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. 2019 Jul 1;11(7):1986-1996.
doi: 10.1093/gbe/evz115.

Loss of Wood Formation Genes in Monocot Genomes

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Free PMC article

Loss of Wood Formation Genes in Monocot Genomes

Danielle Roodt et al. Genome Biol Evol. .
Free PMC article

Abstract

Woodiness (secondary xylem derived from vascular cambium) has been gained and lost multiple times in the angiosperms, but has been lost ancestrally in all monocots. Here, we investigate the conservation of genes involved in xylogenesis in fully sequenced angiosperm genomes, hypothesizing that monocots have lost some essential orthologs involved in this process. We analyzed the conservation of genes preferentially expressed in the developing secondary xylem of two eudicot trees in the sequenced genomes of 26 eudicot and seven monocot species, and the early diverging angiosperm Amborella trichopoda. We also reconstructed a regulatory model of early vascular cambial cell identity and differentiation and investigated the conservation of orthologs across the angiosperms. Additionally, we analyzed the genome of the aquatic seagrass Zostera marina for additional losses of genes otherwise essential to, especially, secondary cell wall formation. Despite almost complete conservation of orthology within the early cambial differentiation gene network, we show a clear pattern of loss of genes preferentially expressed in secondary xylem in the monocots that are highly conserved across eudicot species. Our study provides candidate genes that may have led to the loss of vascular cambium in the monocots, and, by comparing terrestrial angiosperms to an aquatic monocot, highlights genes essential to vasculature on land.

Keywords: Zostera marina; eudicotyledons; monocotyledons; vascular cambium; vasculature; xylogenesis.

Figures

<sc>Fig</sc>. 1.
Fig. 1.
—Heat map representing presence and similarity of the 75 and 5,750 genes preferentially expressed in the xylem tissue of Populus trichocarpa from Hefer et al. (2015). A darker and lighter blue color indicate higher and lower sequence similarity, respectively. Cluster 1 includes genes that are the most conserved across most angiosperm species included in the study. Cluster 2 shows lowest conservation of xylem genes across the monocot species. Cluster 3 represents intermediate conservation across species. The seven monocot species together with the early diverging angiosperm Amborella trichopoda are grouped to the left of the heat map, while the 25 eudicot species are grouped to the right. The three clusters are labeled with a 1, 2, and 3 to the right of the image.
<sc>Fig</sc>. 2.
Fig. 2.
—Early cambial differentiation network constructed from literature (see text for details). The network represents the key genes and hormones involved in vascular cambium differentiation. Black arrows indicate positive regulation, while red lines indicate repression or downregulation. Filled blue bars indicate the conservation of genes in the monocots.
<sc>Fig</sc>. 3.
Fig. 3.
—Selected gene ontology enrichment descriptions of genes from Cluster 1 in figure 1 absent (red) and present (green) in the aquatic monocot Zostera marina. Description of the GO ID is shown in the list on the left, while their corresponding enrichments are indicated in colored circles on the right. Red and green circles represent the enrichment of genes absent and present in Z. marina, respectively. Depth of color and size of the circles indicate the enrichment significance of a particular GO term, with darker color and larger size specifying higher significance, and vice versa.

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