Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts.

chloroplast genome genome databases sequence length taxonomy

Journal

Plants (Basel, Switzerland)
ISSN: 2223-7747
Titre abrégé: Plants (Basel)
Pays: Switzerland
ID NLM: 101596181

Informations de publication

Date de publication:
05 Jan 2023
Historique:
received: 04 11 2022
revised: 31 12 2022
accepted: 03 01 2023
entrez: 21 1 2023
pubmed: 22 1 2023
medline: 22 1 2023
Statut: epublish

Résumé

The development of bioinformatic solutions is guided by biological knowledge of the subject. In some cases, we use unambiguous biological models, while in others we rely on assumptions. A commonly used assumption for genomes is that related species have similar genome sequences. This is even more obvious in the case of chloroplast genomes due to their slow evolution. We investigated whether the lengths of complete chloroplast sequences are closely related to the taxonomic proximity of the species. The study was performed using all available

Identifiants

pubmed: 36678967
pii: plants12020254
doi: 10.3390/plants12020254
pmc: PMC9864865
pii:
doi:

Types de publication

Journal Article

Langues

eng

Subventions

Organisme : Centre of Excellence for Biodiversity and Molecular Plant Breeding
ID : KK.01.1.1.01.0005

Références

Nucleic Acids Res. 2017 Jul 3;45(W1):W6-W11
pubmed: 28486635
Bioinformatics. 2009 Jun 1;25(11):1422-3
pubmed: 19304878
Plant Methods. 2019 May 21;15:50
pubmed: 31139240
Genome Biol Evol. 2020 Oct 1;12(10):1841-1857
pubmed: 32722748
EMBO J. 1986 Sep;5(9):2043-2049
pubmed: 16453699
Bioessays. 1987 Jun;6(6):279-82
pubmed: 3619888
PLoS One. 2013;8(3):e58747
pubmed: 23554920
Ann Bot. 2016 Oct 1;118(5):885-896
pubmed: 27443299
Trends Ecol Evol. 2014 Jan;29(1):33-41
pubmed: 24148292
Genome Biol Evol. 2015 Dec 12;8(1):189-201
pubmed: 26660355
Plant Cell. 2004 Jul;16(7):1661-6
pubmed: 15235123
Mol Gen Genet. 1996 Aug 27;252(1-2):195-206
pubmed: 8804393
Mol Phylogenet Evol. 2012 Oct;65(1):23-34
pubmed: 22643289
Front Genet. 2020 Sep 25;11:576124
pubmed: 33101394
Plant Mol Biol. 2011 Jul;76(3-5):263-72
pubmed: 21327834
Genome Biol Evol. 2017 Jan 1;9(1):64-76
pubmed: 28172771
Methods Mol Biol. 2014;1132:3-38
pubmed: 24599844
Genome Biol. 2020 Sep 10;21(1):241
pubmed: 32912315
Plants (Basel). 2021 Jul 02;10(7):
pubmed: 34371563
BMC Bioinformatics. 2021 Aug 21;22(1):413
pubmed: 34418956
Mol Biol Evol. 1994 Sep;11(5):769-77
pubmed: 7968490
PLoS One. 2013 Nov 18;8(11):e79685
pubmed: 24260278
Mol Biol Evol. 2016 Jun;33(6):1635-8
pubmed: 26921390
Int J Mol Sci. 2019 Jun 03;20(11):
pubmed: 31163646
Mol Biol Evol. 2011 Jan;28(1):583-600
pubmed: 20805190
Syst Biol. 2004 Jun;53(3):384-99
pubmed: 15503669
Nucleic Acids Res. 2017 Feb 28;45(4):e18
pubmed: 28204566
Appl Plant Sci. 2015 Aug 10;3(8):
pubmed: 26312193
Am J Bot. 2006 Feb;93(2):304-18
pubmed: 21646191
Sci Rep. 2017 May 8;7(1):1555
pubmed: 28484234
Plant Mol Biol. 2011 Jul;76(3-5):273-97
pubmed: 21424877
New Phytol. 2017 Apr;214(2):842-851
pubmed: 27991660
Mol Biol Evol. 2006 Nov;23(11):2175-90
pubmed: 16916942
Nat Plants. 2021 Dec;7(12):1571-1578
pubmed: 34845350
Int J Mol Sci. 2022 Sep 16;23(18):
pubmed: 36142721
Proc Natl Acad Sci U S A. 1989 Jun;86(11):4156-60
pubmed: 16594051

Auteurs

Ante Turudić (A)

Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia.
Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia.

Zlatko Liber (Z)

Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia.
Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia.

Martina Grdiša (M)

Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia.
Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia.

Jernej Jakše (J)

Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.

Filip Varga (F)

Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia.
Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia.

Zlatko Šatović (Z)

Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia.
Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia.

Classifications MeSH