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. 2023 May 23;24(11):9126. doi: 10.3390/ijms24119126

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© 2023 by the author.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Evolutionary relationships between TULA-family proteins. The analysis was carried out using the Constraint–based Multiple Protein Alignment Tool [103] with the default alignment parameters. The tree (radial) was built using neighbor-joining method with the evolutionary distances calculated according to Grishin [104]. All sequences have been obtained from the Protein database maintained by the National Library of Medicine, National Center for Biotechnology Information. The TULA-family proteins have been selected for analysis from multiple species representing both vertebrates and invertebrates, which are marked by numbers. Relevant taxonomic groups are indicated. The locus designations of the proteins analyzed are given below. When both TULA-1 and TULA-2 have been analyzed, the locus number for TULA-1 precedes that for TULA-2 in the following list. Placental mammals: human (#1, Homo sapiens: NP_061834.1 and NP_116262.2), chimpanzee (#2, Pan troglodytes: XP_016794065.1 and XP_508828.2), cat domestic (#3, Felis catus: XP_003991416.1 and XP_003992499.1), cow (#4, Bos taurus: NP_001015599.1 and NP_001193057.1), and house mouse (#5, Mus musculus: NP_808491.2 and NP_789830.1). Marsupials: gray short-tailed opossum (#6, Monodelphis domestica; XP_007493239.1 and XP_016289274.1), and koala (#7, Phascolarctos cinereus: XP_020829536.1 and XP_020840539.1). Monotremes: platypus (#8, Ornithorhynchus anatinus: XP_039770616.1 and XP_028931626.1). Birds: chicken (#9, Gallus gallus: XP_004934641.1 and XP_015153661.1), turkey (#10, Meleagris gallopavo: XP_010722714.1 and XP_031412703.1), hooded crow (#11, Corvus cornix cornix: XP_019138194.1 and XP_039420798.1), and common cuckoo (#12, Cuculus canorus: XP_009559175.1 and XP_009555828.1). Reptiles: green anole (#13, Anolis carolinensis: XP_008105681.1 and XP_016850210.1), American alligator (#14, Alligator mississippiensis: XP_019342726.1 and XP_006275146.1), painted turtle (#15, Chrysemys picta bellii: XP_005303759.1 and XP_005303797.1), and brown-spotted pit viper (#16, Protobothrops mucrosquamatus: XP_015677410.1 and XP_015676892.1). Amphibians: African clawed frog (#17, Xenopus laevis: XP_041439474.1 and XP_018081241.1), common toad (#18, Bufo bufo: XP_040278639.1 and XP_040287247.1), and Iberian ribbed newt (#19, Pleurodeles waltl: KAJ1112034.1 and KAJ1175306.1). Fish—sharks: whale shark (#20, Rhincodon typus: XP_048459103.1 and XP_048471549.1), zebra shark (#21, Stegostoma fasciatum: XP_048396616.1 and XP_048417962.1), smaller spotted catshark (#22, Scyliorhinus canicular: XP_038657220.1 and XP_038634591.1), smalltooth sawfish (#23, Pristis pectinate: XP_051870461.1 and XP_051895694.1). Fish—lobe-finned fish (Sarcopterygii): coelacanth (#24, Latimeria chalumnae: XP_014354497.1 partial and XP_005987327.1). Fish—ray-finned fishes (Actinopterygii; the proteins analyzed for ray-finned species are TULA-2a and TULA-2b listed first and second, respectively, for each species, except for the Atlantic salmon, where TULA-2a, TULA-2a’ and TULA-2b are listed): Atlantic salmon (#25, Salmo salar: XP_014069250.1, XP_014017956.1 and XP_014051313.1), zebrafish (#26, Danio rerio: NP_001122227.1 and XP_001923885.2), Nile tilapia (#27, Oreochromis niloticus: XP_013121081.1 and XP_003446846.1), moonfish (#28, Xiphophorus maculatus: XP_023207530.1 and XP_005802954.1), and mudskipper (#29, Boleophthalmus pectinirostris: XP_020782492.1 and XP_020778647.1). For a detailed tree of fish TULA sequences, see Figure 5. Jawless vertebrates: sea lamprey (#30, Petromyzon marinus: XP_032820445.1; only TULA-2 is listed, no TULA-1 has been found). Insects: yellow fever mosquito (#31, Aedes aegypti: XP_021693348.1), honeybee (#32, Apis mellifera: XP_394838.2), powderpost termite (#33, Cryptotermes secundus: XP_023711760.1), fruit fly (#34, Drosophila melanogaster: NP_651202.1), cat flea (#35, Ctenocephalides felis: XP_026468601.1), red flour beetle (#36, Tribolium castaneum: KYB26555.1), desert locust (#37, Schistocerca gregaria: XP_049863752.1), and fall armyworm (#38, Spodoptera frugiperda: XP_050561310.1). Crustacean: Pacific white shrimp (#39, Penaeus vannamei: XP_027239151.1), snow crab (#40, Chionoecetes opilio: KAG0711382.1), Louisiana crawfish (#41, Procambarus clarkii: XP_045594025.1), Hyalella Azteca (#42, Hyalella azteca: XP_047735455.1), striped barnacle (#43, Amphibalanus amphitrite: XP_043215535.1), goose barnacle (#44, Pollicipes pollicipes: XP_037086318.1), and water flea (#45, Daphnia pulex: XP_046453513.1). Chelicerata: deer tick (#46, Ixodes scapularis: XP_029842566.1), Western predatory mite (#47, Galendromus occidentalis: XP_018494053.1), honeybee mite (#48, Varroa destructor: XP_022654098.1), and horse-shoe crab (#49, Limulus polyphemus: XP_022253956.1). Mollusks: Virginia oyster (#50, Crassostrea virginica: XP_022341161.1), California mussel (#51, Mytilus californianus: XP_052075640.1), California sea hare (#52, Aplysia californica: XP_005099706.1), red abalone (#53, Haliotis rufescens: XP_048237131.1), and California two-spot octopus (#54, Octopus bimaculoides: XP_052830112.1). Brachiopods: Lingula anatina (#55, XP_013419245.1). Segmented worms (annelids): marine polychaeta Capitella teleta (#56, ELU07750.1), leach (#57, Helobdella robusta: XP_009015730.1), and tubeworm (#58, Owenia fusiformis: CAH1800724.1). Flat worms: dog tapeworm (#59, Echinococcus granulosus: KAH9282803.1), Chinese liver fluke (#60, Clonorchis sinensis: KAG5444987.1), and blood-fluke (#61, Schistosoma intercalatum: CAH8519421.1). Sponges: Amphimedon queenslandica (#62, XP_019855686.1), and Oopsacas minuta (#63, KAI6655504.1). Cnidarians: fresh-water polyp (#64, Hydra vulgaris: XP_047130900.1). Priapulids: cactus worm (#65, Priapulus caudatus: XP_014678843.1). Hemichordates: acorn worm (#66, Saccoglossus kowalevskii: XP_006821603.1). Echinoderms: Crown-of-thorns starfish (#67, Acanthaster planci: XP_022099247.1), purple sea urchin (#68, Strongylocentrotus purpuratus: XP_030834281.1), and Anneissia japonica (#69, XP_033119264.1). Cephalochordates: Belcher’s lancelet (#70, Branchiostoma belcheri: XP_019620650.1). Tunicates: vase tunicate (#71, Ciona intestinales: XP_026692047.1), rough sea squirt (#72, Styela clava: XP_039248084.1), and Phallusia mammillata (#73, CAB3267428.1).