Despite the large amount of repetitive elements that surround the island, only the rice and maize genome sequences showed post-divergence TE insertions.
1,5% of the total maize ESTs (25.282 sequences) showed significant sequence homology (e-value < 1E-20) with one of the 56 analysed TE families (Additional file 1).
Phylogenetic analysis performed with the deduced NCED amino acid sequences showed that the six maize proteins fell into four monocot clusters that were distinguishable from the eudicot cluster (Fig. 4).
When applying our method to other maize data sets, High- C0 t derived sequences showed the greatest enrichment for low-copy sequences.
When all the treatments were planted to a maize test crop in the third year, herbaceous legume-based sequences showed the highest response to mineral fertilizer N compared with natural fallow-based sequences and continuous fertilized maize.
Blast searches with the rice GW2 protein sequence [GenBank: ABO31101] against the maize high throughput genomic sequence database [ 34] identified two maize bacterial artificial chromosome (BAC) clones, AC212189 on chromosome 4 and AC211190 on chromosome 5, that contain sequences showing high similarity to the rice protein.
Firstly, their cDNA and deduced amino acid sequences show very high sequence homology with SUT2s (90%) and the corresponding proteins (93%), respectively, of rice, barley and maize.
Representative sequences shown.
Although miRNA precursor sequences show high divergence except for miRNAs and miRNAs* regions, we found a predicted homolog for osa-miR159a.2 osa-miR159a.2ches in maize located 21 nucleotides upstream from the predicted maize miR159.
A similar study on genome-wide ASE analysis using massively parallel signature sequencing showed that 60%% of the genes in the maize hybrid meristems exhibited differential allelic expression (Guo et al. 2015).
The deduced amino acid sequence shows high homology with counterpart SnRK2 family members from rice, maize and Arabidopsis, implying the occurrence of SnRK2.8 before separation of monocots and dicots.
