Opsin evolution: update blog

This cluster of web articles on opsin evolution is updated almost daily. Because those changes are hard to track in longish articles, this simple directory and blog of significant changes may be helpful.

• Introduction to the opsin classifier and curated sequence collection
• Key critters: species with genome projects and their photoreceptors
• Ancestral intron reconstruction for ciliary opsins
• Ancestral sequence reconstruction for ciliary opsins
• [http://genomewiki.ucsc.edu/index.php/Opsin_evolution:_alignment 230 opsins aligned: consensus-colored image and searchable text
• Annotation tricks: genes from traces, intron patterns, resolving indels, trimming sequences
• Color vision in the platypus and ancestral mammal
• Tracking significant updates (this page
• Informative coding indels (under development)
• The photoreceptor fossil record (planned)
• Subscholarly opsin literature and defective evolutionary inference (planned)
• Opsin evolution: the bottom line (in progress)
• Comparative genomics of other eye developmental and structural genes (volunteers needed)

Reverse Chronological Update Blog

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.