Opsin evolution: update blog

This cluster of web articles on opsin evolution is updated almost daily. Because those changes are scattered across various long articles, this simple directory of articles and blog of significant changes may be helpful.

• Introduction to the opsin classifier and curated sequence collection
• Key critters with genomics: deuterostomes
• Key critters with genomics: ecdysozoa
• Key critters with genomics: lophotrochozoa
• Key critters with genomics: cnidaria and porifera
• 230 opsins aligned: consensus-colored image and motif searchable text
• Ancestral intron reconstruction for ciliary opsins
• Ancestral status of informative coding indels
• Ancestral sequence reconstruction for ciliary opsins
• LWS: generating locus for imaging opsins
• Encephalopsin and TMT: massive gene loss in mammalian clades
• Melanopsins show gene and exon loss in mammals
• RGR opsin: abrupt change in DRY motif in boreoeutheres
• Peropsin: phyloSNPs (synapomorphies) in persopsin evolution
• Neuropsin (OPN5): 52 deuterostome genes and a novel paralog, Newropsin
• Color vision in the platypus and ancestral mammal
• The cytoplasmic face of opsins and GPCR specificity
• IRBP Interstitial retinol-binding protein modules
• RPE65 rate-limiting step in ciliary opsin regeneration
• Usherin USH2A roles in vision and hearing
• Cadherin CDH23 roles in vision and hearing
• Transducins: comparative genomics of opsin interactions
• Annotation tricks: genes from traces, intron patterns, resolving indels, trimming
• Tracking significant updates (this page)
• The photoreceptor fossil record (planned)
• Opsin evolution: the bottom line (in progress)

Reverse Chronological Update Blog

08 Dec 09: located ur-ciliary opsin of deuterostomes and traced orthologs to fish, frog and lizard, not birds or mammals.
07 Dec 09: aligned 411 opsins in rosetta stone region in TM2
02 Dec 09: major improvements to informative opsin indel section
30 Nov 09: alignment-based refinement of reference sequence collection fixed annotation errors arising from assembly frameshifts
29 Nov 09: added two new RGR sequences from tunicates and a new amphioxus melanopsin 
02 Nov 09: a ciliary opsin from a new cnidarian; revisited acorn worm opsins using newly released assembly

05 Sep 09: comparative genomics applied to potential disease SNPs of USH2A and CDH25
20 Aug 09: new section on molecular commonalities of hearing and vision genes such as PCDH15 and CDH25
05 Aug 09: added section on fibronectin domains of Usher Syndrome components USH2A and GPR98
23 Jul 09: revisited platyhelminthes opsins in view of newly published Schistosoma genome articles

29 Jun 09: found and characterized the first ctenophore opsin
28 Jun 09: separated ecdysozoa and lophotrochozoa articles
27 Jun 09: interaction of opsin cytoplasmic loop C2 and C3 co-evolution with transducin GNAT1
25 Jun 09: updated arthropod melanopsins and their opsin diagnostics; data gap in myriapods, onychophorans, tardigrades
21 Jun 09: updated section on Ciona opsins and their photoreceptors
19 Jun 09: located 6 opsins in aphid genome including Rh7 ortholog
18 Jun 09: recovered complete ciliary opsin and second UV opsin from new Rhodnia assembly
17 Jun 09: comparative genomics of 3rd cytoplasmic loop in melanopsins
16 Jun 09: new section on drosophila opsins focused on 'anatomical orphan' RH7
14 Jun 09: updated Chelicerate opsins, fixed Daphnia gene models, sought Pycnogonida and Onychophora data
10 Jun 09: new section on opsins of ancestral Ecdysozoan, K90 diagnostic of arthropod ultraviolet vision 

19 May 09: analyzed new melanopsin from Acropora (coral) transcriptome project
17 May 09: found new ciliary opsin in Branchiostoma, improved and reclassified the 11 opsins of cephalochordates
09 May 09: hagfish opsins: analyzed their potential impacts on understanding vertebrate vision evolution
08 May 09: documented a diverged tunicate melanopsin with transcript support using K-rhodopsin searching
26 Mar 09: evolutionary analysis of lamprey and amphioxus IRBP modules (interstitial retinol-binding protein RBP3)  
07 Feb 09: integrated sitewide important new chondricthyean sequences for RHO2, LWS1, and LWS2
05 Feb 09: finished massive comparison of cytoplasmic tails of all opsin loci
29 Jan 09: discovered yet another neuropsin NEUR4 that ranges from lamprey to platypus
18 Jan 09: began massive comparative genomic page on structure of opsin cytoplasmic faces and Galpha determinants
06 Jan 09: began new page on origin of RPE65 and its two paralogs BCMO1 and BCO2 (carotenoid processing)

