85 results on '"Hisashi Okuyama"'
Search Results
2. Complete mitochondrial DNA sequence of the Japanese endemic catfish Silurus lithophilus (Siluriformes: Siluridae)
- Author
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Yuu Kishimoto, Hisashi Okuyama, and Jun-ichi Takahashi
- Subjects
next-generation sequencing ,catfish ,lake biwa ,silurus lithophilus ,mitochondrial dna ,Genetics ,QH426-470 - Abstract
The Japanese endemic catfish Silurus lithophilus is distributed only in Lake Biwa, Lake Yogo, and their river drainages. There are four species of the genus Silurus in Japan, of which S. lithophilus has a limited distribution. This catfish needs to be collected for DNA data owing to the lack of information related to its conservation. Here, the complete mitochondrial genome of the S. lithophilus from Lake Biwa in Japan was analyzed using next-generation sequencing. The mitochondrial genome of S. lithophilus was identified as a 16,524 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with one A + T-rich control region. The AT content was 55.89%. The heavy (H)-strand was predicted to have 12 PCGs and 15 tRNA, and 2 rRNA genes, whereas the light (L)-strand was predicted to contain one PCG and seven tRNA genes. The start codons ATG and GTG were found in 13 PCGs. The stop codons TAA, TAG, and AGA were observed in all PCGs, except CytB. All tRNA genes formed typical cloverleaf secondary structures. The molecular phylogenetic relationship, inferred using 13 PCGs (based on the maximum likelihood), was consistent with that reported in previous studies, which predicted a sister relationship between S. lithophilus and S. asotus. The results also clearly indicated that S. lithophilus is a valid species.
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- 2021
- Full Text
- View/download PDF
3. Complete mitochondrial DNA sequence of the Eastern Asian catfish Silurus asotus (Siluriformes: Siluridae) from Lake Biwa in Japan
- Author
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Yuu Kishimoto, Hisashi Okuyama, and Jun-ichi Takahashi
- Subjects
next-generation sequencing ,catfish ,lake biwa ,silurus asotus ,mitochondrial dna ,Genetics ,QH426-470 - Abstract
The east Asian catfish Silurus asotus is a common species living in fresh water in Japan. The complete mitochondrial genome of the S. asotus from Lake Biwa in Japan was analyzed using next-generation sequencing. The mitochondrial genome of S. asotus was identified as a 16,515 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The AT content was 56.1%. Start codons ATG and GTG were found in 13 PCGs. Stop codons TAA, TAG, and AGA were observed in 13 PCGs. The heavy (H)-strand was predicted to have 12 PCGs and 14 tRNA and two rRNA genes, while the light (L)-strand was predicted to contain one PCGs and eight tRNA genes. The molecular phylogenetic analysis showed that S. asotus from Lake Biwa is genetically similar to S. asotus from China.
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- 2022
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- View/download PDF
4. Complete mitochondrial DNA sequence of the East Asian minnow, Pungtungia herzi (Actinopterygii: Cypriniformes)
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Teppei Taniwaki, Misaki Hiroshima, Mihiro Imakita, Yuu Kishimoto, Hisashi Okuyama, and Jun-ichi Takahashi
- Subjects
minnow ,next-generation sequence ,pungtungia herzi ,yodo river ,Genetics ,QH426-470 - Abstract
Some populations of the East Asian minnow Pungtungia herzi Herzenstein, 1892, which are naturally distributed in western Japan, have declined and are considered endangered. However, P. herzi has become a domestic invasive species in eastern Japan. Thus, knowledge of genetic features and phylogenetic relationships of P. herzi is important for conservation of this species and understanding its impact on ecosystems. We analyzed the complete mitochondrial genome using next generation sequencing of the East Asian minnow P. herzi from Yodo River, Osaka Prefecture, Japan. The mitochondrial genome of P. herzi consists of a circular molecule of 16,599 bp that includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region. The heavy (H)-strand was predicted to have 12 PCGs, 14 tRNA, and two rRNA genes, while the light (L)-strand was predicted to contain one PCGs and eight tRNA genes. The average AT content was 57.68%. The genes ATP8 and ATP6, ATP6 and COIII, ND4L and ND4, and ND5 and ND6 shared seven, one, seven, and four nucleotides, respectively. The initiation codons ATG and GTG were found in 12 and one genes, respectively. The termination codons TAA, TAG, incomplete TA–, and single T–– were observed in nine, one, one, and two genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure. The phylogenetic relationships inferred using 13 PCGs (based on the maximum likelihood) were consistent with previous studies that predicted interrelationships of Cypriniformes.
