Chloroplast genome annotation tools

prolegomena to the identification of inverted repeats

Ante Turudić (Author), Zlatko Liber (Author), Martina Grdiša (Author), Jernej Jakše (Author), Filip Varga (Author), Zlatko Šatović (Author)

Abstract

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.

Keywords

chloroplast genome;annotation;inverted repeats;repeat identification;

Data

Language:	English
Year of publishing:	2022
Typology:	1.01 - Original Scientific Article
Organization:	UL BF - Biotechnical Faculty
UDC:	577.2
COBISS:	124702211
ISSN:	1422-0067
Views:	13
Downloads:	4
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	Slovenian
Secondary keywords:	kloroplast;genom kloroplasta;bioinformatika;sekvenciranje genoma;molekularne tehnike;
Type (COBISS):	Article
Pages:	19 str.
Volume:	ǂVol. ǂ23
Issue:	ǂno. ǂ18, art. 10804
Chronology:	2022
DOI:	10.3390/ijms231810804
ID:	16680056