Fig. 8

Key processes and differentially expressed genes (DEGs) differ between Ae. arabicum M⁺ and NM seeds. a Timing of key processes during development and maturation of A. thaliana seeds. Dormancy and desiccation tolerance coincides with changes in water, abscisic acid (ABA) and triacylglycerol (TAG) contents, seed weight, nuclear size and chromatin condensation, endosperm proportion and germinability; Data from [32, 41, 55]. b Selected Ae. arabicum DEG putative ortholog expression during A. thaliana seed development and maturation. Cumulative transcript abundances for A. thaliana putative orthologs of Ae. arabicum 21 histone and 119 ribosomal protein genes (Additional file 3: Figure S4); individual abundances for RNA polymerase II large subunit (AtNRPB1), oleosin AtOLE2 (seed storage), heat shock factor AtHSFA9 (longevity), and AtNYE1 (chlorophyll degradation); data from Arabidopsis eFP browser [74] and [29,30,31]. c Expression of late embryogenesis abundant (LEA) proteins, seed maturation master regulators (AtLEC1, AtLEC2, AtABI3, AtFUS3) and WRINKLED1 (AtWRI1), a transcription factor associated with enhanced fatty acid and TAG biosynthesis during A. thaliana seed maturation; data from Arabidopsis eFP browser and [29,30,31, 58]. d Expression of selected Ae. arabicum DEGs for ribosomal proteins, histones, NRPB1 (RNAseq) and histone acetyltransferase HAC1 (qRT-PCR) in M⁺ and NM seeds. Cumulative RPKM values presented for 21 histone and 119 ribosomal protein genes of Ae. arabicum (Additional file 3: Figure S4). A * indicates a significant difference between M⁺ and NM seeds based on using a t-test (p < 0.05); n.s. means ‘not significant’. e Expression of RNA polymerase II complex and associated factors [50, 51] that mediate transcription including initiation, elongation and processing of transcripts in Ae. arabicum dry seed morphs. Red text indicates factor identified as NM-high DEG with expression ratio (NM / M⁺) indicated. Note core NRPB1/2 transcript abundance and most factors are several-fold higher in NM seeds. f Seed maturation master regulators expression (RNAseq, ABI3 also by qRT-PCR), oleosins, NYE1 and HSFA9 in dry M⁺ and NM Ae. arabicum seeds. g Selected Ae. arabicum LEA expression in dry M⁺ and NM seeds (RNAseq and qRT-PCR). The presented dehydrin is the putative ortholog of At4G39130. Error bars indicate mean ± SEM for qRT-PCR experiments. For the plotted RPKM values of single genes from the RNAseq data we used the result of the DEG detection pipeline (edgeR + NOISeq + DESeq2) as the indicator of significance