Complete mitochondrial DNA sequence,gene organization and genetic variation of control regions in <Emphasis Type="Italic">Parargyrops edita</Emphasis>

ABSTRACT:   The complete nucleotide sequence of the mitochondrial genome of Parargyrops edita was determined by gene amplification using long polymerase chain reaction and direct sequencing techniques. The genome with 16 640 bp contained 37 genes (two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes). The content and order of genes was identical to those in typical teleosts. The major non-coding region of 964 bp in length with several conserved sequence features were identified as the control region (CR). Both COI and ND4 began with a GTG start codon, which is unusual in other fishes. The genetic variation of the CR from 27 wild samples was evaluated. A total of 536 bp consensus sequence of CR was aligned and 26 unique haplotypes were identified. The haplotype diversity (h) was estimated to be 0.997 (standard deviation [SD] 0.011) and nucleotide diversity ( π ) was 0.014 (SD 0.008) for the sample collected from coastal waters of Guangdong Province. It showed a very high level of genetic variation in the sample and also suggested that mtDNA CR sequence analysis can be use to evaluate the genetic diversity and genetic structure of P. edita .     

Complete mitochondrial DNA sequence of the Japanese flying fish <Emphasis Type="Italic">Cypselurus hiraii</Emphasis>

ABSTRACT:   In this study, to develop a technique that enables authentication of processed seafood, the complete nucleotide sequence of the mitochondrial genome for the Japanese flying fish Cypselurus hiraii was determined. Three segments spanning the entire genome were amplified using polymerase chain reaction, and products were subsequently used as templates for direct sequencing with 60 primers. The genome (16 528 base pairs) was found to contain the same 37 genes (two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) as those found in other vertebrate mitochondrial genomes, with the gene order being identical to that typical of vertebrates. A major non-coding region between the tRNA^Pro and tRNA^Phe genes (868 base pairs) appears to be the control (D-loop) region, as it has several conserved blocks characteristic of control regions.     

Complete mitochondrial genome of the sea cucumber Stichopus sp. and its application in the identification of this species

The complete sequence of mitochondrial DNA (mtDNA) from Stichopus sp. (Echinodermata: Holothuroidea: Stichopodidae: Stichopus) was acquired using conventional PCR and long PCR followed by cloning and sequencing. The mtDNA is a circular molecule of 16 257 bp in length, containing the set of 37 genes, including 13 protein‐coding genes (PCGs), 22 tRNA genes and two ribosomal RNA genes. The plus strand consists of 30.9% A, 23.7% C, 16.0% G and 29.3% T bases (AT skew = 0.027; GC skew = ?0.194). All 13 PCGs encode a total of 3782 amino acids and all 22 tRNA genes were predicted to be capable of folding into a clover‐leaf secondary structure. Intergenetic regions in the mitochondrial genome of Stichopus sp. contain 903 bp in total, with the largest continuous region (674 bp, AT% = 58.6) between tRNA‐Thr and tRNA‐Pro. Analysis of phylogenetic relationship of family Stichopodidae and genetic distances (species among the family Stichopodidae and species within Stichopus monotuberculatus group) based on the partial cox1 sequence demonstrates that Stichopus sp. from the South China Sea is a member of S. monotuberculatus complex.     

Genetic comparison between torafugu <Emphasis Type="Italic">Takifugu rubripes</Emphasis> and its closely related species karasu <Emphasis Type="Italic">Takifugu chinensis</Emphasis>

Abstract:   Sequence analyses of mitochondrial (mt) and nuclear genes were performed for genetic comparison between two Takifugu pufferfish species: torafugu T. rubripes and karasu T.  chinensis . With a sequence coverage of 20% in mtDNA, 640, 308, 344, 522 and 697 bp encoding mt 16S ribosomal RNA (rRNA), adenosine triphosphatase 6 ( ATPase 6 ), nicotinamide adenine dinucleotide dehydrogenase subunit 4 ( ND4 ), ND5 and cytochrome b (cyt b ), respectively, among 24 wild torafugu, 24 wild karasu and six hybrid-like samples, 15% of the torafugu identified by external color patterns showed nucleotide sequences consistent with karasu. Meanwhile, sequences of 60% karasu were consistent with those registered for torafugu (AJ421455). As for the hybrid-like samples, two possessed karasu-specific sequences in some base positions while torafugu-specific sequences in others. The remaining hybrid-like samples possessed torafugu-specific sequences. On the other hand, the mt control region did not show such type of consistency. Analysis of nuclear melanocortin receptor genes ( MC1R , MC4R ) among 54 samples showed 99–100% inter- and intraspecific sequence identity. Partial nuclear 18S  rRNA, complete internal transcribed spacer 1 ( ITS1 ), partial 5.8S  rRNA and ITS2 genes showed similar levels of identity, indicating a very low level of variation in their respective gene fragments between the two Takifugu species.     