- Published
- 2020
- Full Text
- View/download PDF
5. Complete mitochondrial DNA sequence of the Japanese endemic catfish Silurus biwaensis (Siluriformes: Siluridae) from Lake Biwa
- Author
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Yuu Kishimoto, Hisashi Okuyama, and Jun-ichi Takahashi
- Subjects
next-generation sequencing ,catfish ,lake biwa ,silurus biwaensis ,mitochondrial dna ,Genetics ,QH426-470 - Abstract
The Japanese endemic catfish Silurus biwaensis is distributed only in Lake Biwa and Yodo river drainages. There are four species of the genus Silurus in Japan, of which S. biwaensis has a most limited distribution. This catfish needs to be collected for DNA data owing to the lack of information related to its phylogenetic relationship. Here, the complete mitochondrial genome of the S. biwaensis from Lake Biwa in Japan was analyzed using next-generation sequencing. The mitochondrial genome of S. biwaensis was identified as a 16,531 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with one A + T-rich control region. The AT content was 55.83%. The heavy (H)-strand was predicted to have 12 PCGs, 14 tRNA, and 2 rRNA genes, whereas the light (L)-strand was predicted to contain one PCG and eight tRNA genes. The start codons ATG, ATC, and GTG were found in 13 PCGs. The stop codons TAA, TAG, and AGA were observed in all PCGs, except CytB and COX3. All tRNA genes formed typical cloverleaf secondary structures. The molecular phylogenetic relationships estimated using 13 PCGs (maximum-likelihood method) indicated that S. biwaensis is genetically distinct from the sympatric species S. asotus and S. lithophilus. This result clearly indicated that S. biwaensis is a valid species.
- Published
- 2021
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6. Analysis of the complete mitochondrial genomes of two dwarf honeybee species, Apis florea and Apis andreniformis (Insecta: Hymenoptera: Apidae), in Thailand
- Author
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Jun-ichi Takahashi, Sureerat Deowanish, and Hisashi Okuyama
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mitochondrial dna ,micrapis ,dwarf honey bee ,next generation sequencing ,Genetics ,QH426-470 - Abstract
The dwarf honeybees Apis florea and Apis andreniformis inhabit the bush and forests of continental Asia and north Africa and some islands of Sundaland and the Philippines. We analysed, for the first time, the complete mitochondrial genomes of two dwarf honeybee species from Thailand using next-generation sequencing. Each mitochondrial genome was a circular and approximately 17 kbp molecule that included 13 protein-coding genes (PCGs), 22 tRNA genes, and two ribosomal RNA genes, along with one A + T-rich control region, besides three tRNA-Ser (AGN) repeats. The AT content values of the mitochondrial genomes of A. florea and A. andreniformis were 86.28% and 85.73%, respectively. The 1150 mutation sites in 13 PCGs differing between A. florea and A. andreniformis in Thailand were evenly distributed throughout their mitochondrial genomes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies, which predicted a sister relationship between A. florea and A. andreniformis.
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- 2018
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7. Complete mitochondrial genome sequence of the broad-winged damselfly, Mnais pruinosa Selys, 1853 (Odonata: Calopterygidae)
- Author
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Hisashi Okuyama, Takuya Kiyoshi, Jun-Ichi Takahashi, and Yoshitaka Tsubaki
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next generation sequence ,damselfly ,mnais pruinosa ,dark-brown-winged morphs ,saga prefecture ,Genetics ,QH426-470 - Abstract
In this study, we analyzed the complete mitochondrial genome of the Mnais pruinosa Selys, 1853 from Saga Prefecture, Japan. The mitochondrial genome of M. pruinosa was identified as a circular molecule of 15,494 bp, and was found to be similar to that of other damselfly species. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, as well as one A + T-rich control region. The genes ATP8 and ATP6 shared seven nucleotides, ATP6 and COIII shared one nucleotide, ND4 and ND4L shared seven nucleotides, and ND6 and Cytb shared one nucleotide. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one; the termination codons TAA, TAG, incomplete TA, and single T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.18%.
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- 2019
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8. Complete mitochondrial DNA sequence of the paper wasp Polistes riparius (Hymenoptera: Vespidae)
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Kazuhisa Yamasaki, Katsuhiko Sayama, Tomoki Oishi, Kanae Nakahama, Masato Yoshioka, Hisashi Okuyama, and Jun-ichi Takahashi
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next generation sequence ,paper wasp ,polistes riparius ,polistinae ,vespidae ,Genetics ,QH426-470 - Abstract
The paper wasp Polistes riparius is distributed in cold regions of northern East Asia to Russia. P. riparius are characterized by having longer cells than those of the closely related P. chinensis, which has a similar life history, as an adaptation to cold regions. The phylogenetic relationships of paper wasps have recently been studied; however, the genetic diversity and population structure of P. riparius has not been determined. The present study is the first to analyze the complete mitochondrial genome using next generation sequencing of P. riparius collected from Sapporo, Hokkaido Prefecture, Japan. The genome consisted of a closed loop that was 16,383 bp-long and included 13 protein coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.54%. The heavy (H)-strand was predicted to have 12 PCGs and 14 tRNA genes, while the light (L)-strand was predicted to contain one PCGs, eight tRNA genes, and two rRNA genes. All PCGs started with ATG. Stop codons were of two types: TAA for 11 genes (ND1, ND2, ND3, ND4L, ND5, ND6, COXI, COXII, COXIII, COB, ATP6 and ATP8) and TAG for two genes (ND3 and ND4). The molecular phylogenetic relationship based on the maximum likelihood method using 13 PCGs was consistent with some previous studies in which a closely relationship between P. riparius and P. jokahamae.
