DOI: 10.5061/dryad.68686
title: Data from: Conserved gene expression programs in developing roots from diverse plants

description: The molecular basis for the origin and diversification of morphological
 adaptations is a central issue in evolutionary developmental biology.
 Here, we defined temporal transcript accumulation in developing roots from
 seven vascular plants, permitting a genome-wide comparative analysis of
 the molecular programs used by a single organ across diverse species. The
 resulting gene expression maps uncover significant similarity in the genes
 employed in roots and their developmental expression profiles. The
 detailed analysis of a subset of 133 genes known to be associated with
 root development in Arabidopsis thaliana indicates that most of these are
 used in all plant species. Strikingly, this was also true for root
 development in a lycophyte (Selaginella moellendorffii), which forms
 morphologically different roots and is thought to have evolved roots
 independently. Thus, despite vast differences in size and anatomy of roots
 from diverse plants, the basic molecular mechanisms employed during root
 formation appear to be conserved. This suggests that roots evolved in the
 two major vascular plant lineages either by parallel recruitment of
 largely the same developmental program or by elaboration of an existing
 root program in the common ancestor of vascular plants.
description: Supplemental DataSet
 1Processed RNA-Seq Gene
 Expression Values in FPKM. Expression data was obtained from six
 angiosperm plant species, from three root development zones (MZ, EZ, and
 DZ), and with three biological replicates each.Supplemental_DataSet1.xlsxSupplemental DataSet 2GreenPhyl Defined Gene Families. Genes IDs are included for the seven vascular plants in this study that are present in the 18110 families defined by the GreenPhyl database.Supplemental_DataSet2.xlsxSupplemental DataSet 3Distribution of Root-Expressed Genes by Family. The number of root-expressed and non-expressed genes from each plant species in each of the 18110 GreenPhyl defined families. Root expressed genes were defined as those exhibiting FPKM ≥ 0.5 in at least one root development zone, with at least 2 of 3 independent biological replicates generating reads.Supplemental_DataSet3.xlsxSupplemental DataSet 4Arabidopsis Genes Preferentially Expressed in Root Developmental Zones. List of Arabidopsis genes preferentially expressed in the meristematic, elongation, and differentiation zones of the primary root. Differential expression analysis was performed by edgeR tag-wise dispersion with upper quartile normalization method (FC ≥ 2 and FDR ≤ 0.05).Supplemental_DataSet4.xlsxSupplemental DataSet 5Clustering of Root-Expressed Genes. Temporal gene expression profile types were assigned by fuzzy C-means clustering.Supplemental_DataSet5.xlsxSupplemental DataSet 6Supergene Expression in Three Development Zones. The expression in the three zones (meristematic (MZ), elongation (EZ), and differentiation (DZ)) of six angiosperm species and the expression profile types (1 - 9) assigned by fuzzy C-Means clustering are presented for all 18110 GreenPhyl-defined families. Supergene expression was generated by summing all the transcript expressions from the same species within a given family. Type 0 indicated less than 2 fold-change across development zones. NA = no gene present or not root-expressed.Supplemental_DataSet6.xlsxSupplemental DataSet 7Supergene Connectivity Values (CNV) for 6161 families possessing root-expressed genes (average FPKM ≥ 0.5 in at least one development zone) from six angiosperm plant species.Supplemental_DataSet7.xlsxSupplemental DataSet 8Processed RNA-Seq Gene Expression Values in FPKM. Expression data was generated for seven vascular plant species, two root development zones (meristematic (MZ) and overlapping elongation/differentiation (EDZ)) with three biological replicates each.Supplemental_DataSet8.xlsxSupplemental DataSet 9Classification of Genes by Expression Profile. Gene expression fold-change types were assigned to each root-expressed genes from seven vascular plant species.Supplemental_DataSet9.xlsxSupplemental_DataSet10Supergene Expression and Profile Types. Supergene expression in two development zones (meristematic (M) and overlapping elongation/differentiation (ED)) of seven vascular species and the expression profile types (1 - 5) assigned by EDZ/MZ fold-change for all 18110 GreenPhyl-defined families.Supplemental DataSet 11Alignment of gene sequences from six angiosperm species. Sequence alignment files are included for each of the phylogenetic trees containing six angiosperm species.Supplemental_DataSet11.zipSupplemental DataSet 12Alignment of gene sequences from five plant species. Sequence alignment files are included for each of the phylogenetic trees containing the five plant species.Supplemental_DataSet12.zip