In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects....In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.展开更多
Pennisetum plants(Pennisetum alopecuroides L.),displaying a dwarfing phenotype along with delayed flowering and mosaic symptom on leaves,were found in Beijing,China.Flexuous filamentous particles with a size of approx...Pennisetum plants(Pennisetum alopecuroides L.),displaying a dwarfing phenotype along with delayed flowering and mosaic symptom on leaves,were found in Beijing,China.Flexuous filamentous particles with a size of approximate 15×850 nm were observed in symptomatic leaves via transmission electron microscopy.Deep sequencing of small RNAs(sRNA)from symptomatic leaves and analysis of sRNA populations were then conducted to determine the genome sequence of the viral agent in diseased plant tissues.It showed that the viral agent had one positive-sense and single-stranded RNA genome,which consisted of 9717 nucleotides(nts)excluding poly(A)tail.The complete viral genome contained a large open reading frame,encoding a polyprotein of 3131 amino acids(aa).Sequence comparison and phylogenetic analysis demonstrated that the viral agent belonged to the genus Potyvirus in the family Potyviridae.In the cladogram it was most closely related to johnsongrass mosaic virus,sharing 72%nt and 65%aa sequence identity.This viral agent was provisionally named pennisetum alopecuroides mosaic virus(PalMV).Subsequently,it was confirmed that PalMV is the causal agent of this new disease in P.alopecuroides by Koch’s postulates and reverse transcription-polymerase chain reaction analysis.Moreover,maize,millet,wheat,sorghum and rice plants were experimentally infected by PalMV via rub inoculation.Consequently,we proposed that PalMV could be a potentially dangerous virus threating a wide range of cereal crops.展开更多
基金supported by National Natural Science Foundation of China(Grant Nos.32370005,32072389)Chongqing Science Funds for Distinguished Young Scientists(Grant No.CSTB2022NSCQ-JQX0027)+3 种基金Innovation Research 2035 Pilot Plan of Southwest University(Grant Nos.SWU-XDPY22002,SWUXDZD22002)Special Fund for Youth Team of Southwest University(Grant No.SWU-XJLJ202310)Chongqing Talents of Exceptional Young Talents Project(Grant No.cstc2022ycjh-bgzxm0143)Chongqing Municipal Training Program of Innovation and Entrepreneurship for Undergraduates(Grant No.S202310635160)。
文摘In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.
基金supported by grants from Ministry of Agriculture and Rural Affairs of China(2018YFD020062)the Chinese Universities Scientific Fund(2019TC064).
文摘Pennisetum plants(Pennisetum alopecuroides L.),displaying a dwarfing phenotype along with delayed flowering and mosaic symptom on leaves,were found in Beijing,China.Flexuous filamentous particles with a size of approximate 15×850 nm were observed in symptomatic leaves via transmission electron microscopy.Deep sequencing of small RNAs(sRNA)from symptomatic leaves and analysis of sRNA populations were then conducted to determine the genome sequence of the viral agent in diseased plant tissues.It showed that the viral agent had one positive-sense and single-stranded RNA genome,which consisted of 9717 nucleotides(nts)excluding poly(A)tail.The complete viral genome contained a large open reading frame,encoding a polyprotein of 3131 amino acids(aa).Sequence comparison and phylogenetic analysis demonstrated that the viral agent belonged to the genus Potyvirus in the family Potyviridae.In the cladogram it was most closely related to johnsongrass mosaic virus,sharing 72%nt and 65%aa sequence identity.This viral agent was provisionally named pennisetum alopecuroides mosaic virus(PalMV).Subsequently,it was confirmed that PalMV is the causal agent of this new disease in P.alopecuroides by Koch’s postulates and reverse transcription-polymerase chain reaction analysis.Moreover,maize,millet,wheat,sorghum and rice plants were experimentally infected by PalMV via rub inoculation.Consequently,we proposed that PalMV could be a potentially dangerous virus threating a wide range of cereal crops.
