These differences remain significant when self-interactions and interactions among proteins encoded by paralogs are removed from the analysis (P = 0.049), or when genes are classified as duplicated or singleton based on whether they present annotated paralogs in the Ensembl plants database release 14 (Kersey et al. 2012) (P = 1.62 × 10−4).
Through comparative analysis we identified and manually curated a further 510 P. yoelii genes which have clear orthologs in the P. falciparum genome, but were not present or incorrectly annotated in the current annotation.
For example, even if 95% of genes were present and correctly annotated in each assembly, we would only expect 77% (0.95) of genes to be present and correctly assigned to sets of orthologous genes in all species (assuming assembly biases are uncorrelated).
c Orthologous sequence present, but ORF annotated in reverse direction.
At present, there are 896 miRNA annotated in the human genome (miRBase Version 14.0).
In total, 182 potentially WRKY-encoding genes were identified and annotated in the present work (Table 1 and Additional file 1).
Given are the protein names, gene model names and protein identification numbers of those loci which were annotated in the present study.
Regarding the domestic dog SAMD9L, this gene is present in NCBI and is annotated in Ensembl, but in this latter database the sequence was missing seventy-four nucleotides when compared to the sequence in NCBI.
Other genes encoding HSPs were also annotated in the present study (Additional file 7), including members from the HSP40, HSP60, HSP70, HSP90 classes; a total of 19 members of HSPs were annotated for P. viridis.
Of the 5'-UTRs from 914 genes annotated in the present study, the 5'-UTRs of the protein kinase PAS_chr3_0850 (GCN2) and PAS_chr2-1_0459 (KOG1), involved in growth control, were selected and monitored for IRES activity.
