendula host tree of Cixi,Zhejiang province,China.On this host tree,we collected additional beetles that appeared to be morphologically intermediate between ALB and CLB.By using a stereoscope,we observed that there were several bumps on the base of the elytra,which was inconsistent with ALB,which typically has a smooth elytral base,but was more like CLB,which has numerous short tubercles on the elytral base.Given their sympatry and intermediate morphology,we hypothesized that these may represent ALB×CLB hybrids.We studied the genomic profiles for 46 samples(ALB,CLB,and putative hybrids)using genotyping-by-sequencing(GBS)providing a reduced representation of the entire genome.Employing principal component analyses on the 163 GBS-derived single nucleotide polymorphism data,we found putative hybrids tightly clustered with ALB,but genetically distinct from the CLB individuals.Therefore,our initial hybrid hypothesis was not supported by genomic data.Further,while mating experiments between adult ALB and CLB were successful in 4 separate years(2017,2018,2020,and 2021),and oviposition behavior was observed,no progeny was produced.Having employed population genomic analysis and biological hybridization experiments,we conclude that the putative hybrids represent newly discovered morphological variants within ALB.Our approach further confirmed the advantage of genome-wide information for Anoplophora species assignment in certain ambiguous classification cases.展开更多
基金This work was supported by grants from the Strategic Prior-ity Research Program,Chinese Academy of Sciences(Grant No.XDA23080000)Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502).
文摘The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color studies.Here,we investigated the divergence between two parental species with different f lower color widely used for azalea breeding.Gapless genome assembly was generated for the yellow-f lowered azalea,Rhododendron molle.Comparative genomics found recent proliferation of long terminal repeat retrotransposons(LTR-RTs),especially Gypsy,has resulted in a 125 Mb(19%)genome size increase in species-specific regions,and a significant amount of dispersed gene duplicates(13402)and pseudogenes(17437).Metabolomic assessment revealed that yellow f lower coloration is attributed to the dynamic changes of carotenoids/f lavonols biosynthesis and chlorophyll degradation.Time-ordered gene co-expression networks(TO-GCNs)and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct f lower pigmentation.B3 and ERF TFs were found dominating the gene regulation of carotenoids/f lavonols characterized pigmentation in R.molle,while WRKY,ERF,WD40,C2H2,and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-f lowered R simsii.This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
基金This study was supported by the Foundation for the Introduction of Talent of Pingdingshan University(PXY-BSQD2016009)the Key Research Project of Colleges and Universities of Henan Province(182102110132,172102110111)+6 种基金the National Natural Science Foundation(31600527)the Fundamental Research Funds for the Central Universities of Beijing Forestry University(2018BLCB08)the Project for the Construction of World Class Universities of Beijing Forestry University(2019XKJS0308)the Scientific Research Foundation for National Natural Science Fund(31600527)Z.L.is funded by a postdoctoral fellowship from the Special Research Fund of Ghent University(BOFPDO2018001701)Y.V.P.acknowledges fundings from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(grant agreement No 833522)from Ghent University(Methusalem funding,BOF.MET.2021.0005.01).
文摘Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.
基金This study was supported by the National Natural Science Foundation(31600527)The Fundamental Research Funds for the Central Universities in Beijing Forestry University(2018BLCB08)+2 种基金the Project of Construction of World Class Universities in Beijing Forestry University(2019XKJS0308)Y.V.d.P.acknowledges funding from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(grant agreement no.833522)from Ghent University(Methusalem funding,BOF.MET.2021.0005.01).
文摘Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be elucidated.Here,we present a chromosome-scale genome assembly of tetraploid scarlet sage(Salvia splendens),one of the most diverse ornamental plants.We found evidence for three WGD events following an older WGD event shared by most eudicots(theγevent).A comprehensive,spatiotemporal,genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries,which could be associated with genomic rearrangements,transposable element proximity discrepancies,coding sequence variation,selection pressure,and transcription factor binding site differences.The observed differences between homoeologs may reflect the first step toward sub-and/or neofunctionalization.This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
基金supported by the Fundamental Research Funds for the Central Universities(No.QNTD202304)National Natural Science Foundation ofChina(No.32171794).
文摘Anoplophora glabripennis(Asian longhorn beetle,ALB)and Anoplophora chinensis(Citrus longhorn beetle,CLB)are native forest pests in China;they have become important international quarantine pests.They are found using the same Salix aureopendula host tree of Cixi,Zhejiang province,China.On this host tree,we collected additional beetles that appeared to be morphologically intermediate between ALB and CLB.By using a stereoscope,we observed that there were several bumps on the base of the elytra,which was inconsistent with ALB,which typically has a smooth elytral base,but was more like CLB,which has numerous short tubercles on the elytral base.Given their sympatry and intermediate morphology,we hypothesized that these may represent ALB×CLB hybrids.We studied the genomic profiles for 46 samples(ALB,CLB,and putative hybrids)using genotyping-by-sequencing(GBS)providing a reduced representation of the entire genome.Employing principal component analyses on the 163 GBS-derived single nucleotide polymorphism data,we found putative hybrids tightly clustered with ALB,but genetically distinct from the CLB individuals.Therefore,our initial hybrid hypothesis was not supported by genomic data.Further,while mating experiments between adult ALB and CLB were successful in 4 separate years(2017,2018,2020,and 2021),and oviposition behavior was observed,no progeny was produced.Having employed population genomic analysis and biological hybridization experiments,we conclude that the putative hybrids represent newly discovered morphological variants within ALB.Our approach further confirmed the advantage of genome-wide information for Anoplophora species assignment in certain ambiguous classification cases.