^aThe table is organized by position of the melanogaster proteins along the chromosomes, as reflected by their names using the chromosomal locations of the genes, e.g. Gr10a is the first Gr gene in the 10th division, which is on the X chromosome. The location of one gene unique to pseudoobscura DpGr93N, is obvious so it is interdigitated in the table. DmGr22b and 22d are polymorphic pseudogenes in melanogaster (see Robertson et al. 2003); the intact versions are used here and in analyses.

^bCG identifiers are provided for all the DmGrs, except the two polymorphic pseudogenes, but the protein isoforms (PA, PB, etc) are only shown for the three alternatively spliced genes - Gr23a, 28b, and 39a. The letters designating the alternatively spliced forms of Gr39a are not in sequential order of the placement of the first exons on the chromosome because historically the last of the four exons was recognized first (see also Figure 3). To avoid confusion FlyBase nomenclature was used which therefore differs from the naming in Clyne et al. (2000) and in Robertson et al. (2003). pseudogenes; with a “N” are genes present only in pseudoobscura.

^cThe DpGrs are given names best reflecting their orthologous or paralogous relationships with the DmOrs. Names ending with a “P” are pseudogenes; with a “N” are genes present only in pseudoobscura.

^dGA identifiers are given for DpGrs when available. Most of these are annotated genes/proteins. When my gene models differ from those in release 1.04 of the Dpse genome annotation in FlyBase as of July 2005 and published in Richards et al. (2005), then the identifier is followed by a “m” for “modified”. Most of these differences are instances where a few N- and/or C-terminal amino acids are missing from the r1.04 versions, but some involve inclusion of open in-frame introns, missing C-terminal exons, or missed GC intron donor splice sites. Some GA identifiers are “place holders” showing where an anticipated orthologous gene model belongs in the Dp genome browser at FlyBase, in which case they are followed by a “n” for “new”. GA identifiers are not available for some genes and all pseudogenes, indicated as “NA”.

^eSome DpGr gene models have N-terminal ORF extensions beyond a potential methionine start codon that aligns with the orthologous DmGr. These have not been included in these length figures, or in the FASTA files or alignments, but the lengths are noted here (Gr10b - 27aa, Gr21a - 55aa, Gr43a - 23aa, Gr61a - 15aa, Gr66a - 20aa, Gr89a – 18aa, and Gr98b - 53aa).

^fPercent identities are based on the “BLAST 2 SEQUENCES” algorithm at NCBI which includes only alignable sequence, so highly divergent proteins that do not completely align full-length are in fact more divergent than they appear herein.

^gRelease 2.0 of the 140Mbp pseudoobscura genome is in 16 major superscaffolds, ranging from entire chromosome arms for 2 and 3, to 4 or 5 superscaffolds for arms XL, XR, and 4, plus 2650 unmapped small scaffolds grouped in a 10.7Mbp “chromosome U”. The locations of the pseudoobscura genes are shown as the major fragment, e.g. “XL_1e” means “XL_group1e”, followed by the location in megabases according to the FlyBase pseudoobscura genome browser.

^hComments on genes include the number of shared introns, whether the gene was lost from, or duplicated in, one or other species, pseudogene status, and alternative splicing. DpGr10b lost intron “XXXXXX”; DpGr36a lost intron “k”; DpGr59e lost intron “1”; the first intron in DpGr59f is phase 2 instead of phase 1 in DmGr59f and other related genes – alternatively DpGr59f might start later; DpGr64b lost intron “r”; DpGr66a has an extra intron – need to figure out if novel or shared with others; Gr68a and Gr94a are both intronless in both species, and both are in introns of other genes (the only other such example is Gr39a), so might have resulted from insertion of reverse transcribed copies of cDNAs in a common ancestor.