- Published
- 2020
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9. Complete mitochondrial DNA sequence of the giant water bug Kirkaldyia deyrolli (Hemiptera: Belostomatidae).
- Author
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Juiki Nakasako, Hisashi Okuyama, Shinya Ohba, and Jun-ichi Takahashi
- Subjects
next generation sequencing ,giant water bug ,kirkaldyia deyrolli ,endangered species ,Genetics ,QH426-470 - Abstract
Giant water bugs (genus Kirkaldyia and Lethocerus) are well known species from aquatic habitats throughout the world’s subtropical and tropical areas. Only one species of the Kirkaldyia deyrolli is distributed in Japan. K. deyrolli has been designated as second category rare species according Law for Conservation of Endangered Species of Wild Fauna and Flora in Japan, in 2019. We analyzed, for the first time, the complete mitochondrial genomes of the giant water bug K. deyrolli from Japan using next-generation sequencing. The mitochondrial genome was a circular and 15,579 bp molecule that included 13 protein-coding genes (PCGs), 22 tRNA genes, and two ribosomal RNA genes, along with one AT-rich control region. The AT content value was 69.55%. The heavy strand was predicted to have nine PCGs and 15 tRNA genes, whereas the light strand was predicted to contain four PCGs, seven tRNA genes, and two rRNA genes. Start codons were variable for all PCGs: four ATA, three ATC, four ATG, two ATT genes as the start codon. Stop codons were of two types: TAA for 12 genes and TAG for one gene. Incomplete stop codon T was identified. The molecular phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies, which predicted a sister relationship to the genus Lethocerus.
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- 2020
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10. Complete mitochondrial DNA sequence of the parasitic honey bee mite Varroa destructor (Mesostigmata: Varroidae)
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Reona Harada, Masato Yoshioka, Hisashi Okuyama, Manabu Kato, Stephen J. Martin, and Jun-ichi Takahashi
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varroa disease ,colony collapse ,apiculture ,beekeeping ,honey bee ,Genetics ,QH426-470 - Abstract
Varroa destructor is a parasite mite of the eastern honey bee Apis cerana, which is native to Asia. The European honey bee Apis mellifera was imported to Asia from Europe and the USA for apiculture in the 19th century. In a short period of time, V. destructor parasitized the artificially introduced honey bees. Varroa destructor was estimated to have spread around the world with A. mellifera when it was exported from Asia to locations worldwide about 50 years ago. The mitochondrial DNA of the parasitic honey bee mite V. destructor was analyzed using next-generation sequencing. The complete mitochondrial genome of V. destructor was identified as a 16,476-bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The heavy strand was predicted to have nine PCGs and 13 tRNA genes, whereas the light strand was predicted to contain four PCGs, nine tRNA genes, and two rRNA genes. All PCGs began with ATA as the start codon, except COIII and CytB, which had ATG as the start codon. Stop codons were of two types: TAA for eight genes and TAG for five genes. Molecular phylogenetic analysis revealed that V. destructor from Japan was genetically distant from that of France. A high base substitution rate of 2.82% was also confirmed between the complete mitochondrial DNA sequences of V. destructor from Japan and the USA, suggesting that one Varroa mite strain found in the USA is not from Japan.
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- 2020
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11. Complete mitochondrial DNA sequence of the alien hornet Vespa velutina (Insecta: Hymenoptera) invading Kyushu Island, Japan
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Ryoichi Takahashi, Hisashi Okuyama, Yûsuke N. Minoshima, and Jun-Ichi Takahashi
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asian hornet ,origin ,genetic distance ,alien species ,kyushu island ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the invasive Asian hornet Vespa velutina from Kyushu Island, Japan. The mitochondrial genome of V. velutina was identified as a circular molecule of 16,388 bp. We predicted that the genome contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with one A + T-rich control region. The average AT content is 81.68%. Molecular phylogenetic analysis using the 13 mitochondrial PCGs from 11 closely related taxa of Vespidae indicated that the V. velutina invading the Japanese Islands of Kyushu and Tsushima have a common origin.
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- 2018
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12. The complete mitochondrial genome of the bumblebee, Bombus hypocrita sapporensis (Insecta: Hymenoptera: Apidae) from Hokkaido Island, Japan
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Mana Nishimoto, Misuzu Umezawa, Hisashi Okuyama, Norikuni Kumano, Tetsuro Nomura, and Jun-ichi Takahashi
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bumblebee ,illumina sequencing ,subspecies ,bombus hypocrita ,hokkaido ,Genetics ,QH426-470 - Abstract
The complete is mitochondrial genome of the Japanese bumblebee Bombus hypocrita sapporensis from Hokkaido Island, Japan is analysed using next generation sequencing. The mitochondrial genome of B. h. sapporensis was observed to be a circular molecule of 15,835 bp. The average AT content in the B. h. sapporensis mitochondrial genome was 85.53%. It was predicted to contain 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The PCGs had ATA, ATG, or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE, trnF, and trnS1. The molecular phylogenetic analysis indicated that the B. h. sapporensis from Hokkaido Island population was most similar to that of the geographically isolated B. h. sapporensis from Rebun Island.
