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Sequence polymorphisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese population
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Sequence polymorphisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese population   (Citations: 26)
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Sequence polymorphisms of the hypervariable mitochondrial DNA (mtDNA) regions HVI and HVII, and coding region polymorphisms were investigated in 211 unrelated individuals from the Japanese population. Sequence comparison of the HVI and HVII regions led to the identification of 169 mitochondrial haplotypes defined by 147 variable positions. Among them 145 types were observed in only 1 individual; the other 24 types were shared by 2 or more individuals. The gene diversity was estimated at 0.9961, and the probability of two randomly selected individuals from the population having identical mtDNA types was 0.86%. We also established phylogenetic haplogroups in the Japanese population based on the coding and control region polymorphisms and compared the haplotypes with those in other Japanese, Korean and Chinese populations. As a result, three new subhaplogroups, G4a, G4b, and N9b, and several haplotypes specific for the Japanese and Korean populations were identified. The present database can be used not only for personal identification but also as an aid for geographic or phenotype (race) estimation in forensic casework in Japan.
Journal: International Journal of Legal Medicine - INT J LEGAL MED , vol. 117, no. 4, pp. 218-225, 2003
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    • ...We did not include variation in the C-stretch in calculating number of haplotypes because this variation frequently shows length heteroplasmy in most haplogroups [9] and haplotypes with a different length of C-stretch are sometimes obtained from biological materials from the same individuals...
    • ...The M7b1 haplotype has been found throughout East and Southeast Asia in the Korean (0.3%) [18-21], Chinese (1.8%) [22-29], Japanese (0.15%) [5, 9, 30-35], Thai (1.9%) [36], Singapore Malay (2.4%) [3], Southern Chinese...
    • ...This motif is frequent in the Island Southeast Asian (8.3%) [15], Aboriginal Taiwanese (4.4% and 7.87%) [39, 40], Aboriginal Malay (5.8%) [14, 41], Singapore Malay (10%) [3], and Vietnamese (2.7%) [38] populations; is rare in the Chinese (0.5%) [22-29], Thai (0.5%) [36], and Southern Chinese Austro-Asiatic and Daic (0.1%) [37] populations; and has never been found in the Japanese [5, 9, 30-35] or Korean [18-21] populations...
    • ...E1a, E1b, and E2 haplogroups have not been found in the Japanese [5, 9, 31-35], Korean [18-21], Chinese [22-29], Thai [36], Southern Chinese Daic and Austro-Asiatic [37], Vietnamese [38], or Aboriginal Malay populations [14, 41]...
    • ...The haplogroup Q1 is a major haplogroup in Melanesia (13.9%) [16] and Polynesia (7.9%) [43], is found at a low frequency in Island Southeast Asia (2.9%) [15], but is rarely found in modern or Aboriginal Malay populations [3, 15]; neither has it been observed in East Asian populations such as the Chinese [22-29], Korean [18-21], Japanese [5, 9, 30-35], Thai [36], Vietnamese [38], Southern Chinese Daic and Austro-Asiatic [37], or Aboriginal ...
    • ...Southern Chinese Daic (1.55%) [38], Singapore Malay (1.5%) [3], Vietnamese (0.53%) [39], Chinese (0.36%) [23- 30], and Island Southeast Asian populations (0.2%) [14], but has never been found in the Aboriginal Malay [14, 15], Southern Chinese Austro-Asiatic [38], Korean, or Japanese populations [5, 9, 19-22, 31-36]...
    • ...The G2a1 lineage is found widely in East Asia, including in Chinese [23-30], Korean [18-21], Japanese [5, 9, 30-35], Central Asian [44], and Southern Chinese Daic populations [37], but not in Southeast Asian populations, such as the Thai [36], Vietnamese [38], Southern Chinese Austro-Asiatic [37], Island Southeast Asian [15], Aboriginal Malay [14, 41], or Singapore Malay populations [3]...
    • ...Regarding the D haplogroup, the same haplotype as that of the D4a3 lineage has been found in East Asia, including in the Korean (0.9%) [18-21], Thai (0.5%) [36], Southern Chinese Daic (0.4%) and Austro-Asiantic (0.8%) [37], Japanese (0.3%) [5, 9, 30-35], and Chinese populations (0.2%) [22-29], but not in the Vietnamese [38], Island Southeast Asian [15], Aboriginal Malay [14, 41], or Singapore Malay populations [3]...
    • ...The same haplotype as that of the D4* lineage (Mal-40) has not been found in East [5, 9, 18-35] or Southeast Asia [16, 36-40], including in the Aboriginal Malay [14, 41] or Singapore Malay populations [3]...
    • ...N9a1 is sporadically found in East Asia [5, 9, 18-35, 37], but has almost never been found in the Thai [36], Vietnamese [38], Island Southeast Asian [15], Aboriginal Taiwanese [39], Singapore Malay [3], or Aboriginal Malay [14, 41] populations...
    • ...Although this lineage is widely distributed but not frequent throughout East Asia, including in the Japanese [5, 9, 30-35], Korean (0.1%) [18-21], Taiwanese Han (0.7%) [22], Daic (1.0%) and Southern Chinese Austro-Asiatic (0.8%) [37], Continental Southern Chinese (1.7%) [23, 27], Vietnamese (1.6%) [38], and Singapore Malay populations (0.5%) [3], it is comparatively frequent in the Aboriginal Taiwanese (5.5%) [39] and Island Southeast ...
    • ... and Singapore Malay populations (0.5%) [3], it is comparatively frequent in the Aboriginal Taiwanese (5.5%) [39] and Island Southeast Asian populations (2.8%) [15 ]. The B4c2 lineage was also comparatively restricted to the Island Southeast Asian (2.2%) [15], Singapore Malay (2.5%) [3], Thai (2.4%) [36], and Southern Chinese Daic (0.8%) and Austro-Asiatic (2.4%) populations [37], but was rare or not found at all in the East Asian [5, 9, ...
    • ...The other B lineages are common haplogroups and are distributed widely in East and Southeast Asian populations [3, 5, 9, 15, 18-39], and some of them (B4a) even further into Oceanian populations [16, 40]...
    • ...Among the four kinds of the present F haplogroup, F1a was very frequent in all East, Continental Southeast, and Island Southeast Asian populations [3, 5, 9, 15, 18-40], but F1a1a was relatively restricted to Continental Southeast and Island Southeast Asia populations [3, 22, 23, 26, 27, 36- 38], including Aboriginal Malays [14, 41]...
    • ...F1a2 seems to be a rare lineage in East and Southeast Asian populations [3, 5, 21, 24, 27, 29, 32, 34, 36-39], and F1a3 is also not frequent in East and Southeast Asian populations [5, 9, 18- 39], but is more frequent in Island Southeast Asian (2.3%) and Singapore Malay populations (2.0%) [3, 15]...
    • ...In the two types of the Southeast Asian R haplogroup, the R22 lineage was mainly found in the Island Southeast Asian population (2.3%) [15], but has rarely been found in other Southeast and East Asian populations [3, 5, 9, 18-35, 37, 39, 40]...
    • ...It is further found in some parts of Island Southeast Asia (0.9%) [15] and in Singapore Malays (1.0%) [3], but it is almost never found in East Asia [5, 9, 18-27, 29-35, 39]...

