Additional file 3: Figure S2. of A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70Â % rule

Phylogenomic dissection of large prokaryotic orders. All largest possible clades are plotted for each taxonomic group. y-axis: average sequence identity between a clade and its sister group (I C-S); x-axis: number of species. A horizontal reference line is drawn corresponding to the average of the singleton I C-S greater than or equal to their third quartile. (TIF 937 kb

Additional file 5: Table S3. of A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70Â % rule

Annotations of top ten clusters with highest sequence identities for each taxonomic group. (XLSX 40 kb

Additional file 8: Figure S3. of A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70Â % rule

Phylogenomic dissection of prokaryotic groups based on clusters generated using the same procedure as for eukaryotes. All largest possible clades are plotted for each taxonomic group. y-axis: average sequence identity between a clade and its sister group (I C-S); x-axis: number of species. A horizontal reference line is drawn corresponding to the average of the singleton I C-S greater than or equal to their third quartile. (TIF 2094 kb

resources

The Zip-file include 8 Folders. Each containing phylogenetic trees and alignments for one dataset

Dating <i>numt</i> insertion.

<p>(A) Dating <i>numt</i> insertion based on a mitochondrial phylogenetic tree (black branches). An arrow indicates time of insertion and the <i>numt</i> branch is shown in red. The methodology can be used only in species where the mitochondrial rate of evolution is lower than the nuclear rate of evolution (e.g., mammals but not plants) and when the <i>numts</i> are long enough (>1 kb) to carry enough evolutionary signal. (B) Dating <i>numt</i> insertion based on patterns of presence and absence on a phylogeny. Few nuclear genomes and their genome alignment are used to identify <i>numt</i> insertions. Species that share the descendant from the common ancestor where the transfer occurred include the <i>numts</i> (red rectangle) whereas this <i>numt</i> is missing in the others.</p

Human polymorphic <i>numts</i> and <i>numts</i> that cause diseases.

<p>Human mitochondrial DNA (NC_001807) is shown in the inner circle, and <i>numt</i> insertions are shown in the outer circle. Polymorphic <i>numts</i> are shown in light green (<i>numts</i> exist in the reference genome) or dark green (<i>numts</i> are missing from the reference genome). <i>Numts</i> causing disease are shown in red. In each case, the reference and the SNP accession numbers (if available) are given. When a <i>numt</i> is inserted within gene, the gene name is indicated (green and red ellipses for polymorphic <i>numts</i> and for <i>numts</i> causing disease, respectively).</p

Blast analysis of 85 mitochondria against their nuclear genomes (BlastN, e-score = 0.0001).

<p>For each organism the number of BLAST hits as well as the unique number of bases in genomes is given (i.e. a base in the genome that has a BLAST hit to two repetitive mitochondria pieces it is count only once in <i>numt</i> content). Other available <i>numt</i> estimates are indicated with their references, where the corresponding search parameters are given.</p

Mechanism of <i>numt</i> insertion.

<p>Mitochondrial DNA has been suggested to get into the nucleus via a few different pathways. (A) The most supported pathway so far involve the degradation of abnormal mitochondria <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000834#pgen.1000834-Campbell1" target="_blank">[53]</a>. Several <i>yme</i> (yeast mitochondrial escape) strains show high level of DNA escape to the nucleus. <i>yme1</i> mutant cause the inactivation of YMe1p protein, a mitochondrial-localized ATP-dependent metallo-protease leading to high escape rate of mtDNA to the nucleus. Mitochondria of <i>yme1</i> strain are taken up for degradation by the vacuole more frequently than the wild-type strain. Other pathways to get mitochondrial DNA into the nucleus were suggested including: (B) lysis of mitochondrial compartment, (C) encapsulation of mitochondrial DNA inside the nucleus, (D) direct physical association between the mitochondria and the nucleus and membrane fusions. (E) Mitochondrial DNA that enters the nucleus can integrate into nuclear chromosomes. mtDNA integrated into the chromosome during the repair of DSBs in a mechanism known as non-homologous end-joining (NHEJ). The insertion involves two DSB repair events. Each can be repaired with or without the involvement of short microhomology. In microhomology-mediated NHEJ, base-pair complements are available between the <i>numt</i> and the chromosome ends, similar to the sticky ends created by restriction enzymes.</p

Additional file 3: of Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method

Contact residues in the SLA class II binding pockets based on HLA contacts (Hc)

S2 - S2.txt

alignment of first and the second codon positions 25246 positions in lengt