鳀科鱼类线粒体全基因组序列结构特征及系统发育信息分析

为了解鳀科鱼类的线粒体全基因组序列结构特征及系统发育信息,以期为进化遗传学研究和分子标记的选取提供参考依据,对已知的10种鳀科鱼类的线粒体全基因组进行分析。结果显示:1)鳀科线粒体基因组全序列长度在16 660 bp到17 069 bp之间,基因组的结构和基因排列顺序与其它硬骨鱼类一致。2)比对后获得一致序列长度为15 704 bp(不含D-loop),其中变异位点5 570个,占所有位点数的35.5%。在编码基因中,序列变异程度和Kimura双参数遗传距离最大的是ND6基因(分别是47.5%和0.276),最小的是tRNA拼接序列(分别为18.7%和0.072)。3)基于Ka-Ks的Z检验和Tajima’s D检验表明蛋白质编码基因主要受到净化选择(即负选择,purifying selection)的作用;其中12个蛋白质编码基因(ND6除外)有强烈的净化选择(Ka/Ks<1),而ND6基因受正选择(positive selection)影响较大(Ka/Ks>1)。4)ND4、ND2和Cytb是进行鳀科鱼类系统发育分析的较为理想的分子标记。     

Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus

ABSTRACT: The complete nucleotide sequence of the mitochondrial genome for the Japanese anchovy Engraulis japonicus (Teleostei: Clupeiformes) was determined. The entire genome was purified by gene amplification using the long polymerase chain reaction (PCR) technique, and products were subsequently used as templates for PCR with 56 fish-versatile primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing of the PCR products demonstrated that the genome (16 675 base pairs [bp]) contained the same 37 mitochondrial genes (two ribosomal RNA, 22 transfer RNA and 13 protein-coding genes) as those found in other vertebrates, with the gene order being identical to that in typical vertebrates. A major non-coding region between the tRNA^Pro and tRNA^Phe genes (1024 bp) was considered to be the control (D-loop) region, as it has several conservative blocks characteristic to this region.     

Complete mitochondrial DNA sequence of ayu Plecoglossus altivelis

SUMMARY: We determined the complete nucleotide sequence of the mitochondrial genome for ayu, Plecoglossus altivelis . Two large DNA fragments covering the entire genome were amplified using a long polymerase chain reaction (PCR) technique, and the products subsequently used as templates for PCR with 57 fish-versatile and five species-specific primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing of the PCR products demonstrated that the genome (16 537 bp) contained the same 37 mitochondrial genes (two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) as those found in other vertebrates, with the gene order identical to that in typical vertebrates. A major non-coding region between the tRNA^Pro and tRNA^Phe genes (857 bp) was considered to be the control region (D-loop), as it has several conservative blocks that are characteristic to this region.     

Complete mitochondrial DNA sequence of Atlantic horse mackerel Trachurus trachurus and molecular identification of two commercially important species T. trachurus and T. japonicus using PCR-RFLP

ABSTRACT:   To characterize and identify mitochondrial DNA (mtDNA) nucleotide sequence variation in two commercially important Trachurus species, Trachurus trachurus and T. japonicus , the complete mtDNA sequence of T. trachurus was determined. The T. trachurus mtDNA consists of 16 559 bp, containing 22 transfer RNA (tRNA) genes, two rRNA genes, and 13 protein-coding genes. Comparing the mtDNA nucleotide sequences of the Trachurus species, a polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method was developed to differentiate these two commercially important species. The primer pair Lt1-ND5 and Ht1-ND5, corresponding to ND5 , was designed to amplify a 360-bp fragment. Following digestion with Eco  RI, the PCR product for T. japonicus resulted in 93- and 267-bp fragments, while T. trachurus lacked a restriction site for Eco  RI. In contrast, after digestion with Hin  fI, the T. trachurus PCR product yielded 44-, 84-, and 232-bp fragments, while the T. japonicus product was not digested. The PCR-RFLP analysis established in the present study was useful for identifying T. trachurus and T. japonicus .     

