Plant viruses in the families Luteoviridae and Geminiviridae are phloem restricted and are transmitted in a persistent,circulative manner by homopteran insects.Using fluorescence 2-D difference gel electrophoresis to ...Plant viruses in the families Luteoviridae and Geminiviridae are phloem restricted and are transmitted in a persistent,circulative manner by homopteran insects.Using fluorescence 2-D difference gel electrophoresis to compare the proteomes of F2 genotypes of Schizaphis graminum segregating for virus transmission ability,we recently discovered a panel of protein biomarkers that predict vector competency.Here we used aphid and whitefly nucleotide and expressed sequence tag database mining to test whether these biomarkers are conserved in other homopteran insects.S.graminum gene homologs that shared a high degree of predicted amino acid identity were discovered in two other aphid species and in the whitefly Bemisia tabaci.Selected reaction monitoring mass spectrometry was used to validate the expression of these biomarkers proteins in multiple aphid vector species.The conservation of these proteins in multiple insect taxa that transmit plant viruses along the circulative transmission pathway creates the opportunity to use these biomarkers to rapidly identify insect populations that are the most efficient vectors and allow them to be targeted for control prior to the spread of virus within a crop.展开更多
Loquat(Eriobotrya japonica)fruit accumulates lignin during postharvest storage under chilling conditions(0℃),while low-temperature conditioning(LTC;5℃for 6 days followed by transfer to 0℃)or heat treatment(HT;40℃f...Loquat(Eriobotrya japonica)fruit accumulates lignin during postharvest storage under chilling conditions(0℃),while low-temperature conditioning(LTC;5℃for 6 days followed by transfer to 0℃)or heat treatment(HT;40℃for 4 h followed by transfer to 0℃)can alleviate lignification.Here we compared transcriptome profiles of loquat fruit samples under LTC or HT to those stored at 0℃at five time points from day 1 to day 8 after treatment.High-throughput transcriptome sequences were de novo assembled into 53,319 unique transcripts with an N50 length of 1306 bp.A total of 2235 differentially expressed genes were identified in LTC,and 1020 were identified in HT compared to 0℃.Key genes in the lignin biosynthetic pathway,including EjPAL2,EjCAD1,EjCAD3,4CL,COMT,and HCT,were responsive to LTC or HT treatment,but they showed different expression patterns during the treatments,indicating that different structural genes could regulate lignification at different treatment stages.Coexpression network analysis showed that these candidate biosynthetic genes were associated with a number of transcription factors,including those belonging to the AP2,MYB,and NAC families.Gene ontology(GO)enrichment analysis of differentially expressed genes indicated that biological processes such as stress responses,cell wall and lignin metabolism,hormone metabolism,and metal ion transport were significantly affected under LTC or HT treatment when compared to 0℃.Our analyses provide insights into transcriptome responses to postharvest treatments in loquat fruit.展开更多
Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a gen...Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.展开更多
The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetrap...The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima ×C. moschata interspecific F1 hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops.展开更多
Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large ...Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large or entire chromosome deletions in the genomes of plants and animals (Zhou et al., 2014;Adikusuma et al., 2017).展开更多
基金supported by NSF BREAD IOS:1109989,USDA-NRI 2007-04567,NSFDBI-0606596USDA-ARS 764 CRIS projects1907-101-16,1907-21000-024/25-00DNIH/NCRR funded Yeast Resource Center P41RR01182
文摘Plant viruses in the families Luteoviridae and Geminiviridae are phloem restricted and are transmitted in a persistent,circulative manner by homopteran insects.Using fluorescence 2-D difference gel electrophoresis to compare the proteomes of F2 genotypes of Schizaphis graminum segregating for virus transmission ability,we recently discovered a panel of protein biomarkers that predict vector competency.Here we used aphid and whitefly nucleotide and expressed sequence tag database mining to test whether these biomarkers are conserved in other homopteran insects.S.graminum gene homologs that shared a high degree of predicted amino acid identity were discovered in two other aphid species and in the whitefly Bemisia tabaci.Selected reaction monitoring mass spectrometry was used to validate the expression of these biomarkers proteins in multiple aphid vector species.The conservation of these proteins in multiple insect taxa that transmit plant viruses along the circulative transmission pathway creates the opportunity to use these biomarkers to rapidly identify insect populations that are the most efficient vectors and allow them to be targeted for control prior to the spread of virus within a crop.
基金supported by grants from the National Natural Science Foundation of China(31630067,11771393,and 11632015)the Natural Science Foundation of Zhejiang Province,China(LR16C150001 and LZ14A010002)+1 种基金the Project of the Science and Technology Department of Zhejiang Province(2016C04001)the US National Science Foundation(IOS-1539831).
文摘Loquat(Eriobotrya japonica)fruit accumulates lignin during postharvest storage under chilling conditions(0℃),while low-temperature conditioning(LTC;5℃for 6 days followed by transfer to 0℃)or heat treatment(HT;40℃for 4 h followed by transfer to 0℃)can alleviate lignification.Here we compared transcriptome profiles of loquat fruit samples under LTC or HT to those stored at 0℃at five time points from day 1 to day 8 after treatment.High-throughput transcriptome sequences were de novo assembled into 53,319 unique transcripts with an N50 length of 1306 bp.A total of 2235 differentially expressed genes were identified in LTC,and 1020 were identified in HT compared to 0℃.Key genes in the lignin biosynthetic pathway,including EjPAL2,EjCAD1,EjCAD3,4CL,COMT,and HCT,were responsive to LTC or HT treatment,but they showed different expression patterns during the treatments,indicating that different structural genes could regulate lignification at different treatment stages.Coexpression network analysis showed that these candidate biosynthetic genes were associated with a number of transcription factors,including those belonging to the AP2,MYB,and NAC families.Gene ontology(GO)enrichment analysis of differentially expressed genes indicated that biological processes such as stress responses,cell wall and lignin metabolism,hormone metabolism,and metal ion transport were significantly affected under LTC or HT treatment when compared to 0℃.Our analyses provide insights into transcriptome responses to postharvest treatments in loquat fruit.
基金supported by grants from the National Key R&D Program of China(No.2021YFD1700101)the National Natural Science Foundation of China(No.32130091 and No.32001923)+2 种基金the science And and Technology Innovation Program of Hunan Province (No.2020WK2014 and No.2020WK2023)the Training Program for Excellent Young Innovators of Changsha(kg2106079)the China Agriculture Research System of MOF and MARA(CARS-16-E19)。
文摘Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.
文摘The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima ×C. moschata interspecific F1 hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops.
基金National Science Foundation grant no. IOS-1546625 (GBM and ZF).
文摘Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large or entire chromosome deletions in the genomes of plants and animals (Zhou et al., 2014;Adikusuma et al., 2017).