Teucrium chamaedrys,commonly known as wall germander,is a small woody shrub native to the Mediterranean region.Its name is derived from the Greek words meaning‘‘ground oak,’’as its tiny leaves resemble those of an...Teucrium chamaedrys,commonly known as wall germander,is a small woody shrub native to the Mediterranean region.Its name is derived from the Greek words meaning‘‘ground oak,’’as its tiny leaves resemble those of an oak tree.Teucrium species are prolific producers of diterpenes,endowing them with valuable properties widely utilized in traditional and modern medicine.Sequencing and assembly of the 3-Gbp tetraploid T.chamaedrys genome revealed 74 diterpene synthase genes,with a substantial number of these genes clustered at four synteny genomic loci,each harboring a copy of a large diterpene biosynthetic gene cluster.Comparative genomics revealed that this cluster is conserved in the closely related species Teucrium marum.Along with the presence of several cytochrome p450 sequences,this region is among the largest biosynthetic gene clusters identified.Teucrium is well known for accumulating clerodane-type diterpenoids,which are produced from a kolavenyl diphosphate precursor.To elucidate the complex biosynthetic pathways of these medicinal compounds,we identified and functionally characterized several kolavenyl diphosphate synthases from T.chamaedrys.The remarkable chemical diversity and tetraploid nature of T.chamaedrys make it a valuable model for studying genomic evolution and adaptation in plants.展开更多
Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome.Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive alleli...Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome.Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous chromosomes.Wild species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding efforts.As a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid potato.Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic load.The StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner.Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.展开更多
基金support of the Neogen Land Grant Prize,an endowed grant program administered by the Office of Research and Innovation at Michigan State University(MSU),which supports graduate students in translating their research into real-world applications that positively impact society and the US economyfunded by a National Science Foundation(NSF)-IMPACTS Training Grant(DGE-1828149)+6 种基金funded by NSF Dimensions of Biodiversity(DEB 1737898)supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number T32 GM110523the US Department of Energy Great Lakes Bioenergy Research Center Cooperative Agreement DESC0018409funding from the Department of Biochemistry and Molecular Biology at MSU and support from AgBioResearch(MICL02454)supported in part by the National Science Foundation under Grant number 1737898funding from the University of Georgia,the Georgia Research Alliance,and Georgia Seed Developmentsupport from the NSF under grant number ISO-2029959.
文摘Teucrium chamaedrys,commonly known as wall germander,is a small woody shrub native to the Mediterranean region.Its name is derived from the Greek words meaning‘‘ground oak,’’as its tiny leaves resemble those of an oak tree.Teucrium species are prolific producers of diterpenes,endowing them with valuable properties widely utilized in traditional and modern medicine.Sequencing and assembly of the 3-Gbp tetraploid T.chamaedrys genome revealed 74 diterpene synthase genes,with a substantial number of these genes clustered at four synteny genomic loci,each harboring a copy of a large diterpene biosynthetic gene cluster.Comparative genomics revealed that this cluster is conserved in the closely related species Teucrium marum.Along with the presence of several cytochrome p450 sequences,this region is among the largest biosynthetic gene clusters identified.Teucrium is well known for accumulating clerodane-type diterpenoids,which are produced from a kolavenyl diphosphate precursor.To elucidate the complex biosynthetic pathways of these medicinal compounds,we identified and functionally characterized several kolavenyl diphosphate synthases from T.chamaedrys.The remarkable chemical diversity and tetraploid nature of T.chamaedrys make it a valuable model for studying genomic evolution and adaptation in plants.
基金We acknowledge financial support from AAFC-Genome Quebec GQAAC-2019-2 to M.V.S.,Agriculture and Agri-Food Canada Genomics Research and Development Initiative grant number J-002367 to H.H.T.and K.M.G.Compute Canada,Research Portals and Platforms(RPP)award to M.V.S,Compute Canada,Resources for Research Groups(RRG)award to M.V.S.,DFG Germany’s Excellence Strategy(EXC2048/1-Project 390686111)to B.U.,Dutch TKI top-sector project Novel genetic and genomic tools for polyploid crops(project numbers BO26.03-009-004 and BO-50-002-022)to P.M.B.,European Union’s Horizon 2020 research and innovation programme under grant agreement no 862858(ADAPT)to C.W.B.B.,Germany Ministry of Education and Research BMBF FKZ031A536C to B.U.,Germany Ministry of Education and Research BMBF FKZ031A536C to M.E.B.,GIZ on behalf of the of the Federal Ministry for Economic Cooperation and Development,Germany to D.Ellis and N.L.A.,National Science Foundation(IOS 2140176)to C.R.B.+6 种基金National Science Foundation NRT-IMPACTS fellowship(1828149)to N.B.,NC Agricultural Research Service to G.C.Y.,NC State University to G.C.Y.,NSF IOS-1929982 to C.R.B.NWO-domein Toegepaste en Technische Wetenschappen MAMY project ID 16889 to C.W.B.B.and N.L.,Potato Variety Management Institute to K.V.and V.S.,State of Minnesota,Minnesota Department of Agriculture to L.M.S.,the United States-Israel Binational Agricultural Research and Development Funds IS-5038-17C and IS-5317-20C to J.J.Texas A&M University to M.I.V.,The Clen P.and Emma L.Atchley Potato Research Faculty Excellence Endowment to J.C.K.,University of Maine to E.H.T.,USDA AFRI NIFA Pre-doctoral Fellowship project 2019-07160 to N.R.K.,USDA Multistate Research Funds accession 1004958 to W.S.D.J.USDA Hatch Act 2019-03162 to C.R.B.,USDA NIFA 2020-67034-31731 to G.H.USDA-NIFA 2016-34141-25707 to L.M.S.,USDA-NIFA-SCRI 2019-51181-30021 to L.M.S.,Dutch TKI top-sector project Genetics Assisted Assembly of Complex Genomes(project number BO-68-001-033-WPR)LWV20.112 Application of sequence-based multi-allelic markers in genetics and breeding of polyploids(project number BO-68-001-042-WPR)Wageningen UR Plant Breeding to R.F.,Wageningen UR Plant Breeding to R.G.F.V.,and Washington State Potato Commission to M.J.F.We would like to thank Emily McCoy and Martin Lague for assistance with data analysis.
文摘Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome.Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous chromosomes.Wild species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding efforts.As a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid potato.Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic load.The StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner.Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.
