Loss of wood formation genes in monocot genomes

Roodt, Danielle; Li, Zhen; Van de Peer, Yves; Mizrachi, Eshchar

Loss of wood formation genes in monocot genomes

dc.contributor.author	Roodt, Danielle
dc.contributor.author	Li, Zhen
dc.contributor.author	Van de Peer, Yves
dc.contributor.author	Mizrachi, Eshchar
dc.contributor.email	eshchar.mizrachi@fabi.up.ac.za	en_ZA
dc.date.accessioned	2020-08-24T08:12:12Z
dc.date.available	2020-08-24T08:12:12Z
dc.date.issued	2019-07
dc.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.
dc.description	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
dc.description.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.	en_ZA
dc.description.department	Biochemistry	en_ZA
dc.description.department	Forestry and Agricultural Biotechnology Institute (FABI)	en_ZA
dc.description.department	Genetics	en_ZA
dc.description.department	Microbiology and Plant Pathology	en_ZA
dc.description.librarian	am2020	en_ZA
dc.description.sponsorship	The National Research Foundation of South Africa, the University of Pretoria Research Development Programme (RDP) and the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement 322739—DOUBLEUP as well as a postdoctoral fellowship from the research fund of UGent.	en_ZA
dc.description.uri	https://academic.oup.com/gbe	en_ZA
dc.identifier.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.	en_ZA
dc.identifier.issn	1759-6653 (online)
dc.identifier.other	10.1093/gbe/evz115
dc.identifier.uri	http://hdl.handle.net/2263/75865
dc.language.iso	en	en_ZA
dc.publisher	Oxford University Press	en_ZA
dc.rights	© The Author(s) 2019. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License.	en_ZA
dc.subject	Vascular cambium	en_ZA
dc.subject	Eudicotyledons	en_ZA
dc.subject	Monocotyledons	en_ZA
dc.subject	Vasculature	en_ZA
dc.subject	Xylogenesis	en_ZA
dc.subject	Zostera marina	en_ZA
dc.title	Loss of wood formation genes in monocot genomes	en_ZA
dc.type	Article	en_ZA