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Molecular Phylogeny of Endogenous Retrovirus HERV-F Family in Japanese and Rhesus Monkeys
Kim, Heui-Soo,Jeon, Seung Heui,Yi, Joo-Mi,Kim, Tae-Hyeong,Kim, Myung-Sook,Hyun, Byung-Hwa,Takenaka, Osamu 한국유전학회 2002 Genes & Genomics Vol.24 No.2
A new human endogenous retroviral family (HERV-F) has recently been identified from the human chromosome 7q31.1-q31.3 that was identical to the XA34 cDNA clone isolated from a human glioma cDNA library with an ERV-9 probe. The current study investigated pol fragments of the HERV-F family from Japanese and rhesus monkeys and compared them with those of the HERV-F (Hu-XA34) family. Fourteen pol fragments of the HERV-F family were detected from the monkeys, which showed a 78.7-95.4% sequence similarity with those of HERV-F (Hu-XA34). Clones FJM-1, FJM-7, FJM-14, and FJM-15 from the Japanese monkey and FRH-1 and FRH-4 from the rhesus monkey exhibited no disruption due to point mutation or insertions/deletions. The ratio of synonymous to non-synonymous substitutions indicated that negative selective pressure was acting on these clones. Therefore, the pol gene sequences could be associated with an active provirus in the monkey genomes. A phylogenetic analysis of the pol fragments from humans and monkeys using the neighbor joining and maximum parsimony methods showed six groups, indicating that either the HERV-F family was amplified at least six times after its original integration into the monkey genome or the occurrence of independent integration events during primate evolution.
Y 염색체의 TSPY 유전자 분석에 의한 신세계원숭이의 분자계통분류
김희수,Takenaka, Osamu 한국유전학회 2001 Genes & Genomics Vol.23 No.3
The Y chromosomal DNA sequences among related genera and species are useful in refining evolutionary classification and represent a valuable source of characters for phylogenetic relationships. In our previous study, we have used testis-specific protein Y (TSPY) gene sequences that have beneficial features for the resolution of the Homo-Pan-Gorilla trichotomy. To understand the phylogenetic relationships among Saimiri-Cebus-Aotus trichotomy in New World monkeys, we have sequenced the first intron of the TSPY gene from the capuchin monkeys, night monkeys, squirrel monkeys, long-haired spider monkeys, and black-handed spider monkey. The TSPY intron has diverged at 180 of the 652 nucleotides positions. The evolutionary rates of nucleotide substitutions per site per year were higher in the TSPY intron than in the ZFY intron within Y-chromosomal DNA. Phylogenetic tree by the neighbor-joining and maximum parsimony methods using the sequence divergence from the TSPY intron was constructed, suggesting that the squirrel monkey and the capuchin monkey showed a sister relationship among New World monkeys.
Kim, Heui-Soo,Takenaka, Osamu,Crow, Timothy J. 부산대학교 유전공학연구소 1999 분자생물학 연구보 Vol.15 No.-
An investigation was undertaken of primate pol gene sequences from a novel endogenous retrovirus family, ERV-W, related to a new human endogenous retrovirus family (HERV-W) that includes multiple sclerosis-associated retrovirus (MSRV) sequences identified in particles recovered from monocyte cultures from patients with multiple sclerosis. The pol gene sequences of the ERV-W family were detected in hominoids and Old World monkeys, but in New World Monkeys, whereas ERV-W long terminal repeat-like elements were detected in all primates (hominoids, Old World monkeys and New World monkeys). Thirty-two pol gene sequences from hominoids and Old World monkeys showed a high degree of sequence identity to MSRV and other HERV-W sequences. Phylogenetic analysis indicated close relationships of pol gene sequences across primate species. The analysis suggests that the ERV-W family has evolved independently but in constrained patterns ('parallel evolution') in different primate species, including man. The ratio of synonymous to non-synonymous substitutions indicated that negative selective pressure is acting on CHW1-1 from chimpanzee, HBW6-6 from baboon and HWX5 from man, sequences that have no disruption by point mutation or insertions/deletions. Therefore, these pol gene sequences could be associated with an active provirus in primates. The findings indicate that the ERV-W family has continued to evolve in the course of the primate radiation and may include members with a capacity to influence gene function and possibly cause disease.
Kim, Heui Soo,Takenaka, Osamu 한국유전학회 1995 Genes & Genomics Vol.17 No.4
Testis specific protein Y-encoded (TSPY) genes from the pongidae (chimpanzee, gorilla, and orangutan) and baboons as an outgroup have been sequenced by PCR amplification and DNA sequencing. The TSPY gene sequences were compared with each other and with the published human sequence (Zhang et al., 1992). Substitutions were detected at 144 of the 755 nucleotide positions compared. Deletions and/or additions were noted at twelve locations. The most divergent representative of higher primates (orangutan) differed from the other three (humans and African apes) by 7.25% (range 6.3∼8.2%). The phylogenetic tree constructed by the neighbor-joining method suggests that human and chimpanzee are more closely related to each other than either of them is to gorilla and the tree also supported by the maximum likelihood and the strict consensus maximum parsimony tree. The number of nucleotide substitutions per site between human and chimpanzee, gorilla, and orangutan for TSPY intron were 0.023, 0.049, and 0.09, respectively. The rates of nucleotide substitutions per site per year were higher in TSPY intron than TSPY exon and higher in the TSPY intron than ZFY intron in homonidae.
일본원숭이의 리보솜 단백질 S4 유전자의 분자적 클로닝 및 진화적 분석
김희수(Heui Soo Kim),(Takashi Kageyama),(Osamu Takenaka) 한국유전학회 2001 Genes & Genomics Vol.23 No.1
N/A We cloned and sequenced the cDNA encoding ribosomal protein S4 (RPS4) from testis cDNA library of the Japanese monkey. The monkey RPS4Y gene encodes a deduced protein of 263 amino acids and share 92.8% and 95.4% amino acid sequence identities with the deduced mouse Rps4 and human RPS4Y. Northern blot analysis of poly (A) mRNA from the Japanese monkey revealed approximately 1.0 kb transcript. Molecular evolutionary rate was 0.2 ∼ 0.3 × 10-9/site/year in the Japanese monkey. This value was at least three fold lower than that of the TSPY and SRY genes of human Y chromosome, suggesting that the RPS4Y gene has been evolved conservatively during primate evolution.