21 Nov 08: added structural comparison of A2a adenosine receptor binding and DRY region
07 Nov 08: considered implication for opsins of new KH Ciona assembly which corrected 5,109 genes
06 Nov 08: added second hemichordate peropsin using new EST release
08 Sep 08: added duplication history and reference sequences for transducins (alpha subunits of heteromeric G proteins)
27 Aug 08: added choanoflagellate genome, no opsins but Gi and Gq class heteromeric G proteins
26 Aug 08: compiled 16 Nematostella non-opsins yet with lysine in retinal position
25 Aug 08: reviewed placozoan genome project and 4 opsins asserted for it
20 Aug 08: added opsins from Rhodnius genome project (traces only)

12 Aug 08: reviewed exciting new developments in cnidarian (Tripedalia) ciliary opsins and transducin binding site
08 Aug 08: recovered very old SWS2 unprocessed pseudogene in Petromyzon (lamprey) and updated key critter article
01 Aug 08: recovered SWS1 unprocessed pseudogene from Petromyzon marinus (lamprey) genome
30 Jul 08: expanded RHO2 collection to 8 teleost fish and one exon from RHO2 of chondrichthyes; lamprey RHO1/2 still muddled
29 Jul 08: evolution of upstream RORB and CRX control regions for LWS and SWS1
28 Jul 08: control region section for LWS; recovered LCR_LWS orthologs for 35 species spanning lamprey to human
27 Jul 08: new echidna data for monotreme opsin evolution; gene tree x species tree showing regressive mammalian opsin evolution 

20 Apr 08: revisited LWS in many more species; expanded ancestral SWS2+ LWS+ linkage species
13 Apr 08: special section on melanopsins in vertebrates: gene loss of MEL2 and gene shrinkage in MEL1
06 Apr 08: expanded TMT class of encephalopsins to 14 species, shark to marsupial, showed lost in all placentals
05 Apr 08: demonstrated massive gene loss of mammalian encephalopsins and placental TMT opsins
27 Mar 08: upgraded lamprey larval section and brought opsin collection to 17 (in 11 orthology classes) 
23 Mar 08: new section aligning 94 LWS and analyzing its PhyloSNPs
17 Mar 08: discovery of a novel opsin occuring from sharks to birds, lost in mammals: newropsin

14 Mar 08: new section on neuropsin comparative genomics 
07 Mar 08: new section on peropsin synapomorphies
20 Feb 08: new section on RGR: clade-defining changes (phyoSNPs), gene loss in marsupial
10 Jan 08: added Tribolium critter section on opsin loss, ommitidia cell gain, non-opsin GPCR content.
09 Jan 08: posted paraphyletic gene tree explanation for 'too many' opsins in Daphnia, Nematostella, and Cladonema: 
opsins duplicated, diverged, neofunctionalized to non-opsin non-photoreceptors nesting within opsins.

08 Jan 08: added key critter section on hydrozoan Cladonema putative opsins.
07 Jan 08: added ancient intron discussion for melanopsins.
05 Jan 08: finished ancient intron section for peropsin group.
04 Jan 08: added new key critters section for hydrozoan Cladonema radiatum,
03 Jan 08: made comparative conservation profile for 54 new cnidarian opsins proposed by Gehring group.

02 Jan 08: added comparative genomics of RGR because of curious loss of DRY motif in boreoeutheres.
31 Dec 07: posted fullscale comparison of ciliary opsin introns
29 Dec 07: extracted scattered elements of the binding pocket for comparative genomic covariance study.
28 Dec 07: added new discussion on peropsins as more than mere photoisomerases and in need of subfamily refinement.
27 Dec 07: recovered new Aplysia and Lottia peropsins orthologous to experimentally studied squid 'retinochrome'.

26 Dec 07: started new page on coding indels and completely rewrote main introductory page.
25 Dec 07: added key critters section for human body louse and its 3 rhabdomeric opsins.
24 Dec 07: fixed arrestin quasi-cognate section and proposed bioinformatic approach to unstudied opsin/arrestin pairs
23 Dec 07: added alignment of C-terminus and comparative genomics of phosphorylation sites vis-a-vis arrestins 
22 Dec 07: upgraded alignment of all opsin sequences, trimmed at one or both ends, color consensus and motif searchable.

21 Dec 07: added an annotation trick that allows trimming and residue selection from the reference opsin set.
20 Dec 07: added comparative genomics discussion of counterion and its switching.
19 Dec 07: added greatly to opsin structure/function in ancient sequence section to explain conserved diagnostic motifs.
18 Dec 07: began new page on ancestral ciliary opsin sequence reconstruction.
17 Dec 07: added new ciliary opsins from Daphnia, Tribolium, Aedes, and Culex genomes.