Complete nucleotide sequences of mitochondrial DNA of long-finned squid Loligo edulis

The complete nucleotide sequence of the mitochondrial genome of long-finned squid Loligo edulis forma kensaki (L. edulis f. kensaki, Teuthida: Myopsida) was determined. It contains 13 protein-coding genes, 12SrRNA, 16SrRNA, and the 22 tRNA genes, and three long noncoding regions. We also determined the mitochondrial genome nucleotide sequence of seasonal brood samples of L. edulis f. budo collected from the western part of the Sea of Japan in the autumn to winter seasons, which showed morphologic discrepancies with L. edulis f. kensaki. Comparison of the two complete sets of mitochondrial DNA data showed that the similarity of the two sequences was as high as 99.9?%, with only eight nucleotide substitutions in coding regions. The complete mitochondrial genome of Loligo edulis f. kensaki from Nagasaki Pref. is 17360?bp and L. edulis f. budo from the Shimane Pref. is 17351?bp. The nucleotide sequences and haplotype patterns in ND1 suggest that L. edulis f. kensaki and L. edulis f. budo share a single genetic background.     

奥利亚罗非鱼线粒体基因组全序列测定与系统进化分析

采用LA-PCR(long amplification polymerase chain reaction)扩增方法获得奥利亚罗非鱼(Oreochromis aureus)线粒体基因组全序列.分析表明,序列全长16 632 bp,包括13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和1个长度为931 bp的主非编码区.A、T、G、C碱基的组成分别为27.89％、25.50％、15.62％、30.99％.基因排列与罗非鱼属的其他物种一致.13个蛋白质基因除COX1用TGT做起始密码子外,其他均以ATG为起始,终止密码子除COX2、Cyt b、ND4为不完整的T,其余基因均以典型的TAA做终止密码子.22个tRNA的二级结构都具有典型三叶草结构.系统发育分析显示,罗非鱼属与丽鱼科(Cichlidae)其他物种分开,聚为单系群,其中奥利亚罗非鱼与尼罗罗非鱼亲缘关系较近,莫桑比克非鱼和罗非鱼KM-2006亲缘关系较近.本研究旨在为进一步利用线粒体基因组分析罗非鱼群体遗传多样性、亲缘关系以及丽鱼科系统进化提供基础依据.     

仿刺参线粒体全基因组序列结构及比较研究

利用已构建的仿刺参cDNA文库得到的线粒体DNA(mtDNA)相关基因序列设计扩增引物,测定了大连仿刺参线粒体基因组全序列,并对其进行了基因构成和进化分析。仿刺参线粒体基因组序列长16 109bp,其基因构成与其他后口动物基本一致,包括37个基因(2个rRNA基因、22个tRNA基因和13个蛋白质编码基因)和3个主要的非编码区。在其37个基因中,ND6、tRNASer(AGN)、tRNAGln、tRNAAla、tRNAVal、TrnaAsp位于L链上,其余均位于H链上。在13个蛋白质编码基因中,除ND1的起始密码子为GTG外,其余均以ATG作为起始密码子;除Cytb以"T"作为终止密码子外,其他蛋白质基因均具有完全的终止密码子,且在已知的棘皮动物线粒体蛋白质基因中,部分基因的起始和终止密码子表现出一定的纲内特异性。比较分析了大连、青岛、威海仿刺参线粒体基因组,三者的基因组成和排列相同,碱基组成相近,蛋白质编码基因的起始和终止密码子完全一致,但存在核苷酸和氨基酸序列的差异。三者的控制区序列存在多个插入/缺失和SNP位点。根据COI、Cytb和ND4计算了三者之间的遗传距离为0.006～0.018,遗传距离分析和系统进化关系分析都显示青岛仿刺参和威海仿刺参的关系较大连仿刺参更近。     

Stock structure of Japanese flounder inferred from morphological and genetic analyses