    S. Maruyama, et al. MtDNA control region sequence polymorphisms and phylogenetic analysis ...

    • ...Therefore, we have carried out a phylogenetic analysis of mtDNA polymorphisms, expanding previous data on Japanese populations [5, 10], by determining basal haplogroup lineages and establishing new lineages by complete...
    • ...In the phylogenetic analysis, the haplogroup motif and private mutations were confirmed by sequencing of additional PCR products and checking against our own previously established database [5] and databases reported by others [10], even when there was little doubt as regards to their accuracy [5, 10]...
    • ...In the phylogenetic analysis, the haplogroup motif and private mutations were confirmed by sequencing of additional PCR products and checking against our own previously established database [5] and databases reported by others [10], even when there was little doubt as regards to their accuracy [5, 10]...
    • ...Because this variation frequently shows length– heteroplasmy in most haplogroups [5] and haplotypes with a different length of C-stretch have been obtained from biological materials from the same individuals, we did not include this variation in calculating number of haplotypes...
    • ...The M7a2 haplogroup lineages have been found in Japanese [5, 10, 18, 19, 25, 26], but not in Koreans and Chinese...
    • ...M11 is rare in Japan [5, 10, 18, 19, 25, 26] and is found in 0.36% of Korean [14, 15, 23, 24] and 0.9% of Chinese populations [9, 16, 17, 20–22]...
    • ...The D4c1b1 control region motif is found in 0.95% of Japanese [5, 10, 18, 19, 25, 26], 0.29% of Korean [14, 15, 23, 24], and 0.15% of Chinese populations [9, 16, 17, 20–22]...
    • ...The control region haplotype of this linage, which includes the A4a1 and A4* haplogroups (16223– 16234/16249–16290–16319–16362), was found in 0.34% of Japanese [5, 10, 18, 19, 26], 0.14% of Korean [23, 24], and 0.18% of Chinese populations [21]...
    • ...This haplogroup branch has only been found in these two samples, and a similar control region haplotype has not yet been found in other Japanese [5, 18, 19, 25, 26], Korean [14, 15, 23, 24], or Chinese populations [9, 16, 17, 20–22]...