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- 2018
- Full Text
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13. A comparison of complete mitochondrial DNA sequences of Mnais costalis Selys, 1869 (Odonata: Calopterygidae) from three different populations (one allopatric and two sympatric)
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Hisashi Okuyama, Takuya Kiyoshi, Jun-Ichi Takahashi, and Yoshitaka Tsubaki
- Subjects
next generation sequence ,damselfly ,mnais costalis ,allopatric population ,sympatric population ,Genetics ,QH426-470 - Abstract
In Japan, two closely-related damselflies, Mnais costalis Selys, 1869 (Odonata: Calopterygidae) and M. pruinosa Selys-Longchamps (Odonata: Calopterygidae), 1853, coexist, and they exhibit geographic variations in wing color, body size, and habitat preference. In this study, we analyzed the complete mitochondrial genome of M. costalis from Saga Prefecture, Japan (sympatric populations that exhibit wing color polymorphism), and compared the genome with M. costalis that exhibit monomorphic orange wing color. The mitochondrial genome of M. costalis from Saga Prefecture was identified as a circular molecule of 15,488 bp, similar to that found in other M. costalis populations. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, along with one A + T-rich control region. Among the PCGs, ATP8 and ATP6, ATP6 and COIII, ND4 and ND4L, and ND6 and Cytb shared seven, one, seven, and one nucleotides, respectively. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one, while the termination codons TAA, TAG, TA, and T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.06%. From a phylogenetic analysis, the loss of wing color polymorphism in monomorphic sympatric populations is likely to occur with the coexistence of two Mnais species.
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- 2019
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14. Complete mitochondrial DNA sequence of the three-keeled pond turtle Mauremys reevesii (Reptilia: Testudines)
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Mari Asami, Hisashi Okuyama, and Jun-ichi Takahashi
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three-keeled pond turtle ,reeve’s pond turtle ,alien species ,next-generation sequencing ,extra base ,Genetics ,QH426-470 - Abstract
The complete mitochondrial genome of the three-keeled pond turtle Mauremys reevesii from Japan was analyzed using next-generation sequencing. The mitochondrial genome of M. reevesii was observed to be a circular molecule of 15,528 bp containing 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The average AT was found to be 61.11%. One extra base was present at the 174th position in the ND3 gene. Molecular phylogenetic analysis revealed that M. reevesii from Japan was few genetically distant from the geographically isolated M. reevesii from South Korea. This turtle might have been exported to Japan from the Korean Peninsula after the Middle Ages.
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- 2019
- Full Text
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15. Complete mitochondrial DNA sequence of the small hive beetle Aethina tumida (Insecta: Coleoptera) from Hawaii
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Jun-ichi Takahashi, Hisashi Okuyama, and Stephen J. Martin
- Subjects
next generation sequence ,small hive beetle ,aethina tumida ,hawaii ,beekeeping ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the small hive beetle Aethina tumida, a major honeybee pest that was accidentally transported to the Hawaii Islands, USA. The mitochondrial genome of A. tumida was identified as a 15,198 bp circular molecule containing 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The average AT content was found to be 76.2%. The heavy strand was predicted to have nine protein-coding and 14 tRNA genes; while the light strand was predicted to contain four protein-coding, eight tRNA, and two rRNA genes. Among the 13 PCGs, the initiation codon ATT was found in five, ATA in three, ATG in four, and TTG in one gene. Six PCGs used TAA as the stop codon, whereas three PCGs used TAG as the stop codon. Incomplete stop codon TA (COIII, ND5, and ND4) and T (COII) were identified. We found that the genetic distance between A. tumida from Hawaii and the beetles’ natural home South Africa, was small, indicating that the Hawaii population may have originated for the South Africa region.
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- 2019
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16. Complete mitochondrial DNA sequence of the endemic Japanese pond turtle Mauremys japonica (Reptilia: Testudines)
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Mari Asami, Hisashi Okuyama, and Jun-ichi Takahashi
- Subjects
next generation sequencing ,extra nucleotide ,near threatened species ,pond turtle ,endemic species ,Genetics ,QH426-470 - Abstract
The complete mitochondrial genome of the Japanese pond turtle Mauremys japonica from Japan was analyzed using next-generation sequencing. The mitochondrial genome of M. japonica was identified as a 16,443 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with 1 A + T-rich control region; the average AT content was 62.82%. One extra base was present at the 174th position in the ND3 gene. The phylogenetic analyses of the complete mitochondrial DNA genes strongly supported the result obtained from the phylogenetic analysis of partial DNA sequences, grouping the monophyletic species within the genus Mauremys.
