Independent pseudogenizations and losses of sox15 during amniote diversification following asymmetric ohnolog evolution

Abstract

Background: Four ohnologous genes (sox1, sox2, sox3, and sox15) were generated by two rounds of whole-genome duplication in a vertebrate ancestor. In eutherian mammals, Sox1, Sox2, and Sox3 participate in central nervous system (CNS) development. Sox15 has a function in skeletal muscle regeneration and has little functional overlap with the other three ohnologs. In contrast, the frog Xenopus laevis and zebrafish orthologs of sox15 as well as sox1-3 function in CNS development. We previously reported that Sox15 is involved in mouse placental development as neofunctionalization, but is pseudogenized in the marsupial opossum. These findings suggest that sox15 might have evolved with divergent gene fates during vertebrate evolution. However, knowledge concerning sox15 in other vertebrate lineages than therian mammals, anuran amphibians, and teleost fish is scarce. Our purpose in this study was to clarify the fate and molecular evolution of sox15 during vertebrate evolution.

Results: We searched for sox15 orthologs in all vertebrate classes from agnathans to mammals by significant sequence similarity and synteny analyses using vertebrate genome databases. Interestingly, sox15 was independently pseudogenized at least twice during diversification of the marsupial mammals. Moreover, we observed independent gene loss of sox15 at least twice during reptile evolution in squamates and crocodile-bird diversification. Codon-based phylogenetic tree and selective analyses revealed an increased d_N/d_S ratio for sox15 compared to the other three ohnologs during jawed vertebrate evolution.

Conclusions: The findings revealed an asymmetric evolution of sox15 among the four ohnologs during vertebrate evolution, which was supported by the increased d_N/d_S values in cartilaginous fishes, anuran amphibians, and amniotes. The increased d_N/d_S value of sox15 may have been caused mainly by relaxed selection. Notably, independent pseudogenizations and losses of sox15 were observed during marsupial and reptile evolution, respectively. Both might have been caused by strong relaxed selection. The drastic gene fates of sox15, including neofunctionalization and pseudogenizations/losses during amniote diversification, might be caused by a release from evolutionary constraints.

Keywords: 2R-WGD; Gene loss; Marsupial; Neofunctionalization; Ohnolog; Ortholog; Pseudogene; Relax; Reptile; d N/d S.

Fig. 1

Incomplete retention of sox15 during amniote evolution. Summary of synteny analysis of (a) mammalian, (b) reptilian, and (c) other gnathostomatan orthologs of sox15 using 56 Gnathostomata species. H. sapiens, Homo sapiens; M. fascicularis, Macaca fascicularis; M. musculus, Mus musculus; O. cuniculus, Oryctolagus cuniculus; F. catus, Felis catus; C. lupus familiaris, Canis lupus familiaris; O. orca, Orcinus orca; B. taurus, Bos taurus; L. africana; Loxodonta africana; M. domestica, Monodelphis domestica; T. vulpecula, Trichosurus vulpecula; S. harrisii, Sarcophilus harrisii; V. ursinus, Vombatus ursinus; P. cinereus, Phascolarctos cinereus; T. cynocephalus, Thylacinus cynocephalus; G. leadbeateri, Gymnobelideus leadbeateri; O. anatinus, Ornithorhynchus anatinus; T. aculeatus, Tachyglossus aculeatus; P. sinensis, Pelodiscus sinensis; G. evgoodei, Gopherus evgoodei; C. picta, Chrysemys picta; D. coriacea, Dermochelys coriacea; A. sinensis, Alligator sinensis; C. porosus, Crocodylus porosus; N. harrisi, Nannopterum harrisi; C. moneduloides, Corvus moneduloides; C. ustulatus, Catharus ustulatus; S. habroptila, Strigops habroptila; P. picta, Paroedura picta; P. muralis, Podarcis muralis; V. komodoensis, Varanus komodoensis; V. berus, Vipera berus; P. vitticeps, Pogona vitticeps; P. obsoletus, Pantherophis obsoletus; N. naja, Naja naja; L. colubrina, Laticauda colubrina; P. pectinata, Pristis pectinata; C. plagiosum, Chiloscyllium plagiosum; C. milii, Callorhinchus milii; E. calabaricus, Erpetoichthys calabaricus; A. ruthenus, Acipenser ruthenus; L. oculatus, Lepisosteus oculatus; S. formosus, Scleropages formosus; D. rerio, Danio rerio; D. clupeoides, Denticeps clupeoides; H. stenolepis, Hippoglossus stenolepis; M. zebra, Maylandia zebra; O. latipes, Oryzias latipes; P. flavescens, Perca flavescens; L. crocea, Larimichthys crocea; T. rubripes, Takifugu rubripes; L. chalumnae, Latimeria chalumnae; G. seraphini, Geotrypetes seraphini; R. bivittatum, Rhinatrema bivittatum; X. tropicalis, Xenopus tropicalis; and X. laevis, Xenopus laevis

Fig. 2

Independent pseudogenizations or losses of sox15 during marsupial or reptilian speciation. a Independent pseudogenization of sox15 during marsupial speciation. (ψ) indicates pseudogenization of sox15. Numbers from the first nucleotide in 225 nucleotide sequences encoding the HMG box are shown in the nucleotide alignment. In-frame stop codons and deletions with frame shift mutation are highlighted by gray boxes. Asterisks denote identical nucleotides among seven species following alignment. MRCA denotes most recent common ancestor. b, c Independent losses of sox15 in two lineages during reptilian speciation: Squamata including lizards and snakes (b) and Archosauromorpha including Testudines, crocodilians, and birds (c). “num. species” denotes the number of species examined in each lineage. Presence or loss of sox15 is shown as + or −. “unknown” indicates that the existence of sox15 was not determined in this analysis

Fig. 3

d_N/d_S (ω) values of four soxB1/G ohnologs (sox15 and sox1-3 s) during vertebrate evolution. A total of 102 gap-containing 930 nucleotide sequences corresponding to 310 codons were used for this tree inference. The GTR + F + R5 model was selected as the best-fit model in this dataset and used for the inference. d_N/d_S (ω) values were calculated using 234 nucleotide sites with gaps deleted on the same nucleotide alignment as the tree inference. The scale bar indicates nucleotide substitutions per site

Fig. 4

Proposed model for molecular evolution of sox15 and its ohnologous members sox1-3 s during vertebrate evolution