16 Dec 07; began new page on ancestral ciliary opsin intron pattern.
14 Dec 07: upgraded sponge photoreceptor account, found final exon of new Platynereis ciliary exon.
13 Dec 07: extended JGI staff models of 3 intronless ciliary encephalopsins from Nematostella to full length.
12 Dec 07: added Nematostella and Hydra sections awaiting clarification.
11 Dec 07: finished larval and adult photoreception in Ciona.

10 Dec 07: expanded section on Ciona to include possible otolith paralogous photoreceptor.
09 Dec 07: added a treatment of two tunicate pinopsin-like opsins and their ancient introns.
08 Dec 07: added a section on intron cross-comparison to the annotation tutorial.
08 Dec 07: added treatment of two platyhelminthes to Lophotrochozoa area.
07 Dec 07: added 2 trematode and 1 planaria opsins, exon pattern matches melanopsin.

06 Dec 07: added cnidarian larval rhabdomeric single-cell eye and adult rhopalium imagery.
05 Dec 07: added Capitella literature survey and a new melanopsin from genome assembly.
04 Dec 07: added Helobedella literature survey and new opsins from genome assembly.
03 Dec 07: added Lottia, reviewed genome assembly, found an opsin but could not locate anything on ocelli.
02 Dec 07: added Aplysia eye anatomy and apparent melanopsin ortholog to key critters.

29 Nov 07: added platynereis story to critters, described second new ciliary opsin.
29 Nov 07: added graphics comparing eye systems in deuts and lophs, illustrated everse and inverse eyes.
29 Nov 07: added sea urchin opsins to critter discussion, graphic of expression in larva and adult.
29 Nov 07: added 6 sea urchin reference opsins by repairing gene models, adding introns, and reclassifying.
28 Nov 07: added Xenoturbella and Convoluta section to basal key critters, no opsins available.

28 Nov 07: upgraded key critters with treatment of Saccoglossus.
28 Nov 07: found first hemichordate opsin, put methods into detailed tutorial.
28 Nov 07: received copywrite permissions for use of handdrawn invertebrate eyes illustrations.
28 Nov 07: added jump navigation to key critters as article is getting fairly long.
27 Nov 07: added scallop Go opsins from an important historic study.
27 Nov 07: reorganized curated sequences into deuterostome, ecdysozoa, lophotrochozoa blocks sorted by receptor type.

                                      2008-2010 site visits   
#pages  topic             22 Apr  12 May  29 Jul  4 Sep  4 Nov 3 Jan  8 Feb  26 Mar 2 Jun  5 Sep  8 Dec
47      main               814      896    1076    1227   1706  1919  2123   2380   2693   3128   3561
14      key deuterostomes    0        0     107     170    250   385   447    631    907   1104   1460
32      key ecdysozoa     1106     1207    1279    1351   1492  1685  1766   2009   2324     98    245
11      key lophotrochozoa   0        0       0       0      0     0     0      0      0    121    305
25      key cnidaria         0        0       0     120    209   320   391    515    731    974   1304
 8      alignment          231      256     304     324    380   429   475    555    636    731    872
10      introns            180      202     252     274    340   396   455    548    637    777    980
 2      indels              97      118     157     179    227   284   322    405    521    634    829
11      ancestral          247      269     318     351    414   476   520    628    765    901   1109
24      LWS                 68      104     169     218    291   338   409    548    665    825   1045
12      encephalopsin       67      110     181     216    286   350   454    625    842   1030   1289
13      melanopsin          24       70     132     160    207   244   317    424    540    651    802
13      RGR phyloSNPs       98      120     181     200    259   299   528    662    822    983   1178 
16      peropsin            89      117     174     195    254   332   381    461    573    710    891
15      neuropsin           83      102     164     188    225   264   390    471    558    672    903
 8      platypus           290      338     488     574    743   868   978   1123   1324   1484   1743
 6      tricks             169      191     304     343    396   468   530    631    769    938   1253
27      cytoplasmic face     0        0       0       0      0     0    91    132    277    445    670
41      RPE, BCO2, BCMO1     0        0       0       0      0     0    85    163    261    447    592 
20      IRBP (RBP3)          0        0       0       0      0     0     0    339    772    968   1202
20      CDH23                0        0       0       0      0     0     0      0      0    162    326
28      USH2A                0        0       0       0      0     0     0      0      0    222    364
17      transducins          0        0       0       0    148   468   378    509    674    918   1164
 3      blog              1178     1329    1798    2158   2610  3179  3412   3960   4599   5436   6211
436     total             4741     5429    7084    8248  10437 12579 14219  17719  21890  26683  30298
        visits per day      31       34      22      31     36    39    49     74     61     50yr   38