The Grape implementation conserves a copy of the exact software and configuration used for a given set of analyses, guaranteeing forward reproducibility.
Martin et al. [ 16] reported that some genes encoding for cyanobacterial proteins and identified in the plant nuclear genome still conserve a copy in the chloroplast genome.
Based on these reports we evaluated the degree of disorder in both nuclear-encoded proteins, which were transferred from the plastid to the nuclear genome, and those transferred to the nucleus that also still conserve a copy in the chloroplast genome.
Since these regions have the same number of copies in 3 relatively distant species, we assumed these were conserved in a copy number neutral stage.
Besides, it has confirmed a pattern of one conserved copy and one accelerated copy for both genes, and has revealed the action of positive selection on several regions of the fast-evolving ago-1b.
Nitric oxide synthase, involved in the biosynthesis of nitric oxide as a defense mechanism, is a highly conserved single copy gene in Arabidopsis, Ricinus, Populus, and Oryza, whereas in H. brasiliensis there are 4 copies.
Instead of aligning the positionally conserved copy of a repetitive DNA segment (a la Mauve), glocal methods construct a multiple alignment of all homologous copies of the repetitive segment, regardless of whether they are orthologous or paralogous.
GI is a highly conserved single copy gene in Arabidopsis, rice and Brachypodium (where it has a proven roles in flowering time [36], [37] and in barley (Table 1).
GBSS1 is a well conserved single copy nuclear gene in the grass family with potential for generating a universal approach to grass fingerprinting.
This assay is based on quantitative-PCR amplification of a 41 bp, 129 bp and 305 bp fragment of a highly conserved single copy gene (KAPA Human Genomic DNA Quantification and QC Kit, Kapa Biosystems).