    C. Nohira, et al. Phylogenetic classification of Japanese mtDNA assisted by complete mit...

    • ...Content and design of the open database The current open database of mtDNAmanager contains 7090 mtDNA control-region sequences grouped in the following five subsets: African (n = 1388), West Eurasian (n = 2857), East Asian (n = 1557), Oceanian and Admixed (n = 1288) [50-62]...

    Hwan Young Lee, et al. mtDNAmanager: a Web-based tool for the management and quality analysis...

    • ...As judging from the HVS-I motifs, the haplogroup M9a contribution alone would, for example, be as high as 6/150 (4.0%) in Nishimaki et al. (43), take intermediate values 5/162 (3.1%) in the HVS-I&II data set of Imaizumi et al. (44) and 5/231 (2.2%) in the HVS-I data set of Tajima et al. (45), but merely 2/211 (0.9%) in the data from Maruyama et al. (46)...

    Qing-Peng Kong, et al. Updating the East Asian mtDNA phylogeny: a prerequisite for the identi...

    • ...In addition, the sequence 16093C–16188.1C–16193.1C–16362C–16390A– 146C–150T–152C–182T–217C, which was reported to be found in some Japanese individuals in haplogroup D5, was observed in one Korean individual, and was assigned to haplogroup D5, as described byMaruyama et al. [26]...
    • ...Also, in reference to Kong et al. [12], G4a inMaruyama et al. [26] corresponds to G1a in the present study...
    • ...The distribution pattern of Korean mtDNA haplogroup frequencies generally parallels to that of the Japanese [13, 26], but showed slight differences versus that of the Chinese [9, 13]...
    • ...The D4* haplogroup occurred at highest frequency in Koreans (15.7% in this study, 16.5% according to Allard et al. [13], and31.9%byMaruyamaetal.[26])andinJapanese(19.6% Allard et al. [13] and 35.5% Maruyama et al. [26]), and was also common in Chinese (6.2% Allard et al. [13] and 14.2% Maruyama et al. [26])...
    • ...The D4* haplogroup occurred at highest frequency in Koreans (15.7% in this study, 16.5% according to Allard et al. [13], and31.9%byMaruyamaetal.[26])andinJapanese(19.6% Allard et al. [13] and 35.5% Maruyama et al. [26]), and was also common in Chinese (6.2% Allard et al. [13] and 14.2% Maruyama et al. [26])...
    • ...The D4* haplogroup occurred at highest frequency in Koreans (15.7% in this study, 16.5% according to Allard et al. [13], and31.9%byMaruyamaetal.[26])andinJapanese(19.6% Allard et al. [13] and 35.5% Maruyama et al. [26]), and was also common in Chinese (6.2% Allard et al. [13] and 14.2% Maruyama et al. [26])...
    • ...However, the G haplogroup and its sub-haplogroups were observed in relatively high frequencies in Koreans (8.6% in the present study and 5.2% by Maruyama et al. [26]) and Japanese populations (10.4% Maruyama et al. [26]), but occurred sparsely in the Chinese (4% Allard et al. [13] and 3.4% Maruyama et al. [26])...
    • ...However, the G haplogroup and its sub-haplogroups were observed in relatively high frequencies in Koreans (8.6% in the present study and 5.2% by Maruyama et al. [26]) and Japanese populations (10.4% Maruyama et al. [26]), but occurred sparsely in the Chinese (4% Allard et al. [13] and 3.4% Maruyama et al. [26])...
    • ...However, the G haplogroup and its sub-haplogroups were observed in relatively high frequencies in Koreans (8.6% in the present study and 5.2% by Maruyama et al. [26]) and Japanese populations (10.4% Maruyama et al. [26]), but occurred sparsely in the Chinese (4% Allard et al. [13] and 3.4% Maruyama et al. [26])...

    Hwan Young Lee, et al. Mitochondrial DNA control region sequences in Koreans: identification ...

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