Project Name Linker amplification for quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples 
Domain (1) viruses
Investigators (2)
Institution University of Arizona
Project Code CAM_P_0000912
Project Type metagenome
Publications (1)


Metagenomics generates and tests hypotheses about dynamics and mechanistic drivers in wild populations, yet commonly suffers from insufficient (<1 ng) starting genomic material for sequencing. Current solutions for amplifying sufficient DNA for metagenomics analyses include linear amplification for deep sequencing (LADS), which requires more DNA than is normally available, linker amplified shotgun libraries (LASLs), which is prohibitively low throughput, and whole genome amplification, which is significantly biased and thus non-quantitative. Here, we adapt the LASL approach to next generation sequencing by offering an alternate polymerase for challenging samples, developing a more efficient sizing step, integrating a "reconditioning PCR" step to increase yield and minimize late-cycle PCR artifacts, and empirically documenting the quantitative capability of the optimized method with both laboratory isolate and wild community viral DNA. Our optimized linker amplification method requires as little as 1 pg of DNA and is the most precise and accurate available, with amplification biases less than 1.5-fold, even for complex samples as diverse as a wild virus community. While optimized here for 454 sequencing, this linker amplification method can be used to prepare metagenomics libraries for sequencing with next-generation platforms, including Illumina and Ion Torrent. The sequences submitted to CAMERA are all those described in the publication.


No assemblies.


Sample Name PI Desc Cart
Pseudoalteromonas phage H105/1 unamplified NA H105-1_unamp
Pseudoalteromonas phage H105/1 15 cycles not reconditioned A NA H105-1_15A
Pseudoalteromonas phage H105/1 15 cycles not reconditioned B NA H105-1_15B
Pseudoalteromonas phage H105/1 15 cycles not reconditioned C NA H105-1_15C
Pseudoalteromonas phage H105/1 18 cycles not reconditioned A NA H105-1_18A
Pseudoalteromonas phage H105/1 18 cycles not reconditioned B NA H105-1_18B
Pseudoalteromonas phage H105/1 18 cycles not reconditioned C NA H105-1_18C
Pseudoalteromonas phage H105/1 20 cycles not reconditioned A NA H105-1_20A
Pseudoalteromonas phage H105/1 20 cycles not reconditioned B NA H105-1_20B
Pseudoalteromonas phage H105/1 20 cycles not reconditioned C NA H105-1_20C
Pseudoalteromonas phage H105/1 25 cycles not reconditioned A NA H105-1_25A
Pseudoalteromonas phage H105/1 25 cycles not reconditioned B NA H105-1_25B
Pseudoalteromonas phage H105/1 25 cycles not reconditioned C NA H105-1_25C
Pseudoalteromonas phage H105/1 30 cycles not reconditioned A NA H105-1_30A
Pseudoalteromonas phage H105/1 30 cycles not reconditioned B NA H105-1_30B
Pseudoalteromonas phage H105/1 30 cycles not reconditioned C NA H105-1_30C
Pseudoalteromonas phage H105/1 15 cycles reconditioned A NA H105-1_15rA
Pseudoalteromonas phage H105/1 15 cycles reconditioned B NA H105-1_15rB
Pseudoalteromonas phage H105/1 15 cycles reconditioned C NA H105-1_15rC
Pseudoalteromonas phage H105/1 18 cycles reconditioned A NA H105-1_18rA
Pseudoalteromonas phage H105/1 18 cycles reconditioned B NA H105-1_18rB
Pseudoalteromonas phage H105/1 18 cycles reconditioned C NA H105-1_18rC
Pseudoalteromonas phage H105/1 20 cycles reconditioned A NA H105-1_20rA
Pseudoalteromonas phage H105/1 20 cycles reconditioned B NA H105-1_20rB
Pseudoalteromonas phage H105/1 20 cycles reconditioned C NA H105-1_20rC
Pseudoalteromonas phage H105/1 25 cycles reconditioned A NA H105-1_25rA
Pseudoalteromonas phage H105/1 25 cycles reconditioned B NA H105-1_25rB
Pseudoalteromonas phage H105/1 25 cycles reconditioned C NA H105-1_25rC
Pseudoalteromonas phage H105/1 30 cycles reconditioned A NA H105-1_30rA
Pseudoalteromonas phage H105/1 30 cycles reconditioned B NA H105-1_30rB
Pseudoalteromonas phage H105/1 30 cycles reconditioned A NA H105-1_30rC
Biosphere2 ocean unamplified A NA B2O_unampA
Biosphere2 ocean unamplified B NA B2O_unampB
Biosphere2 ocean 15 cycles not reconditioned A NA B2O_15A
Biosphere2 ocean 15 cycles not reconditioned B NA B2O_15B
Biosphere2 ocean 15 cycles not reconditioned C NA B2O_15C
Biosphere2 ocean 25 cycles not reconditioned A NA B2O_25A
Biosphere2 ocean 25 cycles not reconditioned B NA B2O_25B
Biosphere2 ocean 25 cycles not reconditioned C NA B2O_25C
Biosphere2 ocean 15 cycles reconditioned A NA B2O_15rA
Biosphere2 ocean 25 cycles reconditioned A NA B2O_25rA


Type Location
Meta  /iplant/home/shared/imicrobe/projects/92/CAM_P_0000912.csv
Meta  /iplant/home/shared/imicrobe/projects/92/sample-attr.tab
Reads  /iplant/home/shared/imicrobe/projects/92/CAM_P_0000912.read.fa
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