Genome group differences in over/underabundance of protein families w/r Daphnia, using Superfamily data (supfam.org) 36 eukaryote genomes from supfam.org were used: 18 invertebrate and 17 vertebrate. Of these 14 are aquatic, 21 are terristrial. Excluded were fungi, plants, protists. Family subset is taken from Daphnia's most significant deviations 38 of 772 families. Score is root mean square deviation from expected gene count (genome x family) contingency table. Significant (p<0.05) t-test results of RMSD are listed between aquatic/terristrial groups, and invert./vert. groups. 4 families have significant aquatic vs terristrial average difference. 28 families have significant invertebrate vs vertebrate average difference. #... 4 deviant families in Daphnia w/ aquatic-terristrial differences "aquatic-terristrial fam sf81320 Rhodopsin-like" ** daphnia overabundant "aquatic-terristrial fam sf51665 Xylose isomerase" ** daphnia overabundant "aquatic-terristrial fam sf53452 beta 1,4 galactosyltransferase (b4GalT1)" ** daphnia overabundant "aquatic-terristrial fam sf54929 Canonical RBD" * underabundant daphnia "aquatic-terristrial fam sf47114 Nucleosome core histones" * daphnia overabundant #..... aquatic Rhodopsins literature ...... Protein Structural Influences in Rhodopsin Evolution Lorraine Marsh* and Carole S. Griffiths Molecular Biology and Evolution 2005 22(4):894-904; doi:10.1093/molbev/msi081 >> has phylo tree separating Rhodopsins of teleost, mammal, amphibian, lizard/lamprey/chicken/alligator groups. "The Asn83 form produces a rhodopsin that is blueshifted relative to the Asp83 form, which may be more adaptive in aquatic environments. " Environmental Genome Shotgun Sequencing of the Sargasso Sea JC Venter, K Remington, JF Heidelberg, AL Halpern, et al. Science. 2004 Apr 2;304(5667):66-74. We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. < **** #... Xylose isomerase >> bacterial papers mostly ... Genetic Analysis of a Novel Pathway for D-Xylose Metabolism in Caulobacter crescentus. Craig Stephens, et al. Journal of Bacteriology, March 2007, p. 2181-2185, Vol. 189, No. 5 ... xylose metabolism has not been further examined in these diverse species. We speculate that they share with C. crescentus a common pathway for D-xylose degradation, encoded in a gene cluster that may have been horizontally transferred in aquatic and/or soil habitats. #.... beta 1,4 galactosyltransferase There are hints in google-search for this of relations to aquatic uses, but I've not pinned down this one (non-free articles have the details :) #... Core nucleosome histones .. important in several nuclear protein functions including these Anti-microbial properties of histone H2A from skin secretions of rainbow trout, Oncorhynchus mykiss - all 4 versions Č JM Fernandes, GD Kemp, MG Molle, VJ Smith - Biochem. J, 2002 - biochemj.org Isolation and identification of antimicrobial components from the epidermal mucus of Atlantic cod (Gadus morhua). Bergsson G, Agerberth B, Jšrnvall H, Gudmundsson GH. FEBS J. 2005 Oct;272(19):4960-9 the antimicrobial proteins were identified as histone H2B..etc. The broad spectra of antimicrobial activities in the cod mucus... contribute to the innate host defence of cod. #.... Organism genomes compared ............... Aquatic-Terristrial Invert/Vert genomes from Supfam.org, feb2008: Sp Taxa Habit Name ax a t Aedes aegypti 44_1a (all transcripts) ag a t Anopheles gambiae 44_3g (all transcripts) ai a t Apis mellifera 37.2d (all transcripts) om a t Bombyx mori bv v t Bos taurus 44_3a (all transcripts) bf i a Branchiostoma floridae 1.0 (Amphioxis: invert/vert transition, aquatic swimmer) ce i t Caenorhabditis elegans WormBase WS147 (all transcripts) cw i t Caenorhabditis briggsae 2 dg v t Canis familiaris 44_2b (all transcripts) i1 i t Capitella sp. I (polychaete worm) c0 i a Ciona savignyi 44_2c (all transcripts) (Urochordata, sea squirt) is i a Ciona intestinalis 44_2e (all transcripts) ie a t Culex pipiens quinquefasciatus da v a Danio rerio 47_7a (all transcripts) d7 a a Daphnia pulex dm a t Drosophila melanogaster FlyBase 4.2 (all transcripts) do a t Drosophila pseudoobscura FlyBase 1.04 gg v t Gallus gallus 44_2b (all transcripts) gc v a Gasterosteus aculeatus 44_1b (all transcripts) (stickleback fish) hs v t Homo sapiens 47_36i (all transcripts) gy i a Lottia gigantea (marine mollusk) ru v t Macaca mulatta 44_10d (all transcripts) op v t Monodelphis domestica 44_5 (all transcripts) mm v t Mus musculus 48_37a (all transcripts) nz a t Nasonia vitripennis nw i a Nematostella vectensis 1.0 (Sea anemone, fresh aquatic preditor worms, insects,) oh v t Ornithorhynchus anatinus 43_1a (all transcripts) ol v a Oryzias latipes 44_1a (all transcripts) (killifish) xp v t Pan troglodytes 44_21c (all transcripts) rn v t Rattus norvegicus 44_34n (all transcripts) tu i a Strongylocentrotus purpuratus (purple sea urchin) to v a Takifugu rubripes 44_4e (all transcripts) tn v a Tetraodon nigroviridis 44_1h (all transcripts) xl v a Xenopus laevis xn v a Xenopus tropicalis 44_41e (all transcripts) Taxon: a,i : invertebrate; v: vertebrate Habit: a: aquatic; t: terristrial