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- 2019
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17. The complete mitochondrial genome of the dusky brown-gray–colored honeybee, Apis mellifera (insecta: Hymenoptera: Apidae) of New Zealand
- Author
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Mito Maeda, Ikumi Nakagawa, Mao Chikano, Hisashi Okuyama, Robert Murray, and Jun-Ichi Takahashi
- Subjects
dusky brown-gray honeybee ,carniolan ,apis mellifera carnica ,new zealand ,subspecies ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the dusky brown-gray–colored honeybee Apis mellifera, collected from North Island, New Zealand. We determined that the mitochondrial genome was a 16,336 bp and predicted 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. The start codon ATA was found in two genes, ATG in four genes, ATT in six genes, and ATC in one gene, whereas the termination codon TAA was observed in all PCGs. The non-coding regions of tRNA-Leu and COII were consistent with the C haplotype of A. mellifera carnica. Phylogenetic analysis suggests a close relationship with the European A. mellifera.
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- 2018
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18. The complete mitochondrial genome of the yellow coloured honeybee Apis mellifera (Insecta: Hymenoptera: Apidae) of New Zealand
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Ikumi Nakagawa, Mito Maeda, Mao Chikano, Hisashi Okuyama, Robert Murray, and Jun-Ichi Takahashi
- Subjects
western honeybee ,illumina sequencing ,apis mellifera ligustica ,new zealand ,subspecies ,Genetics ,QH426-470 - Abstract
The complete mitochondrial genome of the yellow coloured honeybee Apis mellifera from North Island, New Zealand was analyzed using next-generation sequencing. The mitochondrial genome was a 16,349bp circular molecule and was predicted to contain 13 protein-coding genes (PCGs), 22 tRNA genes and two rRNA genes. The initiation codon ATA was found in two genes, ATG in four genes, ATT in six genes, and ATC in one gene, while the termination codon TAA was observed in all the PCGs. Phylogenetic analysis using the sequence of 23 closely related taxa suggested a sister relationship with the Italian strain A. mellifera ligustica.
- Published
- 2018
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19. The complete mitochondrial genome of a Buckfast bee, Apis mellifera (Insecta: Hymenoptera: Apidae) in Northern Ireland
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Hisashi Okuyama, John Hill, Stephen John Martin, and Jun-ichi Takahashi
- Subjects
buckfast bee ,origin ,ireland ,apis mellifera ligustica ,honeybee ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the ‘Buckfast bee’, Apis mellifera, collected from North Ireland, UK. It consisted of a circular molecule of 16,353 bp. The genome contained 13 protein-coding, 22 tRNA, and 2 rRNA genes, along with one A + T-rich control region. The average AT content was 84.9%. The genes ATP8 and ATP6 shared 19 nucleotides. A phylogenetic analysis, suggested that the matriline ‘Buckfast bee’ has remained most closely related to the A. mellifera ligustica race from which it originated in 1917, despite being cross-bred with many other A. mellifera races over the past 100 years.
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- 2018
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20. The complete mitochondrial DNA sequence of endemic honeybee Apis nuluensis (Insecta: Hymenoptera: Apidae) inhabiting Mount Kinabalu in Sabah Province, Borneo Island
- Author
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Jun-Ichi Takahashi, Salim Tingek, and Hisashi Okuyama
- Subjects
endemic species ,illumina sequencing ,borneo ,apis nuluensis ,honeybee ,Genetics ,QH426-470 - Abstract
The cavity-nesting honeybee Apis nuluensis inhabits only the highlands of Mount Kinabalu of Sabah, Borneo Island. The mitochondrial genome is a circular molecule of approximately 1.6 kb that includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.5%. The start codons ATC, ATG, and ATT were found in one, three, and nine genes, respectively, whereas the stop codon TAA was observed in all genes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies that predicted a sister taxon relationship between A. nuluensis and A. cerana.
- Published
- 2017
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21. The complete mitochondrial genome of the cavity-nesting honeybee, Apis cerana (Insecta: Hymenoptera: Apidae) from Borneo
- Author
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Hisashi Okuyama, Salim Tingek, and Jun-ichi Takahashi
- Subjects
asian honeybee ,illumina sequencing ,genetic distance ,apis cerana ,borneo ,Genetics ,QH426-470 - Abstract
The complete mitochondrial genome of the cavity-nesting honeybee Apis cerana from Sabah on Borneo Island was analyzed using next-generation sequencing. The mitochondrial genome of A. cerana was a circular molecule of 15,884 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. cerana mitochondrial genome was 84.4%. It was predicted to contain 13 protein-coding, 22 tRNA, and two rRNA genes, along with one A + T-rich control region.
- Published
- 2017
- Full Text
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22. Complete mitochondrial DNA sequence of the tropical hornet Vespa affinis (Insecta, Hymenoptera)
- Author
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Hisashi Okuyama, Stephen J. Martin, and Jun-Ichi Takahashi
- Subjects
hornet ,illumina sequencing ,repetitive sequence ,monogynous ,polygynous ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the Asian tropical hornet Vespa affinis from Ishigaki Island, Japan. It consisted of a circular molecule with 19,109 bp, which is larger to other hornet species e.g. V. velutina. We predicted the genome contained 13 protein-coding, 22 tRNA, and two rRNA genes, along with one A + T-rich control region. The repetitive sequences were confirmed at multiple positions in the non-coding genes. The initiation codons ATA was found in one, ATG in seven, and ATT in five genes, while the termination codons TAA and TAG were observed 11 and two genes, respectively. The average AT content of the genome was 78.4%.