ABSTRACT:   Stock structure of Japanese flounder Paralichthys olivaceus has been inferred mainly from either morphological or genetic analyses. However, because the results of both analyses did not always agree with each other, an inclusive conclusion has never been obtained. In this study, the stock structure has been inferred from both morphological and genetic analyses using 722 wild Japanese flounder collected from nine locations along the Japanese coast. The dorsal and anal fin ray counts were larger in the southern than in the northern populations. In total, 1041 bp of mitochondrial NADH dehydrogenase subunit-2 ( ND2 ) and 1830 bp of ND5 sequences were aligned. There are 578 variable sites in the concatenated sequence from the two genes, which defined a total of 490 haplotypes. Both results of morphological and genetic analyses indicated that the western Kyushu group, which included the Nagasaki and Kagoshima populations, was divided from the other seven populations. This is the first report to reveal the heterogeneity of the western Kyushu group based on statistical analysis.     

Complete mitochondrial genome sequence of Japanese cockle Fulvia mutica (Cardiidae)

The complete mitochondrial genome (mt-genome) sequence of Fulvia mutica (Veneroida; Cardiidae) was determined. The genome is 19,110 bp in size and contains 42 genes, including the ATP synthase subunit 8 gene (atp8). All genes are on the same strand, as in other marine bivalves. It is extremely different in gene arrangement and size from that of Acanthocardia tuberculata, the only species belonging to Cardiidae with complete genome sequence data. The presence of putative atp8 genes in two additional reported bivalve species, A. tuberculata and Sinonovacula constricta was also inferred by revising their deposited sequence data. It was suggested that atp8 genes of heterodont bivalves could be translated to 37–39 amino acid sequences highly conserved within families, excluding Hiatella arctica with 53 amino acids. The mt-genome of F. mutica also contains two large duplicated regions related to different sequence motifs. One of the regions consists of five nearly identical copies of the 154 bp motif that includes a transfer RNA gene for cysteine. This region exhibited polymorphism in the number of repeats among individuals, suggesting the existence of a variable number of tandem repeats, which was expected to provide valuable information for developing useful genetic markers for phylogenetic study and population genetics.     

艾氏蛇鳗线粒体基因组全序列结构分析和系统发育关系探讨

本研究采用高通量测序技术获得了艾氏蛇鳗(Ophichthus evermanni)线粒体基因组全序列, 并对其结构和特征进行了分析。结果表明, 艾氏蛇鳗线粒体基因组全长 17759 bp, 包含了 13 个蛋白编码基因(PCGs)、22 个转运 RNA 基因(tRNA)、2 个核糖体 RNA 基因(rRNA)、2 个控制区(D-loop)和 1 个轻链复制起始区(O_L)。线粒体 DNA 全序列的碱基组成分别为 A (31.27%)、G (16.19%)、C (26.22%)和 T (26.32%), 其中 A+T 含量(57.59%)大于 G+C 含量 (42.41%), 呈现出明显的 A+T 偏好性。与大多数硬骨鱼类不同, 艾氏蛇鳗线粒体基因组中发生了基因重排现象, ND6 基因和 tRNA-Glu 移到了 tRNA-Thr 和 tRNA-Pro 之间, 且 ND6 基因上游还存在另一个高度同源的 D-loop 区。 tRNA-Gln (Q)、tRNA-Ala (A)、tRNA-Asn (N)、tRNA-Cys (C)、tRNA-Tyr (Y)、tRNA-Ser^UCA (S1)、tRNA-Glu (E)、 tRNA-Pro (P)和 ND6 9 个基因位于 L 链, 其余基因均位于 H 链。除 tRNA-Ser (AGC)外, 其余 21 个 tRNA 均为典型的三叶草二级结构。分别采用邻接法和最大似然法, 基于 12 个蛋白编码基因(ND6 除外)构建了蛇鳗科鱼类系统发育关系树。结果显示艾氏蛇鳗与短尾蛇鳗(O. brevicaudatus)和食蟹豆齿蛇鳗(Pisodonophis cancrivorus)的亲缘关系较近, 蛇鳗属是蛇鳗科鱼类中分化较晚的一个类群。研究结果丰富了蛇鳗科鱼类线粒体基因组数据库, 也为该类群鱼类的系统分类研究提供了参考资料。     

