Young Genes out of the Male： An Insight from Evolutionary Age Analysis of the Pollen Transcriptome

The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis （Betrdn et ah, 2002; Begun et ah, 2007; Dubruille et ah, 2012）, and thus an ＂out of testis＂ hypothesis for the emergence of new genes has been proposed （Vinckenbosch et ah, 2006; Kaessmann, 2010）. However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a num- ber of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and anti- microbial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an ＂innovation incubator＂ for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the ＂new genes out of the male＂ model revealed a common evolu- tionary force that drives reproductive barriers, species specification, and the upgrading of defensive mech- anisms against pathogens.

Mapping theArabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions

Metabolic genome-wide association studies （mGWAS）, whereupon metabolite levels are regarded as traits, can help unravel the genetic basis of metabolic networks. A total of 309Arabidopsis accessions were grown under two independent environmental conditions （control and stress） and subjected to untargeted LC-MS- based metabolomic profiling; levels of the obtained hydrophilic metabolites were used in GWAS. Our two- condition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci （p ≤ 1.0E-08）, 24.39% of which were environment-specific. Interestingly, differently from natural variation in Arabidopsis primary metabolites, which tends to be controlled by a large number of small-effect loci, we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites. The two-condition-based GWAS was fol- lowed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment. Through this integrative approach, we selected 70 key candidate associations between struc- tural genes and metabolites, and experimentally validated eight novel associations, two of them showing differential genetic regulation in the two environments studied. We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different ablotic environments for identifying metabollte-gene associations, providing novel global insights into the metabolic landscape of Arabidopsis.

Analysis of Short-Term Metabolic Alterations in Arabidopsis Following Changes in the Prevailing Environmental Conditions

Although a considerable increase in our knowledge concerning the importance of metabolic adjustments to unfavorable growth conditions has been recently provided, relatively little is known about the adjustments which occur in response to fluctuation in environmental factors. Evaluating the metabolic adjustments occurring under changing environmental conditions thus offers a good opportunity to increase our current understanding of the crosstalk between the major pathways which are affected by such conditions. To this end, plants growing under normal conditions were transferred to different light and temperature conditions which were anticipated to affect （amongst other processes） the rates of photosynthesis and photorespiration and characterized at the physiological, molecular, and metabolic levels following this transition. Our results revealed similar behavior in response to both treatments and imply a tight connec- tivity of photorespiration with the major pathways of plant metabolism. They further highlight that the majority of the regulation of these pathways is not mediated at the level of transcription but that leaf metabolism is rather pre-poised to adapt to changes in these input parameters.

Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures

As sessile organisms,plants are subject to a multitude of environmental variations including several which directly affect their interaction with the atmosphere.Given the indiscriminant nature of Rubisco,the relative rates of photosynthesis and photorespiration are known to be responsive to changes in gas composition.However,comprehensive profiling methods have not yet been applied in order to characterize the wider consequences of these changes on primary metabolism in general.Moreover,although transcriptional profiling has revealed that a subset of photorespiratory enzymes are co-expressed,whether transcriptional responses play a role in short-term responses to atmospheric compositional changes remains unknown.To address these questions,plants Arabidopsis thaliana（Arabidopsis） ecotype Columbia（Col-O） grown under normal air conditions were transferred to different CO_2 and O_2 concentrations and characterized at the physiological,molecular,and metabolic levels following this transition.The results reveal alterations in the components,which are directly involved in,or supporting,photorespiration,including transcripts and metabolite levels.The results further highlight that the majority of the regulation of these pathways is not mediated at the level of transcription and that the photorespiratory pathway is essential also in conditions in which flux through the pathway is minimized,yet suggest that flux through this pathway is not mediated at the level of transcription.