- Published
- 2017
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23. Effects of an hERG Activator, ICA-105574, on Electrophysiological Properties of Canine Hearts
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Mahoko Asayama, Junko Kurokawa, Kiyoshi Shirakawa, Hisashi Okuyama, Toshiki Kagawa, Jun-ichi Okada, Seiryo Sugiura, Toshiaki Hisada, and Tetsushi Furukawa
- Subjects
Therapeutics. Pharmacology ,RM1-950 - Abstract
In short QT syndrome, inherited gain-of-function mutations in the human ether a-go-go-related gene (hERG) K+ channel have been associated with development of fatal arrhythmias. This implies that drugs that activate hERG as a side effect may likewise pose significant arrhythmia risk. hERG activators have been found to have diverse mechanisms of activation, which may reflect their distinct binding sites. Recently, the new hERG activator ICA-105574 was introduced, which disables inactivation of the hERG channel with very high potency. We explored characteristics of this new drug in several experimental models. Patch clamp experiments were used to verify activation of hERG channels by ICA-105574 in human embryonic kidney cells stably-expressing hERG channels. ICA-105574 significantly shortened QT and QTc intervals and monophasic action potential duration (MAP90) in Langendorff-perfused guinea-pig hearts. We also administered ICA-105574 to anesthetized dogs while recording ECG and drug plasma concentrations. ICA-105574 (10 mg/kg) significantly shortened QT and QTc intervals, with a free plasma concentration of approximately 1.7 μM at the point of maximal effect. Our data showed that unbound ICA-105574 caused QT shortening in dogs at concentrations comparable to the half maximal effective concentration (EC50, 0.42 μM) of hERG activation in the patch clamp studies. Keywords:: hERG activator, QT and QTc interval, KCNH2, IKr channel, pro-arrhythmia
- Published
- 2013
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24. Complete mitochondrial genome of the Japanese bumblebee, Bombus hypocrita hypocrita (Insecta: Hymenoptera: Apidae)
- Author
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Mana Nishimoto, Hisashi Okuyama, Takuya Kiyoshi, Tetsuro Nomura, and Jun-ichi Takahashi
- Subjects
illumina’s next seq 500 ,bumblebee ,genetic diversity ,conservation ,Genetics ,QH426-470 - Abstract
In the present report, we describe the complete mitochondrial genome of the common bumblebee, Bombus hypocrita hypocrita, from the Otome Plateau, in Yamanashi Prefecture, Japan. The mitochondrial genome of B. h. hypocrita is a circular molecule of 15,795 bp. It contains 13 protein-coding, 22 tRNA and two rDNA genes. The protein-coding genes had ATA, ATG or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for ND4 and Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE and trnS1.
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- 2017
- Full Text
- View/download PDF
25. The complete mitochondrial genome of the cavity-nesting honeybee, Apis koschevnikovi (Insecta: Hymenoptera: Apidae)
- Author
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Takeshi Wakamiya, Salim Tingek, Hisashi Okuyama, Takuya Kiyoshi, and Jun-ichi Takahashi
- Subjects
asian honeybee ,illumina sequencing ,conservation ,borneo ,apis koschevnikovi ,Genetics ,QH426-470 - Abstract
In this study, we analyzed the complete mitochondrial genome of the cavity-nesting honeybee, A. koschevnikovi. The mitochondrial genome of A. koschevnikovi was observed to be a circular molecule of 15,278 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. koschevnikovi mitochondrial genome was 84%. It was predicted to contain 13 protein-coding, 24 tRNA and two rRNA genes, along with one A + T-rich control region, besides three tRNA-Met repeats.
- Published
- 2017
- Full Text
- View/download PDF
26. Complete mitochondrial DNA sequence of the invasive hornet Vespa velutina (Insecta, Hymenoptera) found in Japan
- Author
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Ryoichi Takahashi, Hisashi Okuyama, Takuya Kiyoshi, and Jun-ichi Takahashi
- Subjects
asian hornet ,illumina sequencing ,genetic distance ,alien species ,invasive species ,Genetics ,QH426-470 - Abstract
In this study, we analyzed the complete mitochondrial genome of the invasive Asian hornet Vespa velutina from Japan. The mitochondrial genome of V. velutina was identified as a circular molecule of 16,765 bp, similar to that in other hornet species. It was predicted to contain 13 protein-coding, 20 tRNA, and two rRNA genes, along with one A + T-rich control region. The initiation codons ATC was found in one, ATG in four, ATT in five, and ATA in three genes, while TAA was the termination codon in all these genes. The average AT content of 13 protein-coding was 82%.
