The Molecular Dialog between Flowering Plant Reproductive Partners Defined by SNP-Informed RNA-Sequencing

The molecular signatures of compatible and incompatible pollination

“…2c). Correlations between another recent SNP-based analysis, which identified pistil- and pollen tube-specific transcripts 8 hour after pollination 20 and the tissue/organ-specific transcripts showed similar trends to our stigma- and pollen-transcripts (Fig. 2c).…”

“…2c. However, while Leydon et al, 2017 used 12 % of reads that had SNPs among the total sequenced reads, in our analysis we took all the RNA-seq reads into account, including those without SNPs 20,21 . This difference in the approaches has likely contributed to making our analysis more exhaustive, as exemplified by the remarkable segregation we found between male transcripts and those derived from female and vegetative tissues (Fig.2 c).…”

“…1). It is worth noting that another SNP-based pipeline has recently been published 20 , identifying transcripts derived from the pistil and pollen tubes collected 8h after compatible pollination. Although we cannot compare the two analyses directly, as pollination time points were different and only compatibility was studied in Leydon et al, both analyses succeeded in distinguishing male and female transcripts as presented in Fig.…”

“…Here, inspired by previous RNA-seq analysis 20 , we developed a new experimental procedure coupled with a bioinformatic analysis of sequencing data to unravel the comprehensive molecular dynamics that occurs both in the stigma and pollen grain following compatible and incompatible pollinations. We took advantage of the SNPs existing between two distinct Arabidopsis thaliana accessions, one used as female (Col-0) and the other as male (C24), to differentiate male and female transcripts based on a new statistical methodology, ASE-TIGAR 21 which can take all sequenced reads in account even those without SNPs while previous study used only reads with SNPs 20 . Our analysis allowed the identification of 80 % of mRNAs according to their parental origin and revealed transcriptional changes occurring specifically in either the stigma or pollen grain/tube.…”

Evolutionary and ecological functional genomics, from lab to the wild

“…Three RNA‐seq papers (Lister et al ., ; Mortazavi et al ., ; Nagalakshmi et al ., ) on Arabidopsis, yeast and mice, respectively, mark the start of this tool's use for functional genomic studies. Contemporarily, RNA‐seq is used at ever‐larger scales for functional characterization of developmental, environmental response and economically important phenotypes (Becker et al ., ; Feng et al ., ; Giacomello et al ., ; Leydon et al ., ; Liu et al ., ), and is often used to validate epigenomic measurements (Wang et al ., ). There are numerous studies that employ whole‐genome gene expression analysis not just for model plant species and crops, but also for lesser‐known plant species including Japanese lawn grass (Xie et al ., ), Cunninghamia lanceolata (Cao et al ., ), mangrove fern (Zhang et al ., ), wild oil‐tea camelia (Chen et al ., ), curry tree (Meena et al ., ) and Banksia (He et al ., ).…”