10.5061/DRYAD.68686
Huang, Ling
University of Michigan-Ann Arbor
Schiefelbein, John
University of Michigan-Ann Arbor
Data from: Conserved gene expression programs in developing roots from
diverse plants
Dryad
dataset
2016
Arabidopsis thaliana
Plant development
Oryza sativa
Zea mays
Selaginella moellendorffii
organ formation
roots
Cucumis sativus
Glycine max
2016-07-27T00:00:00Z
2016-07-27T00:00:00Z
en
https://doi.org/10.1105/tpc.15.00328
74452740 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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