Sour cherry(Prunus cerasus L.)is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant Prunus fruticosa(ground cherry)and Prunus avium(sweet cherry).Here we report a c...Sour cherry(Prunus cerasus L.)is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant Prunus fruticosa(ground cherry)and Prunus avium(sweet cherry).Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency,the predominant cultivar grown in the USA.We also generated a draft assembly of P.fruticosa to use alongside a published P.avium sequence for syntelog-based subgenome assignments for‘Montmorency’and provide compelling evidence P.fruticosa is also an allotetraploid.Using hierarchal k-mer clustering and phylogenomics,we show‘Montmorency’is trigenomic,containing two distinct subgenomes inherited from a P.fruticosa-like ancestor(A and A’)and two copies of the same subgenome inherited from a P.avium-like ancestor(BB).The genome composition of‘Montmorency’is AA’BB and little-to-no recombination has occurred between progenitor subgenomes(A/A’and B).In Prunus,two known classes of genes are important to breeding strategies:the self-incompatibility loci(S-alleles),which determine compatible crosses,successful fertilization,and fruit set,and the Dormancy Associated MADS-box genes(DAMs),which strongly affect dormancy transitions and flowering time.The S-alleles and DAMs in‘Montmorency’and P.fruticosa were manually annotated and support subgenome assignments.Lastly,the hybridization event‘Montmorency’is descended from was estimated to have occurred less than 1.61 million years ago,making sour cherry a relatively recent allotetraploid.The‘Montmorency’genome highlights the evolutionary complexity of the genus Prunus and will inform future breeding strategies for sour cherry,comparative genomics in the Rosaceae,and questions regarding neopolyploidy.展开更多
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
基金This research was funded by AgBioResearch Project GREEEN grant GR19-046the United States Department of Agriculture National Institute of Food and Agriculture(USDA-NIFA)project 2014-51181-22378USDA-NIFA HATCH project 1013242.
文摘Sour cherry(Prunus cerasus L.)is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant Prunus fruticosa(ground cherry)and Prunus avium(sweet cherry).Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency,the predominant cultivar grown in the USA.We also generated a draft assembly of P.fruticosa to use alongside a published P.avium sequence for syntelog-based subgenome assignments for‘Montmorency’and provide compelling evidence P.fruticosa is also an allotetraploid.Using hierarchal k-mer clustering and phylogenomics,we show‘Montmorency’is trigenomic,containing two distinct subgenomes inherited from a P.fruticosa-like ancestor(A and A’)and two copies of the same subgenome inherited from a P.avium-like ancestor(BB).The genome composition of‘Montmorency’is AA’BB and little-to-no recombination has occurred between progenitor subgenomes(A/A’and B).In Prunus,two known classes of genes are important to breeding strategies:the self-incompatibility loci(S-alleles),which determine compatible crosses,successful fertilization,and fruit set,and the Dormancy Associated MADS-box genes(DAMs),which strongly affect dormancy transitions and flowering time.The S-alleles and DAMs in‘Montmorency’and P.fruticosa were manually annotated and support subgenome assignments.Lastly,the hybridization event‘Montmorency’is descended from was estimated to have occurred less than 1.61 million years ago,making sour cherry a relatively recent allotetraploid.The‘Montmorency’genome highlights the evolutionary complexity of the genus Prunus and will inform future breeding strategies for sour cherry,comparative genomics in the Rosaceae,and questions regarding neopolyploidy.
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.
