Automated Annotation Of Plastids And Mitochondria

A Plann for annotation: Automated annotation of plastid and mitochondrial genomes using the program “Plann”

Reference: Huang, Daisie I., and Quentin CB Cronk. "Plann: a command-line application for annotating plastome sequences." Applications in plant sciences 3, no. 8 (2015): 1500026.

Plann is a command line program written in Perl for automated annotation of organelle genomes. Because it is executed from the command line it is easy to incorporate into population genomic pipelines where multiple plastomes within a species are being sequenced by next generation sequencing techniques. Although it was written for, and has been most extensively tested on plastid genomes, it also seems to work for the annotation of chondriomes (mitochondrial genomes).

It was designed to work best when a fully annotated genome of a related species (same genus) is available on GenBank. However, it can make useful initial annotations even when the closest available annotated genome is rather distantly related (e.g. different genus within the same family). However, the more distant the reference from the target the more likely it is that some manual refinement will be necessary to catch unannotated genes.

A good example of the use of Plann is provided by Yin et al. (2016). They sequenced whole plastomes of seven species of Arachis, related to the peanut (Arachis hypogaea). These chloroplast genomes ranged in length from 156,275 to 156,395 bp. Because the plastome of peanut was already well-annotated and available on GenBank the cpDNA annotation could be readily performed with Plann. Propagating the annotation from the reference to the targets was unproblematic. Reference: Yin, D., Wang, Y., Zhang, X., Ma, X., He, X., & Zhang, J. (2017). Development of chloroplast genome resources for peanut (Arachis hypogaea// L.) and other species of Arachis. Scientific Reports, 7(1), 11649.

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