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The evolution of CHROMOMETHYLTRANSFERASES and gene body DNA methylation in plants

ABSTRACT: The evolution of gene body methylation (gbM) and the underlying mechanism is poorly understood. By pairing the largest collection of CHROMOMETHYLTRANSFERASE (CMT) sequences (773) and methylomes (72) across land plants and green algae we provide novel insights into the evolution of gbM and its underlying mechanism. The angiosperm- and eudicot-specific whole genome duplication events gave rise to what are now referred to as CMT1, 2 and 3 lineages. CMTε, which includes the eudicot-specific CMT1 and 3, and orthologous angiosperm clades, is essential for the perpetuation of gbM in angiosperms, implying that gbM evolved at least 236 MYA. Independent losses of CMT1, 2 and 3 in eudicots, and CMT2 and CMTmonocot+magnoliid in monocots suggests overlapping or fluid functional evolution. The resulting gene family phylogeny of CMT transcripts from the most diverse sampling of plants to date redefines our understanding of CMT evolution and its evolutionary consequences on DNA methylation.

ORGANISM(S): Torreya taxifolia Diplazium proliferum Nepenthes bicalcarata Celtis occidentalis Chamaecyparis hodginsii Amentotaxus argotaenia Hypericum perforatum Cephalotaxus harringtonia Papuacedrus papuana Pereskia grandiflora Equisetum Synsepalum dulcificum Cyathea Amentotaxus formosana Selaginella kraussiana Dacrydium balansae Microsorum punctatum Manoao colensoi Psilotum Cissus quadrangularis Impatiens niamniamensis Thuja sutchuenensis Juniperus virginiana Aloe vera Urtica dioica Cyperus papyrus Lupinus angustifolius Encephalartos horridus Yucca brevifolia Gnetum gnemon Kalanchoe tomentosa Dacrycarpus compactus Araucaria Aristolochia grandiflora

PROVIDER: GSE81702 | GEO | 2017/03/16

SECONDARY ACCESSION(S): PRJNA322330

REPOSITORIES: GEO

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Project description:The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ dramatically among angiosperm lineages, but in general, sterile perianth organs surrounding stamens (male reproductive organs) and carpels (female reproductive organs) constitute the basic floral structure. However, the basal angiosperm lineages exhibit spectacular diversity in the number, arrangement, and structure, of floral organs, while the evolutionarily derived monocot and eudicot lineages share a far more uniform floral ground plan. As such, regulatory mechanisms underlying the archetypal floral plan, for instance that of the eudicot genetic model Arabidopsis thaliana, are unlikely to apply to the original flowers. Here we show that broadly overlapping transcriptional programs characterise the floral transcriptome of the basal angiosperm Persea americana (avocado), while floral gene expression domains are typically organ-specific in Arabidopsis. Our findings extend the âfading bordersâ model for basal angiosperms from organ identity genes to the downstream floral transcriptome, and suggest that the combinatorial mechanism for organ identity may not operate in basal angiosperms as it does in Arabidopsis. Furthermore, fading expression of components of the stamen transcriptome in central and peripheral regions of Persea flowers resembles the developmental program of the hypothesized gymnosperm âfloral progenitorâ. Accordingly, in contrast to the canalized organ-specific regulatory apparatus of Arabidopsis, floral development may have been originally regulated by overlapping transcriptional cascades with fading gradients of influence from focal to bordering organs. Expression profiles of inflorescence buds, pre-meiotic floral buds, inner and outer tepals, stamens, carpels, initiating fruit, and leaves were assessed in an interwoven double loop design for eight samples with 16 arrays. Sample materials were collected from two individuals (biological replicates) cultivated on the University of Floridaâs Gainesville campus, and RNA was isolated twice for technical replication. Thus, four RNA extractions from each of the eight tissue types listed above were individually labeled with Cy3 (twice) or Cy5 (twice) and hybridized with four other Cy3 or Cy5 labeled samples as a dual channel array system.

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The evolution of CHROMOMETHYLTRANSFERASES and gene body DNA methylation in plants

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