PMID- 36169620
OWN - NLM
STAT- MEDLINE
DCOM- 20221026
LR  - 20230111
IS  - 1399-3054 (Electronic)
IS  - 0031-9317 (Print)
IS  - 0031-9317 (Linking)
VI  - 174
IP  - 5
DP  - 2022 Sep
TI  - Genome-wide identification, phylogeny, and gene duplication of the epigenetic 
      regulators in Fagaceae.
PG  - e13788
LID - 10.1111/ppl.13788 [doi]
LID - e13788
AB  - Epigenetic regulators are proteins involved in controlling gene expression. 
      Information about the epigenetic regulators within the Fagaceae, a relevant 
      family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With 
      the intent to characterize these proteins in Fagaceae, we searched for orthologs 
      of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers 
      involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and 
      demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were 
      performed in the available genomes, and freely available RNA-seq data were used 
      to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three 
      DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis 
      showed that most of them have the putative characteristic domains found in these 
      protein families, which suggests their conserved function. Additionally, to 
      elucidate the evolutionary history of these genes within Fagaceae, paralogs were 
      identified, and phylogenetic analyses were performed with DNA and histone 
      modifiers. We detected duplication events in all species analyzed with higher 
      frequency in Quercus and Castanea and discuss the evidence of transposable 
      elements adjacent to paralogs and their involvement in gene duplication. The 
      knowledge gathered from this work is a steppingstone to upcoming studies 
      concerning epigenetic regulation in this economically important family of 
      Fagaceae.
CI  - (c) 2022 The Authors. Physiologia Plantarum published by John Wiley & Sons Ltd on 
      behalf of Scandinavian Plant Physiology Society.
FAU - Alves, Sofia
AU  - Alves S
AD  - LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de 
      Agronomia, University of Lisbon, Lisboa, Portugal.
FAU - Braga, Angelo
AU  - Braga A
AD  - Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal.
FAU - Parreira, Denise
AU  - Parreira D
AD  - Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal.
FAU - Alhinho, Ana Teresa
AU  - Alhinho AT
AD  - Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, 
      Portugal.
FAU - Silva, Helena
AU  - Silva H
AD  - Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, 
      Portugal.
FAU - Ramos, Miguel Jesus Nunes
AU  - Ramos MJN
AD  - LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de 
      Agronomia, University of Lisbon, Lisboa, Portugal.
FAU - Costa, Maria Manuela Ribeiro
AU  - Costa MMR
AD  - Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, 
      Portugal.
FAU - Morais-Cecilio, Leonor
AU  - Morais-Cecilio L
AUID- ORCID: 0000-0001-9313-2253
AD  - LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de 
      Agronomia, University of Lisbon, Lisboa, Portugal.
LA  - eng
GR  - POCI-01-0145-FEDER-027980/PTDC/ASP-SIL/27980/2017/Fundacao para a Ciencia e a 
      Tecnologia/
GR  - SFRH/BD/136834/2018/Fundacao para a Ciencia e a Tecnologia/
GR  - SFRH/BD/146660/2019/Fundacao para a Ciencia e a Tecnologia/
GR  - UID/AGR/04129/2020/Fundacao para a Ciencia e a Tecnologia/
GR  - UIDB/04050/2020/Fundacao para a Ciencia e a Tecnologia/
PT  - Journal Article
PL  - Denmark
TA  - Physiol Plant
JT  - Physiologia plantarum
JID - 1256322
RN  - 0 (Histones)
RN  - 0 (DNA Transposable Elements)
RN  - EC 3.5.1.98 (Histone Deacetylases)
RN  - EC 2.1.1.- (Methyltransferases)
SB  - IM
MH  - Phylogeny
MH  - *Histones/genetics/metabolism
MH  - Gene Duplication
MH  - Epigenesis, Genetic
MH  - DNA Transposable Elements
MH  - Ecosystem
MH  - Histone Deacetylases/genetics/metabolism
MH  - *Quercus/metabolism
MH  - Methyltransferases/genetics
PMC - PMC9828519
EDAT- 2022/09/29 06:00
MHDA- 2022/10/27 06:00
PMCR- 2023/01/09
CRDT- 2022/09/28 10:33
PHST- 2022/09/16 00:00 [revised]
PHST- 2022/06/06 00:00 [received]
PHST- 2022/09/21 00:00 [accepted]
PHST- 2022/09/29 06:00 [pubmed]
PHST- 2022/10/27 06:00 [medline]
PHST- 2022/09/28 10:33 [entrez]
PHST- 2023/01/09 00:00 [pmc-release]
AID - PPL13788 [pii]
AID - 10.1111/ppl.13788 [doi]
PST - ppublish
SO  - Physiol Plant. 2022 Sep;174(5):e13788. doi: 10.1111/ppl.13788.