Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts

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 ob...
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Autor*in:	Ante Turudić [verfasserIn] Zlatko Liber [verfasserIn] Martina Grdiša [verfasserIn] Jernej Jakše [verfasserIn] Filip Varga [verfasserIn] Zlatko Šatović [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	genome databases chloroplast genome sequence length taxonomy

Übergeordnetes Werk:	In: Plants - MDPI AG, 2013, 12(2023), 2, p 254
Übergeordnetes Werk:	volume:12 ; year:2023 ; number:2, p 254

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/plants12020254

Katalog-ID:	DOAJ081721498

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allfields	10.3390/plants12020254 doi (DE-627)DOAJ081721498 (DE-599)DOAJe1316cc3aeb34b07a5cad835b6487292 DE-627 ger DE-627 rakwb eng QK1-989 Ante Turudić verfasserin aut Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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 <i<RefSeq</i< sequences from the asterid and rosid clades. In general, chloroplast length distributions are narrow at both the family and genus levels. In addition, clear biological explanations have already been reported for families and genera that exhibit particularly wide distributions. The main factors responsible for the length variations are parasitic life forms, IR loss, IR expansions and contractions, and polyphyly. However, the presence of outliers in the distribution at the genus level is a strong indication of possible inaccuracies in sequence assembly. genome databases chloroplast genome sequence length taxonomy Botany Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In Plants MDPI AG, 2013 12(2023), 2, p 254 (DE-627)737288345 (DE-600)2704341-1 22237747 nnns volume:12 year:2023 number:2, p 254 https://doi.org/10.3390/plants12020254 kostenfrei https://doaj.org/article/e1316cc3aeb34b07a5cad835b6487292 kostenfrei https://www.mdpi.com/2223-7747/12/2/254 kostenfrei https://doaj.org/toc/2223-7747 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2023 2, p 254
spelling	10.3390/plants12020254 doi (DE-627)DOAJ081721498 (DE-599)DOAJe1316cc3aeb34b07a5cad835b6487292 DE-627 ger DE-627 rakwb eng QK1-989 Ante Turudić verfasserin aut Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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 <i<RefSeq</i< sequences from the asterid and rosid clades. In general, chloroplast length distributions are narrow at both the family and genus levels. In addition, clear biological explanations have already been reported for families and genera that exhibit particularly wide distributions. The main factors responsible for the length variations are parasitic life forms, IR loss, IR expansions and contractions, and polyphyly. However, the presence of outliers in the distribution at the genus level is a strong indication of possible inaccuracies in sequence assembly. genome databases chloroplast genome sequence length taxonomy Botany Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In Plants MDPI AG, 2013 12(2023), 2, p 254 (DE-627)737288345 (DE-600)2704341-1 22237747 nnns volume:12 year:2023 number:2, p 254 https://doi.org/10.3390/plants12020254 kostenfrei https://doaj.org/article/e1316cc3aeb34b07a5cad835b6487292 kostenfrei https://www.mdpi.com/2223-7747/12/2/254 kostenfrei https://doaj.org/toc/2223-7747 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2023 2, p 254
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allfieldsGer	10.3390/plants12020254 doi (DE-627)DOAJ081721498 (DE-599)DOAJe1316cc3aeb34b07a5cad835b6487292 DE-627 ger DE-627 rakwb eng QK1-989 Ante Turudić verfasserin aut Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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 <i<RefSeq</i< sequences from the asterid and rosid clades. In general, chloroplast length distributions are narrow at both the family and genus levels. In addition, clear biological explanations have already been reported for families and genera that exhibit particularly wide distributions. The main factors responsible for the length variations are parasitic life forms, IR loss, IR expansions and contractions, and polyphyly. However, the presence of outliers in the distribution at the genus level is a strong indication of possible inaccuracies in sequence assembly. genome databases chloroplast genome sequence length taxonomy Botany Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In Plants MDPI AG, 2013 12(2023), 2, p 254 (DE-627)737288345 (DE-600)2704341-1 22237747 nnns volume:12 year:2023 number:2, p 254 https://doi.org/10.3390/plants12020254 kostenfrei https://doaj.org/article/e1316cc3aeb34b07a5cad835b6487292 kostenfrei https://www.mdpi.com/2223-7747/12/2/254 kostenfrei https://doaj.org/toc/2223-7747 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2023 2, p 254
