Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are ...Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species.We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×J.regia using a novel combination of single-molecule sequencing and optical genome mapping technologies.The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions.Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long.The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them transcribed.Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes.Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other.The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes.Given the importance of J.microcarpa×J.regia hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution.We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.展开更多
Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the whe...Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path （MTP） of 3176 BAC clones from the short arm ofAe. tauschii chromosome 3 （At3DS）. The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B （Ta3BS） is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element （TE） bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D （Ta3DS）, there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.展开更多
Soil-borne plant pathogens represent a serious threat that undermines commercial walnut(Juglans regia)production worldwide.Crown gall,caused by Agrobacterium tumefaciens,and Phytophthora root and crown rots,caused by ...Soil-borne plant pathogens represent a serious threat that undermines commercial walnut(Juglans regia)production worldwide.Crown gall,caused by Agrobacterium tumefaciens,and Phytophthora root and crown rots,caused by various Phytophthora spp.,are among the most devastating walnut soil-borne diseases.A recognized strategy to combat soil-borne diseases is adoption of resistant rootstocks.Here,resistance to A.tumefaciens,P.cinnamomi,and P.pini is mapped in the genome of Juglans microcarpa,a North American wild relative of cultivated walnut.Half-sib J.microcarpa mother trees DJUG 31.01 and DJUG 31.09 were crossed with J.regia cv.Serr,producing 353 and 400 hybrids,respectively.Clonally propagated hybrids were genotyped by sequencing to construct genetic maps for the two populations and challenged with the three pathogens.Resistance to each of the three pathogens was mapped as a major QTL on the long arm of J.microcarpa chromosome 4D and was associated with the same haplotype,designated as haplotype b,raising the possibility that the two mother trees were heterozygous for a single Mendelian gene conferring resistance to all three pathogens.The deployment of this haplotype in rootstock breeding will facilitate breeding of a walnut rootstock resistant to both crown gall and Phytophthora root and crown rots.展开更多
Cassava is a highly resilient tropical crop that produces large,starchy storage roots and high biomass.However,how did cassava’s remarkable environmental adaptability and key economic traits evolve from its wild spec...Cassava is a highly resilient tropical crop that produces large,starchy storage roots and high biomass.However,how did cassava’s remarkable environmental adaptability and key economic traits evolve from its wild species remain unclear.In this study,we obtained near complete telomere-to-telomere genome assemblies and their haplotype forms for the cultivar AM560,the wild ancestors FLA4047 and W14,constructed a graphic pan-genome of 30 representatives with a size of 1.15 Gb,and built a clarified evolutionary tree of 486 accessions.A comparison of structural variations and single-nucleotide variations between the ancestors and cultivated cassavas reveals predominant expansions and contractions of numbers of genes and gene families,which are mainly driven by transposons.Significant selective sweeping occurred in 122 footprints of genomes and affects 1,519 domesticated genes.We identify selective mutations in MeCSK and MeFNR2 that could promote photoreactions associated with MeNADP-ME in C4 photosynthesis in modern cassava.Coevolution of retard floral primordia and initiation of storage roots may arise from MeCOL5 variants with altered bindings to MeFT1,MeFT2,and MeTFL2.Mutations in MeMATE1 and MeGTR occur in sweet cassava,and MeAHL19 has evolved to regulate the biosynthesis,transport,and endogenous remobilization of cyanogenic glucosides in cassava.These extensive genomic and gene resources provided here,along with the findings on the evolutionary mechanisms responsible for beneficial traits in modern cultivars,lay a strong foundation for future breeding improvements of cassava.展开更多
Many fungal and oomycete pathogens differentiate a feeding structure named the haustorium to extract nutrition from the plant epidermal cell. The atypical resistance （R） protein RPW8.2 activates salicylic acid （SA...Many fungal and oomycete pathogens differentiate a feeding structure named the haustorium to extract nutrition from the plant epidermal cell. The atypical resistance （R） protein RPW8.2 activates salicylic acid （SA）-dependent, haustorium-targeted defenses against Golovinomyces spp., the causal agents of powdery mildew diseases on multiple plant species. How RPW8.2 activates defense remains uncharacterized. Here, we report that RPWS.2 interacts with the phytochrome-associated protein phosphatase type 2C （PAPP2C） in yeast and in planta as evidenced by co- immunoprecipitation and bimolecular fluorescence complementation assays. Down-regulation of PAPP2C by RNA interfer- ence （RNAi） in Col-0 plants lacking RPWS.2 leads to leaf spontaneous cell death and enhanced disease resistance to powdery mildew via the SA-dependent signaling pathway. Moreover, down-regulation of PAPP2C by RNAi in the RPW8.2 background results in strong HR-like cell death, which correlates with elevated RPWS.2 expression. We further demonstrate that hemagglutinin （HA）-tagged PAPP2C prepared from tobacco leaf cells transiently transformed with HA-PAPP2C possesses phosphatase activity. In addition, silencing a rice gene （Os04g0452000） homologous to PAPP2C also results in spontaneous cell death in rice. Combined, our results suggest that RPW8.2 is functionally connected with PAPP2C and that PAPP2C negatively regulates SA-dependent basal defense against powdery mildew in Arabidopsis.展开更多
基金supported by USDA/NIFA/SCRI under grant number 59-5306-2-333 and by the California Walnut Board.
