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Towards the well-tempered chloroplast DNA sequences
ID Turudić, Ante (Author), ID Liber, Zlatko (Author), ID Grdiša, Martina (Author), ID Jakše, Jernej (Author), ID Varga, Filip (Author), ID Šatović, Zlatko (Author)

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Abstract
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 This link opens in a new window
UDC:602
ISSN on article:2223-7747
DOI:10.3390/plants10071360 This link opens in a new window
COBISS.SI-ID:69203459 This link opens in a new window
Publication date in RUL:30.03.2022
Views:1174
Downloads:94
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Record is a part of a journal

Title:Plants
Shortened title:Plants
Publisher:MDPI
ISSN:2223-7747
COBISS.SI-ID:523345433 This link opens in a new window

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

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