Towards the well-tempered chloroplast DNA sequences

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

With the development of next-generation sequencing technology and bioinformatics tools, the process of assembling DNA sequences has become cheaper and easier, especially in the case of much shorter organelle genomes. The number of available DNA sequences of complete chloroplast genomes in public genetic databases is constantly increasing and the data are widely used in plant phylogenetic and biotechnological research. In this work, we investigated possible inconsistencies in the stored form of publicly available chloroplast genome sequence data. The impact of these inconsistencies on the results of the phylogenetic analysis was investigated and the bioinformatic solution to identify and correct inconsistencies was implemented. The whole procedure was demonstrated using five plant families (Apiaceae, Asteraceae, Campanulaceae, Lamiaceae and Rosaceae) as examples.

• Language: English
• Keywords: chloroplast genome, genome assembly, standardization, cyclic shift, inversion
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: 14 str.
• Numbering: Vol. 10, iss. 7, art. 1360
• PID: 20.500.12556/RUL-135742
• UDC: 602
• ISSN on article: 2223-7747
• DOI: 10.3390/plants10071360
• COBISS.SI-ID: 69203459
• Publication date in RUL: 30.03.2022

Record is a part of a journal

• Title: Plants
• Shortened title: Plants
• Publisher: MDPI
• ISSN: 2223-7747
• COBISS.SI-ID: 523345433

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.
• Licensing start date: 02.07.2021

Secondary language

• Language: Slovenian
• Keywords: bioinformatika, kloroplasti, genom, sekvenciranje genoma, filogenetske analize, filogenetske metode

Projects

• Funder: Other - Other funder or multiple funders
• Project number: KK.01.1.1.01.0005
• Name: Biodiversity and Molecular Plant Breeding