Artificial cyanophages are considered to be an effective biological method to control harmful cyanobacterial bloom.However,no synthetic cyanophage genome has been constructed and where its obstacles are unclear.Here,w...Artificial cyanophages are considered to be an effective biological method to control harmful cyanobacterial bloom.However,no synthetic cyanophage genome has been constructed and where its obstacles are unclear.Here,we survey a stretch of 16 kb length sequence of cyanophage A-4L that is unclonable in Escherichia coli.We test 12 predicted promoters of cyanophage A-4L which were verified all active in E.coli.Next,we screen for eight ORFs that hindered the assembly of intermediate DNA fragments in E.coli and describe that seven ORFs in the 16 kb sequence could not be separately cloned in E.coli.All of unclonable ORFs in high-copy-number plasmid were successfully cloned using low-copy-number vector,suggesting that these ORFs were copy-number-dependent.We propose a clone strategy abandoned the promotor and the start codon that could be applied for unclonable ORFs.Last,we de novo synthesized and assembled the full-length genome of cyanophage A-4L.This work deepens the understanding of synthetic cyanophages studies.展开更多
Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bod...Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bodies and limitations in virus discovery techniques. In this study, we conducted a 1-year survey of phytoplankton virus communities by collecting surface water monthly from an inland lake(East Lake) in China between May 2012 and April 2013. We examined four phytoplankton viruses, i.e., myoviruses, podoviruses, siphoviruses, and phycodnaviruses, and seven sets of primers were used to target conserved genes within these four species. In this year-long investigation, a total of 358 different virus-related sequences from four virus families were obtained. All virus families were detected in all months, except for cyanopodoviruses, which were only identified during eight of the 12 months surveyed. Moreover, virus abundance and diversity changed dynamically over time. Phylogenetic analysis revealed that the majority of viral sequences from East Lake, China displayed distinct clustering patterns compared with published sequences. These results supported the existence of a highly diverse and unique phytoplankton virus community in East Lake, China.展开更多
基金supported by the grants from the National Key Research and Development Program of China (No.2018YFA0903000)the National Natural Science Foundation of China (31901019)and the China Postdoctoral Science foundation (2021M692389).
文摘Artificial cyanophages are considered to be an effective biological method to control harmful cyanobacterial bloom.However,no synthetic cyanophage genome has been constructed and where its obstacles are unclear.Here,we survey a stretch of 16 kb length sequence of cyanophage A-4L that is unclonable in Escherichia coli.We test 12 predicted promoters of cyanophage A-4L which were verified all active in E.coli.Next,we screen for eight ORFs that hindered the assembly of intermediate DNA fragments in E.coli and describe that seven ORFs in the 16 kb sequence could not be separately cloned in E.coli.All of unclonable ORFs in high-copy-number plasmid were successfully cloned using low-copy-number vector,suggesting that these ORFs were copy-number-dependent.We propose a clone strategy abandoned the promotor and the start codon that could be applied for unclonable ORFs.Last,we de novo synthesized and assembled the full-length genome of cyanophage A-4L.This work deepens the understanding of synthetic cyanophages studies.
基金financial support from Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-YW-Z-0954, KSCX2-EW-Z-3)
文摘Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bodies and limitations in virus discovery techniques. In this study, we conducted a 1-year survey of phytoplankton virus communities by collecting surface water monthly from an inland lake(East Lake) in China between May 2012 and April 2013. We examined four phytoplankton viruses, i.e., myoviruses, podoviruses, siphoviruses, and phycodnaviruses, and seven sets of primers were used to target conserved genes within these four species. In this year-long investigation, a total of 358 different virus-related sequences from four virus families were obtained. All virus families were detected in all months, except for cyanopodoviruses, which were only identified during eight of the 12 months surveyed. Moreover, virus abundance and diversity changed dynamically over time. Phylogenetic analysis revealed that the majority of viral sequences from East Lake, China displayed distinct clustering patterns compared with published sequences. These results supported the existence of a highly diverse and unique phytoplankton virus community in East Lake, China.
