Loss of wood formation genes in monocot genomes
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Authors
Roodt, Danielle
Li, Zhen
Van de Peer, Yves
Mizrachi, Eshchar
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Abstract
Woodiness (secondary xylemderived from vascular cambium) has been gained and lostmultiple 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 xylemof 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 Zosteramarina 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 xylemin themonocots
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.
Description
Supplementary Figures:
Fig. S1: Comprehensive list of gene ontology enrichment descriptions for Cluster 1 in Figure 1 absent (red) and present (green) in Zostera marina. GO category (Biological Process, Cellular Component or Molecular Function) is shown in the left column and description of the GO ID in the middle column. The corresponding enrichments are indicated in the coloured circles. Red and green circles represent enrichment of genes absent and present in Z. marina, respectively. Depth of colour and circle size indicate the enrichment significance of a particular GO term, with darker colour and larger size specifying higher significance, and vice versa.
Fig. S2: Three heat maps representing similarity of genes present in the H, E1 and E2 expressions clusters from Sundell et al. (2017). A darker and lighter blue colour indicate higher and lower sequence similarity, respectively. Cluster 1 on each heat map includes genes that are the most conserved across most angiosperm species included in the study. Cluster 2 on each heat map shows lowest conservation of xylem genes across the monocot species. Cluster 3 on each heat map 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 maps, while the 25 eudicot species are grouped to the right. The three clusters in each heat map are labelled with a 1, 2, and 3 to the right of the image.
Fig. S3: Summary of the enrichment results obtained for Cluster 1 in Figure 1 after summarising the results with REViGO (Supek et al. 2011). GO category (Biological Process, Cellular Component or Molecular Function) is shown in the left column and description of the GO ID in the middle column. The corresponding enrichments are indicated with diamonds. The size of the diamonds indicates the enrichment significance of a particular GO term, with larger diamonds signifying higher significance, and vice versa.
Fig. S4: Summary of the enrichment results obtained for Cluster 3 in Figure 1. GO category (Biological Process, Cellular Component or Molecular Function) is shown in the left column and description of the GO ID in the middle column. The corresponding enrichments are indicated with diamonds. The size of the diamonds indicates the enrichment significance of a particular GO term, with larger diamonds signifying higher significance, and vice versa.
Fig. S5: The conservation of secondary cell wall development genes from Hussey et al. (2013). The three tiers as well as structural genes are indicated, and the level of conservation shown in the blue bar to the left.
Supplementary Tables: Table S1: Eudicot specific gene list Table S2: Populus trichocarpa and Arabidopsis thaliana gene IDs for genes found in the three heat map clusters from Figure 1 Table S3: Arabidopsis thaliana gene IDs for cluster 2 genes from Figure 1 with low sequence similarity compared to Amborella trichopoda Table S4: Gene descriptions of Arabidopsis thaliana genes present in Cluster 1 from Figure 1 Table S5: Gene descriptions of Arabidopsis thaliana genes present in Cluster 2 from Figure 1 Table S6: Gene descriptions of Arabidopsis thaliana genes present in Cluster 3 from Figure 1 Table S7: Gene names and Arabidopsis thaliana gene IDs for genes included in Figure 2 (The early cambial differentiation network) Table S8: Arabidopsis thaliana gene IDs for cluster 1 genes from Figure 1 absent from the genome of Zostera marina Table S9: Arabidopsis thaliana gene IDs for cluster 2 genes from Figure 1 absent from the genome of Zostera marina Table S10: Arabidopsis thaliana gene IDs for cluster 3 genes from Figure 1 absent from the genome of Zostera marina
Supplementary Tables: Table S1: Eudicot specific gene list Table S2: Populus trichocarpa and Arabidopsis thaliana gene IDs for genes found in the three heat map clusters from Figure 1 Table S3: Arabidopsis thaliana gene IDs for cluster 2 genes from Figure 1 with low sequence similarity compared to Amborella trichopoda Table S4: Gene descriptions of Arabidopsis thaliana genes present in Cluster 1 from Figure 1 Table S5: Gene descriptions of Arabidopsis thaliana genes present in Cluster 2 from Figure 1 Table S6: Gene descriptions of Arabidopsis thaliana genes present in Cluster 3 from Figure 1 Table S7: Gene names and Arabidopsis thaliana gene IDs for genes included in Figure 2 (The early cambial differentiation network) Table S8: Arabidopsis thaliana gene IDs for cluster 1 genes from Figure 1 absent from the genome of Zostera marina Table S9: Arabidopsis thaliana gene IDs for cluster 2 genes from Figure 1 absent from the genome of Zostera marina Table S10: Arabidopsis thaliana gene IDs for cluster 3 genes from Figure 1 absent from the genome of Zostera marina
Keywords
Vascular cambium, Eudicotyledons, Monocotyledons, Vasculature, Xylogenesis, Zostera marina
Sustainable Development Goals
Citation
Roodt, D., Li, Z., Van de Peer, Y. et al. 20119, 'Loss of wood formation genes in monocot genomes', v, vol. 11, no. 7, pp. 1986-1996.