- Published
- 2017
- Full Text
- View/download PDF
27. Complete mitochondrial DNA sequence of the East Asian minnow, Pungtungia herzi (Actinopterygii: Cypriniformes)
- Author
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Mihiro Imakita, Misaki Hiroshima, Jun-ichi Takahashi, Yuu Kishimoto, Teppei Taniwaki, and Hisashi Okuyama
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,Actinopterygii ,Endangered species ,Zoology ,Biology ,Minnow ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,biology.animal ,Cypriniformes ,Genetics ,Pungtungia herzi ,East Asia ,Molecular Biology ,Sequence (medicine) - Abstract
Some populations of the East Asian minnow Pungtungia herzi Herzenstein, 1892, which are naturally distributed in western Japan, have declined and are considered endangered. However, P. herzi has be...
- Published
- 2020
28. Complete mitochondrial genome of the Japanese bumblebee
- Author
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Mana, Nishimoto, Hisashi, Okuyama, Takuya, Kiyoshi, Tetsuro, Nomura, and Jun-Ichi, Takahashi
- Subjects
conservation ,bumblebee ,genetic diversity ,Illumina’s Next Seq 500 ,Mitogenome Announcement ,Research Article - Abstract
In the present report, we describe the complete mitochondrial genome of the common bumblebee, Bombus hypocrita hypocrita, from the Otome Plateau, in Yamanashi Prefecture, Japan. The mitochondrial genome of B. h. hypocrita is a circular molecule of 15,795 bp. It contains 13 protein-coding, 22 tRNA and two rDNA genes. The protein-coding genes had ATA, ATG or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for ND4 and Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE and trnS1.
- Published
- 2021
29. The complete mitochondrial DNA sequence of endemic honeybee
- Author
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Jun-Ichi, Takahashi, Salim, Tingek, and Hisashi, Okuyama
- Subjects
illumina sequencing ,Borneo ,parasitic diseases ,Endemic species ,honeybee ,Mitogenome Announcement ,Apis nuluensis ,Research Article - Abstract
The cavity-nesting honeybee Apis nuluensis inhabits only the highlands of Mount Kinabalu of Sabah, Borneo Island. The mitochondrial genome is a circular molecule of approximately 1.6 kb that includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.5%. The start codons ATC, ATG, and ATT were found in one, three, and nine genes, respectively, whereas the stop codon TAA was observed in all genes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies that predicted a sister taxon relationship between A. nuluensis and A. cerana.
- Published
- 2021
30. The complete mitochondrial genome of the cavity-nesting honeybee
- Author
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Hisashi, Okuyama, Salim, Tingek, and Jun-Ichi, Takahashi
- Subjects
genetic distance ,Borneo ,Asian honeybee ,Illumina sequencing ,Mitogenome Announcement ,Research Article ,Apis cerana - Abstract
The complete mitochondrial genome of the cavity-nesting honeybee Apis cerana from Sabah on Borneo Island was analyzed using next-generation sequencing. The mitochondrial genome of A. cerana was a circular molecule of 15,884 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. cerana mitochondrial genome was 84.4%. It was predicted to contain 13 protein-coding, 22 tRNA, and two rRNA genes, along with one A + T-rich control region.
- Published
- 2021
31. The complete mitochondrial genome of the bumblebee
- Author
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Mana, Nishimoto, Misuzu, Umezawa, Hisashi, Okuyama, Norikuni, Kumano, Tetsuro, Nomura, and Jun-Ichi, Takahashi
- Subjects
Mito Communication ,Hokkaido ,Illumina sequencing ,subspecies ,Bumblebee ,Bombus hypocrita ,Research Article - Abstract
The complete is mitochondrial genome of the Japanese bumblebee Bombus hypocrita sapporensis from Hokkaido Island, Japan is analysed using next generation sequencing. The mitochondrial genome of B. h. sapporensis was observed to be a circular molecule of 15,835 bp. The average AT content in the B. h. sapporensis mitochondrial genome was 85.53%. It was predicted to contain 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The PCGs had ATA, ATG, or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE, trnF, and trnS1. The molecular phylogenetic analysis indicated that the B. h. sapporensis from Hokkaido Island population was most similar to that of the geographically isolated B. h. sapporensis from Rebun Island.
- Published
- 2021
32. Analysis of the complete mitochondrial genomes of two dwarf honeybee species
- Author
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Jun-Ichi, Takahashi, Sureerat, Deowanish, and Hisashi, Okuyama
- Subjects
Mito Communication ,Micrapis ,next generation sequencing ,dwarf honey bee ,Mitochondrial DNA ,Research Article - Abstract
The dwarf honeybees Apis florea and Apis andreniformis inhabit the bush and forests of continental Asia and north Africa and some islands of Sundaland and the Philippines. We analysed, for the first time, the complete mitochondrial genomes of two dwarf honeybee species from Thailand using next-generation sequencing. Each mitochondrial genome was a circular and approximately 17 kbp molecule that included 13 protein-coding genes (PCGs), 22 tRNA genes, and two ribosomal RNA genes, along with one A + T-rich control region, besides three tRNA-Ser (AGN) repeats. The AT content values of the mitochondrial genomes of A. florea and A. andreniformis were 86.28% and 85.73%, respectively. The 1150 mutation sites in 13 PCGs differing between A. florea and A. andreniformis in Thailand were evenly distributed throughout their mitochondrial genomes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies, which predicted a sister relationship between A. florea and A. andreniformis.
