Plann: A command‐line application for annotating plastome sequences

Abstract

Premise of the study:Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome.Methods and Results:Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann’s output can be used in the National Center for Biotechnology Information’s tbl2asn to create a Sequin file for GenBank submission.Conclusions:Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved.

Hybridization‐facilitated genome merger and repeated chromosome fusion after 8 million years

“…As the novoplasty software did not yield a circularized assembly for R. cretica , we first used velvet 1.2.1 (Zerbino and Birney, ) to assemble reads into contigs with a wide range of kmers (from 79 to 145, with a step size of 11), and then merged these contigs by aligning them to the chloroplast genome of M. pygmaea in geneious 8.0.5 (Kearse et al ., ). The annotation was performed with plann 1.1.1 (Huang and Cronk, ) using the annotation of the M. pygmaea plastome as a reference, aided by manual refinement in sequin (Clark et al ., ). The Aragorn web interface (Laslett and Canback, ) was used to predict tRNAs.…”

Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes

“…We then applied Velvet v.1.2.10 (Zerbino and Birney, 2008) to assemble these reads into the complete plastid genomes, and gaps were filled with GapCloser v.1.12 (http://soap.genomics.org.cn/index.html). We finally annotated the chloroplast genomes using Plann v.1.1.2 (Huang and Cronk, 2015) and manually corrected for start and stop codons and for intron/exon boundaries to match gene predictions with Geneious v.R.8.1.4 (Kearse et al, 2012) and Sequin v.15.10 (http://www.ncbi.nlm.nih.gov/Sequin/) based on Arabidopsis thaliana chloroplast genome as a reference annotation. The visual images about annotation information were generated by OGDRAW v.1.1 (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al, 2013).…”

Characterization of the complete chloroplast genome of Allium prattii

“…The resulting contigs were linked based on overlapping regions after being aligned to A. cepa (KM088013) and visualized using Geneious version 11.0.4 (Kearse et al 2012). Annotation was performed using Plann (Huang and Cronk 2015) which is a command-line application for annotating plastome sequences. A maximum-likelihood (ML) tree with 1000 bootstrap replicates was inferred using MEGA7.0 (Kumar et al 2016) from alignments created by the MAFFT (Katoh et al 2002) using plastid genomes of 10 species.…”