Opsin evolution: update blog: Difference between revisions
From genomewiki
Jump to navigationJump to search
Tomemerald (talk | contribs) mNo edit summary |
(remove self reference link to this page, leave label for reference in bold) |
||
Line 19: | Line 19: | ||
* [[Opsin_evolution:_transducins|Transducins: comparative genomics of opsin interactions]] | * [[Opsin_evolution:_transducins|Transducins: comparative genomics of opsin interactions]] | ||
* [[Opsin_evolution:_annotation_tricks|Annotation tricks: genes from traces, intron patterns, resolving indels, trimming]] | * [[Opsin_evolution:_annotation_tricks|Annotation tricks: genes from traces, intron patterns, resolving indels, trimming]] | ||
* | * <B>Tracking significant updates (this page)</B> | ||
* The photoreceptor fossil record (planned) | * The photoreceptor fossil record (planned) | ||
* Comparative genomics of other eye developmental and structural genes (volunteers needed) | * Comparative genomics of other eye developmental and structural genes (volunteers needed) |
Revision as of 23:18, 25 March 2009
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: protostomes
- 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
- 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)
- Comparative genomics of other eye developmental and structural genes (volunteers needed)
- Opsin evolution: the bottom line (in progress)
Reverse Chronological Update Blog 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.
2008-2009 site visits #pages topic 22 Apr 12 May 29 Jul 4 Sep 4 Nov 3 Jan 8 Feb 47 main 814 896 1076 1227 1706 1919 2123 14 key deuterostomes 0 0 107 170 250 385 447 19 key protostomes 1106 1207 1279 1351 1492 1685 1766 25 key cnidaria 0 0 0 120 209 320 391 8 alignment 231 256 304 324 380 429 475 10 introns 180 202 252 274 340 396 455 2 indels 97 118 157 179 227 284 322 11 ancestral 247 269 318 351 414 476 520 24 LWS 68 104 169 218 291 338 409 12 encephalopsin 67 110 181 216 286 350 454 13 melanopsin 24 70 132 160 207 244 317 13 RGR phyloSNPs 98 120 181 200 259 299 528 16 peropsin 89 117 174 195 254 332 381 15 neuropsin 83 102 164 188 225 264 390 8 platypus 290 338 488 574 743 868 978 6 tricks 169 191 304 343 396 468 530 27 cytoplasmic face 0 0 0 0 0 0 91 41 RPE, BCO2, BCMO1 0 0 0 0 0 0 85 13 transducins 0 0 0 0 148 468 378 3 blog 1178 1329 1798 2158 2610 3179 3412 327 total 4741 5429 7084 8248 10437 12579 14219 per day 31 34 22 31 36 39 49