Tab. S4 Top 10 down-regulated transcripts in lily pollen compared to vegetative
tissue. The Lilium longiflorum pollen transcripts (access. no. ERP002303) were compared
with the vegetative tissue transcriptome of oriental lily (access. no. SRX250152).
Pollen transcript unigene
log2-fold
identifier
change
Unigene7226
-11.1
L. longiflorum chloroplast, complete genome
Unigene24307
-10.1
light harvesting protein 1
Unigene25484
-9.8
photosystem II oxygen evoling complex protein 1
Unigene13730
-9.7
L. longiflorum chloroplast, complete genome
Unigene11792
-8.9
glutamine synthetase
Unigene9929
-8.8
Unknown
Unigene11119
-8.8
glutamine synthetase
Unigene16580
-8.6
L. longiflorum chloroplast, complete genome
Unigene2046
-8.3
L. longiflorum chloroplast, complete genome
Unigene2749
-8.2
ATP synthase CF0 subunit, chloroplast
Annotation (BLAST)
biological process
cellular component
molecular function
Fig.S1 Classification of the lily pollen transcriptome to GO classes. Sequences were classified
to groups of the GO (Gene Ontology) data base. The number of identified sequences (number
of genes) for each class is given in logarithmic scale.
Fig.S2 Organization of lily pollen sequences into functional categories (bin classes) using the
Mercator software.
A
B
C
Fig.S3 Classification of the transcriptome to mayor metabolic pathways by MAPMAN. Each box
presents an unigene which was classified into the given pathway categories. A. Lilium pollen
transcriptome data. B. Transcriptome data obtained from 6 different Lilium oriental hybrid tissues
(Du et al., 2014). Grey dots: BIN classses without any identified unigene or gene C. Up- (green) and
down-regulated (red) lily pollen transcripts compared with the transcript numbers of Lilium
oriental hybrid tissue. Data from Tab. S3 were used to construct Fig. S3C.
PATHWAYS MAPPINGS
EXPERIMENTS
Fig. S4 How to visualize your own pollen transcriptome with MAPMAN. The appropriate data and
pathways are given as packed files (lilyPollenRNAseq_supplements_Lang_etal_2014.zip) and should
be unpacked and copied into the indicated directories of the MAPMAN software.
Fig. S5 Comparison between pollen sequences and sporophytic tissue sequences / Amborella
genome. The percentage of identified Arabidopsis pollen genes from Loraine et al. (2013, orange),
the percentage of identified unigenes of the present study (Lilium pollen, Lang et al., dark red), the
Amborella CDSs (olive green), Lilium oriental hybrid tissue (Du et al., green) and Lilium longiflorum
leaf tissue (Shahin et al., 2012, blue-green) were compared. The percentages of identified genes
were calculated for each MAPMAN Bin class 1 to 34.
A
B
C
D
E
Fig. S6 MA plots of comparison between pollen unigenes and transcripts of the vegetative tissue
pool. A. MA plot of Lilium pollen versus Lilium oriental hybrid tissue (L-6Tis). The log2 fold change is
plotted against the log2 of the average expression. According to the assumption that under most
experimental conditions the bulk of genes of an organism are not responding differentially, the cloud
of points centers around a log2 fold change of 0 (black dots). Red dots indicate pollen unigenes with
estimated changes in expression level (P < 0.01) .
B. and C. The middle panel shows similar plots but pollen and L-6Tis reads were mapped to the
respective unigenes (B) , or mapped to the unigenes and length differences were corrected (C).
D. and E. Finally, the lower panel shows the plots for the analysis Lilium pollen versus the 454 read
dataset of Shahin et al. (2012) using once again their unigenes without correcting for length (D) and
with a unigene length correction (E). For (B)-(E) a trendline was added for illustration
Fig. S7 Molecular phylogenetic analysis of
plasma membrane H+ ATPase sequences
from Lilium pollen and sporophytic Lilium
tissue using maximum likelihood method.
Assembled amino acid sequences with
homologies to P-type PM H+ ATPases were
aligned with MUSCLE and a phylogenetic tree
was generated using Mega 6 software [3].
Sequences from pollen transcripts (L-pollen),
leaf transcripts (L-leaf) and from pooled tissue
(L-6Tis) were compared. The full-length ORFs
of the pollen PM H+ ATPases LilHA1
(AY029190) and LilHA2 (EF397610.2) were
included which clustered only with pollen
transcripts (red circle).
The following settings were used for
generation of the phylogenetic tree:
Maximum Likelihood method based on the
Poisson correction model [1]. The bootstrap
consensus tree inferred from 500 replicates
[2] is taken to represent the evolutionary
history of the sequences analyzed [2].
Branches corresponding to partitions
reproduced in less than 50% bootstrap
replicates are collapsed. Initial tree(s) for the
heuristic search were obtained automatically
by applying Neighbor-Join and BioNJ
algorithms to a matrix of pairwise distances
estimated using a JTT model, and then
selecting the topology with superior log
likelihood value. The analysis involved 23
amino acid sequences. There were a total of
1042 positions in the final dataset.
Evolutionary analyses were conducted in
MEGA6 [3].
1. Zuckerkandl E. and Pauling L. (1965). Evolutionary
divergence and convergence in proteins. In Evolving
Genes and Proteins, V. Bryson, H.J. Vogel (eds.), pp. 97166. Academic Press, New York.
2. Felsenstein J. (1985). Confidence limits on phylogenies:
An approach using the bootstrap. Evolution 39:783-791.
3. Tamura K., Stecher G., Peterson D., Filipski A., and
Kumar S. (2013). MEGA6: Molecular Evolutionary
Genetics Analysis version 6.0. Molecular Biology and
Evolution 30: 2725-2729.