allfieldsSound	10.3390/plants12020254 doi (DE-627)DOAJ081721498 (DE-599)DOAJe1316cc3aeb34b07a5cad835b6487292 DE-627 ger DE-627 rakwb eng QK1-989 Ante Turudić verfasserin aut Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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 <i<RefSeq</i< sequences from the asterid and rosid clades. In general, chloroplast length distributions are narrow at both the family and genus levels. In addition, clear biological explanations have already been reported for families and genera that exhibit particularly wide distributions. The main factors responsible for the length variations are parasitic life forms, IR loss, IR expansions and contractions, and polyphyly. However, the presence of outliers in the distribution at the genus level is a strong indication of possible inaccuracies in sequence assembly. genome databases chloroplast genome sequence length taxonomy Botany Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In Plants MDPI AG, 2013 12(2023), 2, p 254 (DE-627)737288345 (DE-600)2704341-1 22237747 nnns volume:12 year:2023 number:2, p 254 https://doi.org/10.3390/plants12020254 kostenfrei https://doaj.org/article/e1316cc3aeb34b07a5cad835b6487292 kostenfrei https://www.mdpi.com/2223-7747/12/2/254 kostenfrei https://doaj.org/toc/2223-7747 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2023 2, p 254
language	English
source	In Plants 12(2023), 2, p 254 volume:12 year:2023 number:2, p 254
sourceStr	In Plants 12(2023), 2, p 254 volume:12 year:2023 number:2, p 254
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institution	findex.gbv.de
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callnumber-first	Q - Science
author	Ante Turudić
spellingShingle	Ante Turudić misc QK1-989 misc genome databases misc chloroplast genome misc sequence length misc taxonomy misc Botany Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts
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topic_title	QK1-989 Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts genome databases chloroplast genome sequence length taxonomy
topic	misc QK1-989 misc genome databases misc chloroplast genome misc sequence length misc taxonomy misc Botany
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title	Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts
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title_full	Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts
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title_sort	variation in chloroplast genome size: biological phenomena and technological artifacts
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title_auth	Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts
abstract	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 <i<RefSeq</i< sequences from the asterid and rosid clades. In general, chloroplast length distributions are narrow at both the family and genus levels. In addition, clear biological explanations have already been reported for families and genera that exhibit particularly wide distributions. The main factors responsible for the length variations are parasitic life forms, IR loss, IR expansions and contractions, and polyphyly. However, the presence of outliers in the distribution at the genus level is a strong indication of possible inaccuracies in sequence assembly.
abstractGer	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 <i<RefSeq</i< sequences from the asterid and rosid clades. In general, chloroplast length distributions are narrow at both the family and genus levels. In addition, clear biological explanations have already been reported for families and genera that exhibit particularly wide distributions. The main factors responsible for the length variations are parasitic life forms, IR loss, IR expansions and contractions, and polyphyly. However, the presence of outliers in the distribution at the genus level is a strong indication of possible inaccuracies in sequence assembly.
abstract_unstemmed	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 <i<RefSeq</i< sequences from the asterid and rosid clades. In general, chloroplast length distributions are narrow at both the family and genus levels. In addition, clear biological explanations have already been reported for families and genera that exhibit particularly wide distributions. The main factors responsible for the length variations are parasitic life forms, IR loss, IR expansions and contractions, and polyphyly. However, the presence of outliers in the distribution at the genus level is a strong indication of possible inaccuracies in sequence assembly.
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title_short	Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts
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Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts

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