鲂属鱼类线粒体基因组的比较及其系统发育分析

基于GenBank中团头鲂线粒体基因组全序列和三角鲂、厚颌鲂、广东鲂的部分线粒体基因组序列,设计引物扩增出三角鲂、厚颌鲂和广东鲂3种鱼线粒体基因组全序列,同时对4种鲂属鱼类线粒体基因组全序列进行了比较分析。结果表明,4种鲂属鱼类线粒体基因组基因排列顺序完全相同,排列紧密,均包含13个蛋白质编码基因、22个tRNA、2个rRNA、1个非编码控制区(D-loop区)和1个轻链复制起始区(OL区)。除ND6和8个tRNA在L链上编码外,其余的基因均在H链上编码。4种鲂属线粒体基因组13个蛋白质编码基因中,均呈现出较强的A+T偏向性和C碱基偏好。全序列比对结果显示,共有758个变异位点,其中非简约性信息位点有691个,占总变异位点的91.16%,简约性信息位点有67个,仅占总变异位点的8.84%。22个tRNA基因中只有11个存在种间变异,共23个变异位点,主要发生在tRNA三叶草结构的TΨC和DHU臂环上。13个蛋白质编码基因中共检测出626个变异位点,这些变异主要发生在密码子第三位,占总变异位点的82.59%,其中变异位点数最多的是Cyt b基因,达84个,其次是ND 4基因(83个)。因此,Cyt b和ND4基因可作为备选的分子标记,用于鲂属群体间的遗传学研究。基于4种鲂属鱼类线粒体基因组全序列构建的ML树和BI树均显示,三角鲂与厚颌鲂的亲缘关系最近,团头鲂与它们的亲缘关系相对较近,而广东鲂与前述3种鲂属鱼类的亲缘关系均较远。     

黄条鰤线粒体全基因组测序及结构特征分析

通过二代测序、软件拼接获得中国黄海海域黄条鰤(Seriola aureovittata)线粒体基因组全序列。其序列全长为16609 bp,碱基组成分别为A(26.68%)、G(17.84%)、C(30.12%)和T(25.36%);共有13条蛋白编码基因, 22个tRNA基因, 2个rRNA基因,除NAD6、trnQ、trnA、trnN、trnC、trnY、trnS、trnE、trnP外,其余基因均在H链上编码。黄条鰤线粒体基因组全序列与蛋白编码基因的A+T含量分别为52.05%和51.085%,具有明显的AT偏好性。线粒体基因中存在2个散在重复序列,分别位于NAD1基因序列正义链的中游和COX2基因序列反义链的上游。在其22个tRNA基因中,除了tRNAGly外,均具有典型的三叶草二级结构。黄条鰤线粒体基因组的蛋白编码基因起止位点与密码子除COX1、NAD5外,均与日本海域出产的黄条鰤(Seriola lalandi)完全吻合,且COX1、NAD5基因皆短于日本黄条鰤;两者间存在一定的遗传差异。基于18种隶属于13属的鲹科鱼类线粒体基因组全序列构建系统发生树,可知小甘鲹(Seriolina nigrofasciata)、黄条鰤、五条鰤(Seriola quinqueradiata)、高体鰤(Seriola dumerili)、长鳍鰤(Seriola rivoliana)同属一近支,且黄条鰤与五条鰤亲缘关系最近,与小甘鲹进化距离较远。     

青鱼线粒体ND4L的SNP筛选及在两种体色群体中的分布

为了分析青鱼线粒体蛋白编码基因与体色性状的相关性,从而筛选出与体色相关的SNP分子标记。本研究选取了5尾广东佛山灰色青鱼和5尾扬州邗江正常体色黑色青鱼群体的皮肤组织,通过qPCR检测13个线粒体蛋白质编码基因在两种颜色群体皮肤组织中的表达量,并进行显著性分析。对表达差异最明显的蛋白编码基因CDS区序列设计引物,并选取78尾佛山灰色青鱼样本和92尾邗江黑色青鱼样本进行测序,根据测序峰图筛选出SNP位点。结果发现：13个线粒体蛋白质编码基因中COII基因表达量最高,ND5基因表达量最低,ND4L基因在两种体色青鱼中的表达差异最为明显。在对170尾青鱼样本的线粒体ND4L基因上共检测到了2个SNP位点,位于编码区,且都为同义突变。卡方检验表明,252bp(C/T)处的SNP位点在两种体色青鱼群体中的等位基因频率和基因型频率都有极显著的差异(p＜0.01),243bp(A/G)处的SNP位点在两种体色青鱼群体中的等位基因频率和基因型频率差异不显著(p＞0.05),因此线粒体ND4L基因中的SNP位点C252T与青鱼体色显著相关。本研究中成功找到一个与青鱼体色相关的SNP分子标记,可以在青鱼的养殖和育种中提供理论分子层面的指导和帮助。     

