1. Volume 8, Issue 6, Pages 935-945 (June 2015)
Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome 
Xiao Cui, Yang Lv, Miaolin Chen, Zoran Nikoloski, David Twell, Dabing Zhang 
Molecular Plant 
Volume 8, Issue 6, Pages (June 2015)
DOI: /j.molp
Copyright © 2015 The Author Terms and Conditions

2. Figure 1
Phylostratigraphic Profiles and General Features of Rice and Arabidopsis Genes.
Numbers in parentheses show the number of genes in each phylostratum (PS1–PS13). The numbers of genes in major phylostrata are proportional to the size of the filled circles. Here, we define old genes as genes from PS1 to PS3 (blue) and new genes as those from PS11 to PS13 (red).
(A) Phylostratigraphic profile of rice genes.
(B) Phylostratigraphic profile of Arabidopsis genes.
(C) Gene features of new genes and old genes. The observed differences of gene features between new genes and old genes are significant at the level (permutation test). ∗∗∗ denotes that the difference is statistically significant with P <
(D) Percentage of genes with/without known function annotations in new genes (red) and old genes (blue).
PS, phylostratum; Cell.org, cellular organism; TSOG, taxon-specific orphan genes; SSOG, species-specific gene; Osa, Oryza sativa; Ath, Arabidopsis thaliana.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

3. Figure 2
Gene Ontology (GO) Enrichment for Old Genes and Young Genes in Arabidopsis.
(A) The top 10 most significant biological process GO terms of old genes.
(B) Significant biological process GO terms of young genes.
(C) The top 10 most significant cellular component GO terms of old genes.
(D) Significant cellular component GO terms of young genes.
Number of query genes in each GO term and their enrichment against all genes in the same GO term are shown in parentheses.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

4. Figure 3
Transcriptome Age Index (TAI) Profiles across Different Groups of Tissues.
(A and B) The TAI profiles across 18 tissue groups in rice (A) and 22 tissues groups in A. thaliana (B). The observed patterns of TAI are significant (P < 0.0001), tested by permutation test.
(C and D) Relative expression values of the old genes (PS1–PS3) and young genes (PS11–PS13) across different tissues in rice (C) and A. thaliana (D).
Pre-anther, anther before meiosis; mei-anther, anther at meiotic stage; uni-pollen, pollen at uni-cellular stage; bi-pollen, pollen at bi-cellular stage; tri-pollen, pollen at tri-cellular stage; m-pollen, mature pollen; germ-pollen, germinating pollen; v-apex, vegetative shoot apex; r-apex, reproductive shoot apex.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

5. Figure 4
Transcriptome Divergence Index (TDI) Profiles across Different Tissues.
(A) Rice.
(B) Arabidopsis.
(C and D) Relative expression values of young genes with syntenic evidence across different tissues in rice (C) and A. thaliana (D).
The orange areas highlight data for the male germ cell and male gametophyte. Higher TDI value indicates more divergent transcriptome.
Pre-anther, anther before meiosis; mei-anther, anther at meiotic stage; uni-pollen, pollen at uni-cellular stage; bi-pollen, pollen at bi-cellular stage; tri-pollen, pollen at tri-cellular stage; m-pollen, the mature pollen grain stage; germ-pollen, germinating pollen; v-apex, vegetative shoot apex; r-apex, reproductive shoot apex.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

6. Figure 5
Correlation between TAI and Expression Patterns of Different Groups of Transcripts.
(A) Scatter plot of TAI versus average absolute expression values of probes across different tissues. Colors indicate classification of tissues in groups. Genic probes match genes; inter-genic probes match inter-genic regions; anti-sense probes match anti-sense strand of genes. TAI is slightly negatively correlated with absolute average expression levels of genic probe sets (β = −0.101, R2 = 0.67, P < 2.2e−16), but strongly correlated with anti-sense (β = 1.714, R2 = 0.98, P < 2.2e−16) and inter-genic probe sets (β = 1.107, R2 = 0.94, P < 2.2e−16).
(B) Violin plot showing the distribution of correlation coefficients between TAI and expression level of different groups of genes. All, all genes on the microarray; Old, old genes (PS1–PS3); Young, young genes (PS11–PS13); TE, transposable element; Type I, retrotransposons; Type II, DNA transposons.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

7. Figure 6 The Out of Male Model for Emergence of New Genes.
The special chromatin state of non-coding regions in post-meiotic male gametes facilitates promiscuous transcription, which in turn provides raw material for the emergence of new genes. Young genes tend to be firstly expressed in male gametophyte. Male gametophyte competition acts as a pilot trial or proving ground for the function of new genes, eliminating gametes that carry harmful genetic changes and fixing changes with neutral or beneficial effects. In the longer term, some young genes may gain regulatory elements of promoters and expression in sporophytic tissues.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions