Supporting Information
Tab. S1 Identified sequences of unigenes in 5’ to 3’direction (Tab_S1_POLLEN_RNAseq_poolUnigene_5-3.txt)
Tab. S2. Classification of unigenes of the TCA cycle (Tab_S2_POLLEN_RNAseq_metabolism
_TCA.xls)
Tab.
S3.
Comparison
between
pollen
unigenes
versus
vegetative
tissue
transcripts.(Tab_S3_pollen_vegTissueCompare_001.xls)
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).
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 Organisation of lily pollen sequences into functional categories (Bin classes) using the
Mercator software.
Fig.S3 Classification of the transcriptome to 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
Fig. S4How to visualize your own pollen transcriptome with MAPMAN. The appropriate data and
pathways are given as packed files (lilypollenRNAseq.7z) 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.
1
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).
2