Chloroplast genome annotation tools : prolegomena to the identification of inverted repeats

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

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.

• Language: English
• Keywords: chloroplast genome, annotation, inverted repeats, repeat identification
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2022
• Number of pages: 19 str.
• Numbering: Vol. 23, no. 18, art. 10804
• PID: 20.500.12556/RUL-141760
• UDC: 577.2
• ISSN on article: 1422-0067
• DOI: 10.3390/ijms231810804
• COBISS.SI-ID: 124702211
• Publication date in RUL: 07.10.2022

Record is a part of a journal

• Title: International journal of molecular sciences
• Shortened title: Int. j. mol. sci.
• Publisher: MDPI
• ISSN: 1422-0067
• COBISS.SI-ID: 2779162

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: kloroplast, genom kloroplasta, bioinformatika, sekvenciranje genoma, molekularne tehnike