CSCs identified from overlapping EvoPrints were annotated to include gene name hyphenated with consecutive numbers and were named based on their proximity to the nub and pdm genes.
However, it is worth noting that we observed a mRNA, BC035062, that is annotated to include an exon contained within the common 'intronic' duplication, suggesting these events may affect a splice variant.
For example, two drought-responsive miRNAs, osa-miR166e-3p osa-miR166e-3p osa-miR166e-3pa-miR169r-3p* [miRBase:MIMAT0000639], and osa-miR169r-3p* osa-miR169r-3p* osa-miR169r-3p*et alkaline neutral invertase and UDP-glucose 4-epimerase respectively, where each target are annotated to several GO biological processes including root development and carbohydrate metabolic process.
In the little brown bat, the Lalba gene is embedded in a large genomic fragment that was not annotated to include c12orf41 (although our BLAST searches did identify a very small fragment with strong similarity).
Seven SSRs could be annotated to developmental processes (including the flowering time gene FCA).
Among genes in 42.5 kb genomes with a GC content of 43.5%, 16 out of 47 open-reading frames (ORFs) were annotated to known functions, including RNA polymerase (RNAP) and phage structure proteins.
Add2 is annotated to several GO categories, including ' positive regulation of protein binding' and ' actin filament bundle assembly'.
Some of non-classical secreted proteins have been annotated to facilitate cellular activities including those associated with mobile genetic elements (transposases or phage associated; Additional file 3: Table S3) that may be moon-lighting [ 36].
As shown in Figure 2C, 28,556 unigenes were annotated to 4 top-hit species, including Glycine max, Arabidopsis thaliana, Medicago truncatula and Populus trichocarpa.
A list of SVAs from the repeat masker track of UCSC genome browser (http://genome.ucsc.edu/index.html) with Hg19 was generated and then manually annotated to include any components of the SVA that had not been included.