Species identification of <Emphasis Type="Italic">Pinctada imbricata</Emphasis> using intergenic spacer of nuclear ribosomal RNA genes and mitochondrial 16S ribosomal RNA gene regions

ABSTRACT:   For pearl production, pearl oyster seeds from foreign pearl oysters as well as hybrids between native and such foreign pearl oysters are produced in Japanese hatcheries. However, it is very difficult to identify these pearl oysters and hybrids based on morphological measurements. Thus, a molecular identification method for distinguishing Atlantic pearl oysters Pinctada imbricata from the Indian-Pacific pearl oyster group including P. martensii and P. fucata , was developed. The polymerase chain reaction (PCR) products of the partial intergenic spacer (IGS) of nuclear ribosomal RNA (rRNA) genes exhibited length polymorphism between P. imbricata (590 bp) and the other two species (427 bp). The restriction fragment length polymorphism analysis of the PCR products (PCR-RFLP) cleaved with Mse  I observed in the IGS of nuclear rRNA genes also gave different profiles between P. imbricata and the other two species. The difference in PCR-RFLP using Alu  I was also detected in the mitochondrial 16S rRNA gene regions between P. imbricata and the other two species. Thus, the method developed enables the distinction of P. imbricata from P. martensii and P. fucata .     

Species identification method for <Emphasis Type="Italic">Scombrops boops</Emphasis> and <Emphasis Type="Italic">Scombrops gilberti</Emphasis> based on polymerase chain reaction-restriction fragment length polymorphism analysis of mitochondrial DNA

ABSTRACT:   Gnomefish Scombrops boops and Scombrops gilberti are commercially important fishes in Japan, but these species are often confused in the markets because of their morphological similarity. To identify these two species, we performed nucleotide sequencing and restriction fragment length polymorphism (RFLP) analysis on 16S ribosomal RNA (rRNA) gene and the control region in mitochondrial DNA. Five and 12 nucleotide substitutions were observed between species in the 777-bp 16S rRNA gene and 471-bp control region, respectively. Diagnostic restriction sites for discriminating between S. boops and S. gilberti were found in the 16S rRNA gene, but not in the control region. Polymerase chain reaction (PCR)–RFLP analysis using two enzymes, Eco NI and Mva I, clearly discriminated between S. boops and S. gilberti identified by meristic characters. The PCR–RFLP analysis identified most of the 168 Scombrops young caught in the coastal waters of the Izu and Miura peninsulas as S. boops , suggesting that S. gilberti juveniles are rare in this area.     

Low genetic variability in an endangered population of fiddler crab <Emphasis Type="Italic">Uca arcuata</Emphasis> on Okinawajima Island: analysis of mitochondrial DNA

ABSTRACT:   Restriction fragment length polymorphism analysis was performed on polymerase chain reaction-amplified DNA fragments containing the D-loop , ND2 , and CO I genes of fiddler crab Uca arcuata mitochondrial DNA. In total, 316 individuals from six populations in Japan and two populations in Taiwan were analyzed using five restriction endonucleases ( Afa I, Bcn I, Cfr 13I, Hae III and Hin fI), yielding 85 haplotypes. Samples were taken from Nakagusuku Bay, Okinawajima Island, which is the only known distribution of U. arcuata in the Ryukyu Archipelago. The Okinawajima Island population is isolated geographically from others and showed a marked low genetic variability ( h  = 0.2539, π  = 0.0005) and significant differentiation from other population samples in haplotype composition. We suggest that a substantial decrease in the genetic variability of the Okinawajima Island population was caused by genetic drift under the conditions of small population size and low gene flow from other populations. It is important to conserve the intertidal zone in Nakagusuku Bay for the maintenance of this endangered population.