Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis

Kitano, Takashi; Noda, Reiko; Takenaka, Osamu; Saitou, Naruya

doi:10.1016/j.ympev.2009.02.023

Cited by 17 publications

(12 citation statements)

References 22 publications

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“…We used previously published data: in humans, 60 individuals of European ancestry (CEU), 60 individuals of South East Asian ancestry (CHB + JPT) and 59 individuals of Sub-Saharan ancestry (YRI) (30), 31 olive baboons (Papio anubis) (27), 13 macaques (seven cynomolgus or crabeating macaques, Macaca fascicularis and six rhesus macaques, Macaca mulatta) (24), 17 gibbons (five agile gibbons, Hylobates agilis and 12 whitehanded gibbons, Hylobates lar), and six siamangs (Symphalangus syndactylus) (25). In addition, we sequenced hominoid samples from Lincoln Park Zoo (40) (SI Acknowledgments): 10 bonobos (Pan paniscus), 35 western chimpanzees (Pan troglodytes), 31 lowland western gorillas (Gorilla gorilla), and nine orangutans (Pongo pygmaeus: three orangutans from Sumatra, two from Borneo, and four hybrids).…”

Section: Methodsmentioning

confidence: 99%

“…Remarkably, the A, B, and H antigens exist not only in humans but in many other primates (reviewed in ref. 22), and the same two amino acids are responsible for A and B enzymatic specificity in all sequenced species (8,18,(23)(24)(25). Thus, primates not only share their ABO blood group, but also the same genetic basis for the A/B polymorphism.…”

Section: Neuroscience Psychological and Cognitive Sciencesmentioning

confidence: 99%

“…That different species share the same two A/B alleles could be the result of convergent evolution in many lineages or of an ancestral polymorphism stably maintained for millions of years and inherited across (at least a subset of) species. The two possibilities have been debated for decades, with a consensus emerging that A is ancestral and the B allele has evolved independently at least six times in primates (in human, gorilla, orangutan, gibbon/siamang, macaque, and baboon) (8,25,26), in particular, that the human A/B polymorphism arose more recently than the split with chimpanzee (8, 20) (SI Methods, SI Note S2). We show instead that the remarkable distribution of ABO alleles across species reflects the persistence of an old ancestral polymorphism that originated at least 20 million years (My) ago and is shared identical by descent by humans and gibbons as well as among distantly related Old World monkeys.…”

Section: Neuroscience Psychological and Cognitive Sciencesmentioning

confidence: 99%

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The ABO blood group is a trans-species polymorphism in primates

Ségurel

Thompson²,

Flutre

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

138

177

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Fig. 1. The phylogenetic distribution of ABO phenotypes and genotypes. Shown is a phylogenetic tree of primate species, with a summary of phenotypic/ genotypic information given in the first column, and the genetic basis for the A versus B phenotype provided in the second column (functionally important codons at positions 266 and 268 are in uppercase letters). See Dataset S1 for the source of information about phenotypes/genotypes. Only species with available divergence times are represented here (34 of 40). The phylogenetic tree is drawn to scale, with divergence times (on the x axis) in millions of years taken from ref. 29. OWM, Old World monkeys; NWM, New World monkeys. Under a model of convergent evolution, these data suggest that A is the ancestral allele, and a turnover (e.g., a neutral substitution) occurred on the branch leading to Old World monkeys. If instead, B were ancestral, all Old World monkeys would have had to serendipitously converge from ATG to TTG to encode a leucine, whereas all New World monkeys and hominoids would have had to converge to the CTG codon.

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Section: Methodsmentioning

confidence: 99%

Section: Neuroscience Psychological and Cognitive Sciencesmentioning

confidence: 99%

Section: Neuroscience Psychological and Cognitive Sciencesmentioning

confidence: 99%

See 1 more Smart Citation

The ABO blood group is a trans-species polymorphism in primates

Ségurel

Thompson²,

Flutre

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

138

177

View full text Add to dashboard Cite

show abstract

“…Furthermore, this study indicates that the ERV-DC7 env region has undergone several multistep events, such as gene mutations like parallel substitutions and recombination among alleles, since its integration. We hypothesize that ERV genes gradually evolved into host genes and that several intermediate alleles have contributed to this process through the independent acquisitions of mutations and recombination events, such as host gene evolutions (67) (Fig. 11).…”

Section: Fig 11mentioning

confidence: 99%

Ancestral Mutations Acquired in Refrex-1, a Restriction Factor against Feline Retroviruses, during its Cooption and Domestication

Ito

Baba

Kawasaki

et al. 2016

J Virol

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Endogenous retroviruses (ERVs) are remnants of ancestral retroviral infections of germ cells. Retroviral endogenization is an adaptation process for the host genome, and ERVs are gradually attenuated or inactivated by mutation. However, some ERVs that have been "domesticated" by their hosts eventually gain physiological functions, such as placentation or viral resistance. We previously reported the discovery of Refrex-1, a soluble antiretroviral factor in domestic cats that specifically inhibits infection by feline leukemia virus subgroup D (FeLV-D), a chimeric virus of FeLV, and a feline ERV, ERV-DC. Refrex-1 is a truncated envelope protein (Env) encoded by both ERV-DC7 and ERV-DC16 proviral loci. Here, we reconstituted ancestral and functional Env from ERV-DC7 and ERV-DC16 envelope genes (env) by inducing reverse mutations. Unexpectedly, ERV-DC7 and ERV-DC16 full-length Env (ERV-DC7 fl and ERV-DC16 fl), reconstructed by removing stop codons, did not produce infectious viral particles. ERV-DC7 fl and ERV-DC16 fl were highly expressed in cells but were not cleaved into surface subunits (SU) and transmembrane subunits, nor were they incorporated into virions. G407R/N427I-A429T and Y431D substitutions within the SU Cterminal domain of ERV-DC7 fl and ERV-DC16 fl, respectively, caused these dysfunctions. The residues glycine 407 and tyrosine 431 are relatively conserved among infectious gammaretroviruses, and their substitution causes the same dysfunctions as the tested retroviruses. Our results reveal that specific mutations within the SU C-terminal domain suppressed Env cleavage and incorporation into virions and indicate that these mutations contributed to the domestication of Refrex-1 through multistep events that occurred in the postintegration period. IMPORTANCEDomestic cats are colonized with various exogenous retroviruses (exRVs), such as feline leukemia virus (FeLV), and their genomes contain numerous ERVs, some of which are replication-competent proviruses. The feline hosts, exRVs, and ERVs have complicated genetic interactions and provide an interesting field model for triangular relationships: recombination between FeLV and ERV-DC, which is a feline ERV, generated FeLV-D, a chimeric virus, and FeLV-D is restricted by Refrex-1, an antiretroviral factor corresponding to truncated Env of ERV-DC7 and ERV-DC16. Here, we reconstructed ancestral, functional Env from ERV-DC7 and ERV-DC16 env by inducing reverse mutations to elucidate how Refrex-1 was generated from its ancestor. Our results reveal that they were repeatedly inactivated by mutations preventing Env maturation. Our results provide insights into how ERVs were "domesticated" by their hosts and identify the mutations that mediated these evolutions. Notably, experiments that restore inactivated ERVs might uncover previously unrecognized features or properties of retroviruses. E ndogenous retroviruses (ERVs) are present in all vertebrate genomes and are thought to be the remnants of ancestral germ line infections by exogenous retroviruses (exRVs)...

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“…Notes: Seven sequence names are from Kitano et al (2009). When nucleotide of a sequence is identical with that of the outgroup sequence (SI-2), a dot is given.…”

mentioning

confidence: 99%