文摘Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species.We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×J.regia using a novel combination of single-molecule sequencing and optical genome mapping technologies.The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions.Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long.The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them transcribed.Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes.Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other.The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes.Given the importance of J.microcarpa×J.regia hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution.We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.
基金supported by funding from the National Natural Science Foundation of China(Nos.31290210,31210103902)the Unites States National Science Foundation grant(No.IOS 1238231)+1 种基金the USDA-Agricultural Research Service CRIS project(No.5325-21000-019)the Ministry of Education of China(111 project)
文摘Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path （MTP） of 3176 BAC clones from the short arm ofAe. tauschii chromosome 3 （At3DS）. The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B （Ta3BS） is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element （TE） bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D （Ta3DS）, there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.
基金This work was supported in part by USDA NIFA-SCRI grants no.59-5306-2-333 and 2018-51181-28437the California Walnut Board,USDA ARS Project:2032-22000-016-00D,and NIFA-Hatch 1010599.
文摘Soil-borne plant pathogens represent a serious threat that undermines commercial walnut(Juglans regia)production worldwide.Crown gall,caused by Agrobacterium tumefaciens,and Phytophthora root and crown rots,caused by various Phytophthora spp.,are among the most devastating walnut soil-borne diseases.A recognized strategy to combat soil-borne diseases is adoption of resistant rootstocks.Here,resistance to A.tumefaciens,P.cinnamomi,and P.pini is mapped in the genome of Juglans microcarpa,a North American wild relative of cultivated walnut.Half-sib J.microcarpa mother trees DJUG 31.01 and DJUG 31.09 were crossed with J.regia cv.Serr,producing 353 and 400 hybrids,respectively.Clonally propagated hybrids were genotyped by sequencing to construct genetic maps for the two populations and challenged with the three pathogens.Resistance to each of the three pathogens was mapped as a major QTL on the long arm of J.microcarpa chromosome 4D and was associated with the same haplotype,designated as haplotype b,raising the possibility that the two mother trees were heterozygous for a single Mendelian gene conferring resistance to all three pathogens.The deployment of this haplotype in rootstock breeding will facilitate breeding of a walnut rootstock resistant to both crown gall and Phytophthora root and crown rots.
基金supported by grants from the National Key R&D Program of China(2018YFD1000501)the National Natural Science Foundation of China-CG joint foundation(3181101517)the startup funds for the double first-class disciplines of crop science in Hainan University(RZ2100003362).
文摘Cassava is a highly resilient tropical crop that produces large,starchy storage roots and high biomass.However,how did cassava’s remarkable environmental adaptability and key economic traits evolve from its wild species remain unclear.In this study,we obtained near complete telomere-to-telomere genome assemblies and their haplotype forms for the cultivar AM560,the wild ancestors FLA4047 and W14,constructed a graphic pan-genome of 30 representatives with a size of 1.15 Gb,and built a clarified evolutionary tree of 486 accessions.A comparison of structural variations and single-nucleotide variations between the ancestors and cultivated cassavas reveals predominant expansions and contractions of numbers of genes and gene families,which are mainly driven by transposons.Significant selective sweeping occurred in 122 footprints of genomes and affects 1,519 domesticated genes.We identify selective mutations in MeCSK and MeFNR2 that could promote photoreactions associated with MeNADP-ME in C4 photosynthesis in modern cassava.Coevolution of retard floral primordia and initiation of storage roots may arise from MeCOL5 variants with altered bindings to MeFT1,MeFT2,and MeTFL2.Mutations in MeMATE1 and MeGTR occur in sweet cassava,and MeAHL19 has evolved to regulate the biosynthesis,transport,and endogenous remobilization of cyanogenic glucosides in cassava.These extensive genomic and gene resources provided here,along with the findings on the evolutionary mechanisms responsible for beneficial traits in modern cultivars,lay a strong foundation for future breeding improvements of cassava.
基金grants from the National Research Initiative of the USDA Cooperative State Research,Education and Extension Service to S.X.，G.L.W.，a grant from the National Science Foundation (grant number IOS-0842877) to S.X
文摘Many fungal and oomycete pathogens differentiate a feeding structure named the haustorium to extract nutrition from the plant epidermal cell. The atypical resistance （R） protein RPW8.2 activates salicylic acid （SA）-dependent, haustorium-targeted defenses against Golovinomyces spp., the causal agents of powdery mildew diseases on multiple plant species. How RPW8.2 activates defense remains uncharacterized. Here, we report that RPWS.2 interacts with the phytochrome-associated protein phosphatase type 2C （PAPP2C） in yeast and in planta as evidenced by co- immunoprecipitation and bimolecular fluorescence complementation assays. Down-regulation of PAPP2C by RNA interfer- ence （RNAi） in Col-0 plants lacking RPWS.2 leads to leaf spontaneous cell death and enhanced disease resistance to powdery mildew via the SA-dependent signaling pathway. Moreover, down-regulation of PAPP2C by RNAi in the RPW8.2 background results in strong HR-like cell death, which correlates with elevated RPWS.2 expression. We further demonstrate that hemagglutinin （HA）-tagged PAPP2C prepared from tobacco leaf cells transiently transformed with HA-PAPP2C possesses phosphatase activity. In addition, silencing a rice gene （Os04g0452000） homologous to PAPP2C also results in spontaneous cell death in rice. Combined, our results suggest that RPW8.2 is functionally connected with PAPP2C and that PAPP2C negatively regulates SA-dependent basal defense against powdery mildew in Arabidopsis.
