Fig 1.
Junction sequences of R2 elements.
R2 family name, flanking 28S rRNA gene sequences (28S rDNA) with terminal sequences of R2, common name of the origin, and classification are shown from left to right. 28S rRNA gene sequences are in bold and shaded. (A) Both 5′ and 3′ junctions of non-avian R2 copies. (B) 3′ junctions of R2 copies detected by PCR. Scientific names and common English names of the origins of R2 elements are as follows: R2-1_MLe, Mnemiopsis leidyi (sea walnut); R2-1_SK, Saccoglossus kowalevskii (acorn worm); R2NS-1_CGi, Crassostrea gigas (Pacific oyster); R2-2_SMed, Schimidtea mediterranea (planarian); R2-1_SP, Strongylocentrotus purpuratus (purple sea urchin); R2-1_LV, Lythechinus variegatus (green sea urchin); R2-1_GA, Gasterosteus aculeatus (three-spined stickleback); R2-1_SSa, Salmo salar (Atlantic salmon); R2-1_AMi, Alligator mississippiensis (American alligator); R2-1_Crp, Crocodilus porosus (saltwater crocodile); R2-1_Gav, Gavialis gangeticus (gharial); R2Pp, Pungitius pungitius pungitius (nine-spined stickleback); R2Ao, Anarhichas orientalis (Bering wolffish); R2Cm, Crystallichthys matsushimae (snailfish); R2Om, Oryzias melastigma (marine medaka); R2Tcc, Tylosurus crocodilus crocodilus (houndfish); R2Tch, Theragra chalcogramma (Alaska pollock); R2Tla-B, Tanakia lanceolata (bitterling); R2Raa, Rhodeus atremius atremius (Kyushu bitterling); R2Ac, Amia calva (bowfin); R2Ar, Acipenser ruthenus (sterlet); R2Em, Eublepharis macularius (leopard gecko); R2Ec, Elaphe climacophora (Japanese rat snake); R2Sqj, Squatina japonica (Japanese angel shark).
Fig 2.
The phylogenetic distributions of R2 in vertebrates and birds.
(A) The R2 distribution in vertebrates focusing on actinopterygian fish. (B) R2 distribution in birds. Orders are shown with common names in parentheses. Asterisks indicate the presence of R2 in at least one species. Order names in blue indicate groups that we analyzed by PCR. Perciformes is not monophyletic and thus shown divided. Fish phylogeny is based on [31–33][34,35] while avian phylogeny is based on [36].
Fig 3.
Junction sequences of avian R2 elements.
The R2 family name or accession number (if the characterized sequence was short), flanking 28S rRNA gene sequence with terminal sequence of R2, common name of the origin, and classification are shown from left to right. The 28S ribosomal RNA gene sequences are in bold and shaded. (A) 5′ junctions. (B) 3′ junctions. Scientific names and common English names of the origins of R2 elements are as follows: R2-1_TG, Taeniopygia guttata (zebrafinch); R2-1_GFo, Geospiza fortis (medium ground finch); R2-1_FAl, Ficedula albicollis (collared flycatcher); R2-1_ZA, Zonotrichia albicollis (white-throated sparrow); R2-1_CBr, Corvus brachyrhynchos (American crow); R2-1_ZLM, Zosterops lateralis melanops (silvereye); R2-1_ACh, Acanthisitta chloris (rifleman); R2-1_SCa, Serinus canaria (Atlantic canary); R2-1_MVi, Manacus vitellinus (golden-collared manakin); R2-1_MUn and R2-2_MUn, Melopsittacus undulatus (budgerigar); R2-1_FCh, Falco cherrug (saker falcon); R2-1_FPe, Falco peregrinus (peregrine falcon); R2-1_PPu, Picoides pubescens (downy woodpecker); R2-1_CSt, Colius striatus (speckled mousebird); R2-1_TAl, Tyto alba (barn owl); R2-1_ACC, Aquila chrysaetos canadensis (golden eagle); R2-1_LDi, Leptosomus discolor (cuckoo roller); R2-1_HAl and R2-2_HAl, Haliaeetus albicilla (white-tailed eagle) and H. leucocephalus (bald eagle); R2-1_CAu, Cathartes aura (Turkey vulture); R2-1_NNi and R2-2_NNi, Nipponia nippon (Asian crested ibis); R2-1_PCar, Phalacrocorax carbo (great cormorant); R2-1_EGa, Egretta garzetta (little egret); R2-1_AFo, Aptenodytes forsteri (emperor penguin); R2-1_PAd, Pygoscelis adeliae (Adelie penguin); R2-1_GSt, Gavia stellata (red-throated loon); R2-1_PLe, Phaethon lepturus (white-tailed tropicbird); R2-1_CVo, Charadrius vociferus (killdeer); R2-1_CPu, Calidris pugnax (ruff); R2-1_BRG, Balearica regulorum gibbericeps (grey crowned crane); R2-1_OHo, Opisthocomus hoazin (hoatzin); R2-1_CCa, Caprimulgus carolinensis (nightjar); R2-2_CMa, Chlamydotis macqueenii (McQueen’s bustard); R2-1_CCan and R2-2_CCan, Cuculus canorus (common cuckoo); R2-1_MUni, Mesitornis unicolor (brown mesite); R2-1_PGu, Pterocles gutturalis (yellow-throated sandgrouse); R2-1_PRR, Phoenicopterus ruber ruber (American flamingo); R2-1_PCr, Podiceps cristatus (great crested grebe); R2-1_TGut, Tinamus guttatus (white-throated tinamou).
Fig 4.
A phylogenetic tree of R2 families based on the protein alignment from motif 5 of the RT domain to the C-terminus.
Bootstrap values above 50% are shown at branches. R2 family names and their origins are shown as leaves. R2 families from Chordata are colored in red, those from Arthropods in blue, those from Platyhelminthes in green and those from other animals in black. Clusters of R2 families that can be assigned to reported subclades are indicated by vertical lines with names whilst clusters not assigned to reported subclades are indicated by vertical lines without names. The magenta bar indicates the cluster having a 28S rRNA gene-like sequence in the 3′ UTR.
Fig 5.
Apparent movement of 5′ insertion sites of R2.
(A) Alignment of 5′ and 3′ junction sequences. Nucleotides of 28S rRNA genes are in bold and shaded while nucleotides identical to 28S rRNA genes inside of R2 elements are only shaded. Patterned boxes above the sequences correspond to the regions with the same patterned boxes in (B). R2Gs, R2Pt, R2Bs-B, R2Bs-A, and R2Sb are phylogenetically closely related and it is likely that their 3′ 28S-like sequences were acquired in their common ancestor. (B) Schematic diagram around the insertion sites of canonical R2 and R2Gs. Patterned boxes indicate the regions of 28S rRNA genes. Scientific names and common English names of the origins of R2 elements are as follows: R2Gs, Grammistes sexlineatus (goldenstriped soapfish); R2Pt, Parapristipoma trilineatum (chicken grunt); R2Bs-A and R2Bs-B, Beryx splendens (splendid alfonsino); R2Sb, Stethojulis bandanesis (red shoulder wrasse); R2Kp, Konosirus punctatus (dotted gizzard shad); R2Op, Oxyurichthys papuensis (arrowfin gobies).