Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities.

ABSTRACT:

Premise of the study

DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants.

Methods

To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants.

Results

Perfor

SUBMITTER: Harbert RS 

PROVIDER: S-EPMC5895191 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature