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Citation for Study 22409

Citation title: "Tangled history of a multigene family: the evolution of Isopentenyltransferase genes".

Study name: "Tangled history of a multigene family: the evolution of Isopentenyltransferase genes".

This study is part of submission 22409 (Status: Published).

Citation

Nishii K., Wright F., Chen Y., & Moeller M. 2018. Tangled history of a multigene family: the evolution of Isopentenyltransferase genes. PLOS ONE, 13(8): e0201198.

Authors

• Nishii K. (submitter) +441315527171
• Wright F.
• Chen Y.
• Moeller M.

Abstract

ISOPENTENYLTRANSFERASE (IPT) genes play important roles in the initial steps of cytokinin synthesis, exist in plant and pathogenic bacteria, and form a multigene family in plants. Protein domain searches revealed that bacteria and plant IPT proteins were to assigned to different protein domains families in the Pfam database, namely Pfam IPT (IPTPfam) and Pfam IPPT (IPPTPfam) families, both are closely related in the P-loop NTPase clan. To understand the origin and evolution of the genes, a species matrix was assembled across the tree of life and intensively in plant lineages. The IPTPfam domain was only found in few bacteria lineages, whereas IPPTPfam is common except in Archaea and Mycoplasma bacteria. The bacterial IPPTPfam domain miaA genes were shown as ancestral of eukaryotic IPPTPfam domain genes. Plant IPTs diversified into class I, class II tRNA-IPTs, and Adenosine-phosphate IPTs; the class I tRNA-IPTs appeared to represent direct successors of miaA genes were found in all plant genomes, whereas class II tRNA-IPTs originated from eukaryotic genes, and were found in prasinophyte algae and in euphyllophytes. Adenosine-phosphate IPTs were only found in angiosperms. Gene duplications resulted in gene redundancies with ubiquitous expression or diversification in expression. In conclusion, it is shown that IPT genes have a complex history prior to the protein family split, and might have experienced losses or HGTs, and gene duplications that are to be likely correlated with the rise in morphological complexity involved in fine tuning cytokinin production.

Keywords

Cytokinins; gene evolution; ISOPENTENYLTRANSFERASE; IPPT domain; IPT domain; multigene family; Pfam

External links

• DOI: 10.1371/journal.pone.0201198
• Other URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201198

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S22409
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref28643,
  	 author = {Kanae  Nishii and Frank  Wright and Yun-Yu  Chen and Michael  Moeller},
  	 title = {Tangled history of a multigene family: the evolution of Isopentenyltransferase genes},
  	 year = {2018},
  	 keywords = {Cytokinins; gene evolution; ISOPENTENYLTRANSFERASE; IPPT domain; IPT domain; multigene family; Pfam},
  	 doi = {10.1371/journal.pone.0201198},
  	 url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201198},
  	 pmid = {},
  	 journal = {PLOS ONE},
  	 volume = {13},
  	 number = {8},
  	 pages = {e0201198},
  	 abstract = {ISOPENTENYLTRANSFERASE (IPT) genes play important roles in the initial steps of cytokinin synthesis, exist in plant and pathogenic bacteria, and form a multigene family in plants. Protein domain searches revealed that bacteria and plant IPT proteins were to assigned to different protein domains families in the Pfam database, namely Pfam IPT (IPTPfam) and Pfam IPPT (IPPTPfam) families, both are closely related in the P-loop NTPase clan. To understand the origin and evolution of the genes, a species matrix was assembled across the tree of life and intensively in plant lineages. The IPTPfam domain was only found in few bacteria lineages, whereas IPPTPfam is common except in Archaea and Mycoplasma bacteria. The bacterial IPPTPfam domain miaA genes were shown as ancestral of eukaryotic IPPTPfam domain genes. Plant IPTs diversified into class I, class II tRNA-IPTs, and Adenosine-phosphate IPTs; the class I tRNA-IPTs appeared to represent direct successors of miaA genes were found in all plant genomes, whereas class II tRNA-IPTs originated from eukaryotic genes, and were found in prasinophyte algae and in euphyllophytes. Adenosine-phosphate IPTs were only found in angiosperms. Gene duplications resulted in gene redundancies with ubiquitous expression or diversification in expression. In conclusion, it is shown that IPT genes have a complex history prior to the protein family split, and might have experienced losses or HGTs, and gene duplications that are to be likely correlated with the rise in morphological complexity involved in fine tuning cytokinin production.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 28643
  AU  - Nishii,Kanae 
  AU  - Wright,Frank 
  AU  - Chen,Yun-Yu 
  AU  - Moeller,Michael 
  T1  - Tangled history of a multigene family: the evolution of Isopentenyltransferase genes
  PY  - 2018
  KW  - Cytokinins; gene evolution; ISOPENTENYLTRANSFERASE; IPPT domain; IPT domain; multigene family; Pfam
  UR  - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201198
  N2  - ISOPENTENYLTRANSFERASE (IPT) genes play important roles in the initial steps of cytokinin synthesis, exist in plant and pathogenic bacteria, and form a multigene family in plants. Protein domain searches revealed that bacteria and plant IPT proteins were to assigned to different protein domains families in the Pfam database, namely Pfam IPT (IPTPfam) and Pfam IPPT (IPPTPfam) families, both are closely related in the P-loop NTPase clan. To understand the origin and evolution of the genes, a species matrix was assembled across the tree of life and intensively in plant lineages. The IPTPfam domain was only found in few bacteria lineages, whereas IPPTPfam is common except in Archaea and Mycoplasma bacteria. The bacterial IPPTPfam domain miaA genes were shown as ancestral of eukaryotic IPPTPfam domain genes. Plant IPTs diversified into class I, class II tRNA-IPTs, and Adenosine-phosphate IPTs; the class I tRNA-IPTs appeared to represent direct successors of miaA genes were found in all plant genomes, whereas class II tRNA-IPTs originated from eukaryotic genes, and were found in prasinophyte algae and in euphyllophytes. Adenosine-phosphate IPTs were only found in angiosperms. Gene duplications resulted in gene redundancies with ubiquitous expression or diversification in expression. In conclusion, it is shown that IPT genes have a complex history prior to the protein family split, and might have experienced losses or HGTs, and gene duplications that are to be likely correlated with the rise in morphological complexity involved in fine tuning cytokinin production.
  L3  - 10.1371/journal.pone.0201198
  JF  - PLOS ONE
  VL  - 13
  IS  - 8
  ER  -