  Context-dependent identification of orthologs customarily relies on conserved
gene order or whole-genome sequence alignment. It is shown here that
short-range context--as short as single maximal matches--also provides an
effective means to identify orthologs within whole genomes. On pristine
(un-repeatmasked) mammalian whole-genome assemblies we perform a genome
"intersection" that in general consumes less than one thirtieth of the
computation time required by commonly used methods for whole-genome alignment,
and we extract "non-embedded maximal matches," maximal matches that are not
embedded into other maximal matches, as potential orthologs. An ortholog
identified via non-embedded maximal matches is analogous to a "positional
ortholog" or a "primary ortholog" as defined in previous literature; such
orthologs constitute homologs derived from the same direct ancestor whose
ancestral positions in the genome are conserved. At the nucleotide level,
non-embedded maximal matches recapitulate most exact matches identified by a
Lastz net alignment. At the gene level, reciprocal best hits of genes
containing non-embedded maximal matches recover one-to-one orthologs annotated
by Ensembl Compara with high selectivity and high sensitivity; these reciprocal
best hits additionally include putatively novel orthologs not found in Ensembl
(e.g. over two thousand for human/chimpanzee). The method is especially
suitable for genome-wide identification of orthologs.
