Evolutionary dynamics of protein domain architecture in plants

Xue Cheng Zhang, Zheng Wang, Xinyan Zhang, Mi Ha Le, Jianguo Sun, Dong Xu, Jianlin Cheng, Gary Stacey

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

Background: Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results: Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions: Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing the notion that plant genomes have undergone dynamic evolution.

Original languageEnglish (US)
Article number6
JournalBMC Evolutionary Biology
Volume12
Issue number1
DOIs
StatePublished - Jan 18 2012
Externally publishedYes

Fingerprint

plant architecture
genome
protein
proteins
ploidy
biogeography
microorganism
microorganisms
history

Keywords

  • domain architecture
  • evolutionary dynamics
  • genetic origin
  • plant lineage

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics

Cite this

Zhang, X. C., Wang, Z., Zhang, X., Le, M. H., Sun, J., Xu, D., ... Stacey, G. (2012). Evolutionary dynamics of protein domain architecture in plants. BMC Evolutionary Biology, 12(1), [6]. https://doi.org/10.1186/1471-2148-12-6

Evolutionary dynamics of protein domain architecture in plants. / Zhang, Xue Cheng; Wang, Zheng; Zhang, Xinyan; Le, Mi Ha; Sun, Jianguo; Xu, Dong; Cheng, Jianlin; Stacey, Gary.

In: BMC Evolutionary Biology, Vol. 12, No. 1, 6, 18.01.2012.

Research output: Contribution to journalArticle

Zhang, XC, Wang, Z, Zhang, X, Le, MH, Sun, J, Xu, D, Cheng, J & Stacey, G 2012, 'Evolutionary dynamics of protein domain architecture in plants', BMC Evolutionary Biology, vol. 12, no. 1, 6. https://doi.org/10.1186/1471-2148-12-6
Zhang, Xue Cheng ; Wang, Zheng ; Zhang, Xinyan ; Le, Mi Ha ; Sun, Jianguo ; Xu, Dong ; Cheng, Jianlin ; Stacey, Gary. / Evolutionary dynamics of protein domain architecture in plants. In: BMC Evolutionary Biology. 2012 ; Vol. 12, No. 1.
@article{6075d302eb8b4a099428ab32bb23cbf7,
title = "Evolutionary dynamics of protein domain architecture in plants",
abstract = "Background: Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results: Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65{\%} of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions: Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing the notion that plant genomes have undergone dynamic evolution.",
keywords = "domain architecture, evolutionary dynamics, genetic origin, plant lineage",
author = "Zhang, {Xue Cheng} and Zheng Wang and Xinyan Zhang and Le, {Mi Ha} and Jianguo Sun and Dong Xu and Jianlin Cheng and Gary Stacey",
year = "2012",
month = "1",
day = "18",
doi = "10.1186/1471-2148-12-6",
language = "English (US)",
volume = "12",
journal = "BMC Evolutionary Biology",
issn = "1471-2148",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Evolutionary dynamics of protein domain architecture in plants

AU - Zhang, Xue Cheng

AU - Wang, Zheng

AU - Zhang, Xinyan

AU - Le, Mi Ha

AU - Sun, Jianguo

AU - Xu, Dong

AU - Cheng, Jianlin

AU - Stacey, Gary

PY - 2012/1/18

Y1 - 2012/1/18

N2 - Background: Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results: Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions: Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing the notion that plant genomes have undergone dynamic evolution.

AB - Background: Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results: Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions: Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing the notion that plant genomes have undergone dynamic evolution.

KW - domain architecture

KW - evolutionary dynamics

KW - genetic origin

KW - plant lineage

UR - http://www.scopus.com/inward/record.url?scp=84862792374&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84862792374&partnerID=8YFLogxK

U2 - 10.1186/1471-2148-12-6

DO - 10.1186/1471-2148-12-6

M3 - Article

C2 - 22252370

AN - SCOPUS:84862792374

VL - 12

JO - BMC Evolutionary Biology

JF - BMC Evolutionary Biology

SN - 1471-2148

IS - 1

M1 - 6

ER -