We examined the sequence conservation of sno-lncRNAs by calculating PhastCons scores from multiple alignments of primate genomes.
It has been shown that the genes encoding evolutionarily conserved protein, duplicated in multiple sites along primate genomes, might contribute to interspecies phenotypic differences [ 14].
Using the results of BLAST-search we extracted orthologous gene sequences from the most recent assemblies of primate genomes and made multiple alignment using ClustalW algorithm [ 16].
For instance, the availability of genome sequence data for multiple primate species has shown that that our own genetic material is expanded by ~5% during the past 35 40 million years (divergence of New and Old World monkeys) of evolution through segmental duplications (SDs) and rearrangement events [ 42, 43].
To analyze L1PA7 and L1P3 expansion in the NWM genomes, we initially selected L1PA7 elements with intact open reading frame 2 (Oregionsginns in all of the primate genomes, and we conducted a multiple alignment of DNA sequences of their ORF2 regions using CLUSTALW2 (parameters: -type=dna -quicktree).
To elucidate the differences between L1PA7 in Platyrrhini and Catarrhini, we performed a multiple alignment of L1PA7 ORF2p across all complete elements in the seven primate genomes.
The conservation of micSeqs in multiple primate species provides an opportunity to locate their exact position in the human genome at the resolution of single nucleotide.
The total number of DDX11L gene copies ranges from 16 to 19 in the analyzed individuals (see the FISH analysis in the " DDX11L genes are present in multiple copies in primates' genomes" paragraph), even though these copies were collectively found in 18 different sites (see table 1).
Dr. Monaco said he had started a collaboration with Dr. Svante Paabo of Leipzig, Germany, who is studying the chimpanzee and other primate genomes.
The genomes of the common chimpanzee (2005) and bonobo (2012), orangutan (2011), gorilla (2012), and macaque monkey (2007) have already been identified, and the determination of other primate genomes is well underway.
