Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway

Genome Biology and Evolution
Lu MaAndrew R Leitch

Abstract

The RNA-directed DNA methylation (RdDM) pathway can be divided into three phases: 1) small interfering RNA biogenesis, 2) de novo methylation, and 3) chromatin modification. To determine the degree of conservation of this pathway we searched for key genes among land plants. We used OrthoMCL and the OrthoMCL Viridiplantae database to analyze proteomes of species in bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms. We also analyzed small RNA size categories and, in two gymnosperms, cytosine methylation in ribosomal DNA. Six proteins were restricted to angiosperms, these being NRPD4/NRPE4, RDM1, DMS3 (defective in meristem silencing 3), SHH1 (SAWADEE homeodomain homolog 1), KTF1, and SUVR2, although we failed to find the latter three proteins in Fritillaria persica, a species with a giant genome. Small RNAs of 24 nt in length were abundant only in angiosperms. Phylogenetic analyses of Dicer-like (DCL) proteins showed that DCL2 was restricted to seed plants, although it was absent in Gnetum gnemon and Welwitschia mirabilis. The data suggest that phases (1) and (2) of the RdDM pathway, described for model angiosperms, evolved with angiosperms. The absence of some features of RdDM in F. persica may be associated wit...Continue Reading

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Citations

Dec 3, 2016·Proceedings of the National Academy of Sciences of the United States of America·Israel AusinHaifeng Wang
Dec 21, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Wencai Wang, Xianzhi Zhang
Feb 15, 2018·Genes·Jaume PellicerIlia J Leitch
Aug 25, 2017·Genome Biology·Chenjiang YouXuemei Chen
Nov 4, 2016·G3 : Genes - Genomes - Genetics·Daniel Gonzalez-IbeasJill L Wegrzyn
Jul 1, 2020·Plant Cell Reports·R Wambui MbichiTao Wan
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Jul 14, 2019·BMC Plant Biology·Liuling PeiMaojun Wang
Dec 18, 2016·Genes & Development·Sylvie LahmyThierry Lagrange
Jun 15, 2019·BMC Genomics·Juan Pablo A OrtizSilvina C Pessino
Oct 28, 2019·Essays in Biochemistry·Sunil K Kenchanmane RajuChad E Niederhuth
Oct 9, 2020·PLoS Genetics·Robert M Erdmann, Colette L Picard
Jan 15, 2021·Current Opinion in Plant Biology·Eleanore J Ritter, Chad E Niederhuth
Mar 8, 2016·Current Opinion in Plant Biology·Alexandros Bousios, Brandon S Gaut
Aug 5, 2021·Scientific Reports·Sergio Alan Cervantes-PérezLuis Herrera-Estrella

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Datasets Mentioned

BETA
AT3G43920
AT5G20320
U42416.1

Methods Mentioned

BETA
electrophoresis

Software Mentioned

MUSCLE
RAxML
ImageQuant
CyMATE
TransDecoder
BLASTp
OrthoMCL
trimAl
Trinity

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