Comparative analysis of citrus polyembryonic and monoembryonic ovule transcriptomes identifies candidate transcripts related to nucellar embryony initiation

Next-generation sequencing was employed to compare transcriptomic profiling of ovules at and prior to the appearance of nucellar embryony initial cells. To exclude the unwanted genetic background noise and variations among years, two biological replicates for each sample were set by sampling in two consecutive years from two pairs of polyembryonic and monoembryonic cultivars, i.e. one pair of mandarin and the other of grapefruit/pummelo. In that manner, 71 embryo-type enriched transcripts were determined by overlaying differentially expressed transcripts, derived from pairwise comparisons between polyembryonic and monoembryonic cultivars in each basic taxa, which revealed commonly genes that indeed regulated nucellar embryogenesis. Transcriptome profiling indicated that cell wall remodelling transcripts, such as pectinesterase, endochitinase, glucan endo-1,3-ß-glucosidase precursor, UDP-glucosyltransferase and laccase were significantly enriched in the polyembryonic cultivars. The expression of transcription factors containing AP2/ERF and WRKY domains were also up-regulated in polyembryonic cultivars compared with monoembryonic cultivars. In addition, the embryo-type enriched transcripts were associated with hormone regulation and signal transduction, as well as carbohydrate metabolism. Overall design: A total of 16 mRNA-Seq libraries were constructed, for the ovules of the two paired citrus varieties PK/CM and GF/PU at pre-NEI and NEI stages, with biological replicates. For each stage, trancriptomes were compared between the poly- and mono-embryonic genotype within each pair. The overlapped differentially expressed genes between the two pairs were identified as factors involved in nucellar embryogenesis of citrus