Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats

The development of next-generation sequencing technology and the increasing amount of sequencing data have brought the bioinformatic tools used in genome assembly into focus. The final step of the process is genome annotation, which works on assembled genome sequences to identify the location of gen...

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Bibliographic Details
Published inInternational journal of molecular sciences Vol. 23; no. 18; p. 10804
Main Authors Turudić, Ante, Liber, Zlatko, Grdiša, Martina, Jakše, Jernej, Varga, Filip, Šatović, Zlatko
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 16.09.2022
MDPI
Subjects
annotation
Annotations
Chloroplast DNA
chloroplast genome
Chloroplasts
Chloroplasts - genetics
DNA, Chloroplast - genetics
Genes
Genome, Chloroplast
Genomes
Inverted repeat
inverted repeats
Microsatellite Repeats - genetics
Molecular Sequence Annotation
Next-generation sequencing
Nucleotide sequence
Phylogeny
repeat identification
annotation
repeat identification
inverted repeats
chloroplast genome
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Summary:The development of next-generation sequencing technology and the increasing amount of sequencing data have brought the bioinformatic tools used in genome assembly into focus. The final step of the process is genome annotation, which works on assembled genome sequences to identify the location of genome features. In the case of organelle genomes, specialized annotation tools are used to identify organelle genes and structural features. Numerous annotation tools target chloroplast sequences. Most chloroplast DNA genomes have a quadripartite structure caused by two copies of a large inverted repeat. We investigated the strategies of six annotation tools (Chloë, Chloroplot, GeSeq, ORG.Annotate, PGA, Plann) for identifying inverted repeats and analyzed their success using publicly available complete chloroplast sequences of taxa belonging to the asterid and rosid clades. The annotation tools use two different approaches to identify inverted repeats, using existing general search tools or implementing stand-alone solutions. The chloroplast sequences studied show that there are different types of imperfections in the assembled data and that each tool performs better on some sequences than the others.
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content type line 23
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms231810804