- Published
- 2021
33. Complete mitochondrial DNA sequence of the tropical hornet
- Author
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Hisashi, Okuyama, Stephen J, Martin, and Jun-Ichi, Takahashi
- Subjects
Illumina sequencing ,repetitive sequence ,monogynous ,polygynous ,Mitogenome Announcement ,Hornet ,Research Article - Abstract
We analyzed the complete mitochondrial genome of the Asian tropical hornet Vespa affinis from Ishigaki Island, Japan. It consisted of a circular molecule with 19,109 bp, which is larger to other hornet species e.g. V. velutina. We predicted the genome contained 13 protein-coding, 22 tRNA, and two rRNA genes, along with one A + T-rich control region. The repetitive sequences were confirmed at multiple positions in the non-coding genes. The initiation codons ATA was found in one, ATG in seven, and ATT in five genes, while the termination codons TAA and TAG were observed 11 and two genes, respectively. The average AT content of the genome was 78.4%.
- Published
- 2021
34. Complete mitochondrial DNA sequence of the invasive hornet
- Author
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Ryoichi, Takahashi, Hisashi, Okuyama, Takuya, Kiyoshi, and Jun-Ichi, Takahashi
- Subjects
genetic distance ,illumina sequencing ,alien species ,Mitogenome Announcement ,Asian hornet ,Research Article ,invasive species - Abstract
In this study, we analyzed the complete mitochondrial genome of the invasive Asian hornet Vespa velutina from Japan. The mitochondrial genome of V. velutina was identified as a circular molecule of 16,765 bp, similar to that in other hornet species. It was predicted to contain 13 protein-coding, 20 tRNA, and two rRNA genes, along with one A + T-rich control region. The initiation codons ATC was found in one, ATG in four, ATT in five, and ATA in three genes, while TAA was the termination codon in all these genes. The average AT content of 13 protein-coding was 82%.
- Published
- 2021
35. Complete mitochondrial DNA sequence of the East Asian minnow
- Author
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Teppei, Taniwaki, Misaki, Hiroshima, Mihiro, Imakita, Yuu, Kishimoto, Hisashi, Okuyama, and Jun-Ichi, Takahashi
- Subjects
next-generation sequence ,Pungtungia herzi ,Minnow ,Mitogenome Announcement ,Research Article ,Yodo River - Abstract
Some populations of the East Asian minnow Pungtungia herzi Herzenstein, 1892, which are naturally distributed in western Japan, have declined and are considered endangered. However, P. herzi has become a domestic invasive species in eastern Japan. Thus, knowledge of genetic features and phylogenetic relationships of P. herzi is important for conservation of this species and understanding its impact on ecosystems. We analyzed the complete mitochondrial genome using next generation sequencing of the East Asian minnow P. herzi from Yodo River, Osaka Prefecture, Japan. The mitochondrial genome of P. herzi consists of a circular molecule of 16,599 bp that includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region. The heavy (H)-strand was predicted to have 12 PCGs, 14 tRNA, and two rRNA genes, while the light (L)-strand was predicted to contain one PCGs and eight tRNA genes. The average AT content was 57.68%. The genes ATP8 and ATP6, ATP6 and COIII, ND4L and ND4, and ND5 and ND6 shared seven, one, seven, and four nucleotides, respectively. The initiation codons ATG and GTG were found in 12 and one genes, respectively. The termination codons TAA, TAG, incomplete TA–, and single T–– were observed in nine, one, one, and two genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure. The phylogenetic relationships inferred using 13 PCGs (based on the maximum likelihood) were consistent with previous studies that predicted interrelationships of Cypriniformes.
- Published
- 2021
36. A comparison of complete mitochondrial DNA sequences of
- Author
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Hisashi, Okuyama, Takuya, Kiyoshi, Jun-Ichi, Takahashi, and Yoshitaka, Tsubaki
- Subjects
sympatric population ,Mnais costalis ,damselfly ,Next generation sequence ,Mitogenome Announcement ,allopatric population ,Research Article - Abstract
In Japan, two closely-related damselflies, Mnais costalis Selys, 1869 (Odonata: Calopterygidae) and M. pruinosa Selys-Longchamps (Odonata: Calopterygidae), 1853, coexist, and they exhibit geographic variations in wing color, body size, and habitat preference. In this study, we analyzed the complete mitochondrial genome of M. costalis from Saga Prefecture, Japan (sympatric populations that exhibit wing color polymorphism), and compared the genome with M. costalis that exhibit monomorphic orange wing color. The mitochondrial genome of M. costalis from Saga Prefecture was identified as a circular molecule of 15,488 bp, similar to that found in other M. costalis populations. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, along with one A + T-rich control region. Among the PCGs, ATP8 and ATP6, ATP6 and COIII, ND4 and ND4L, and ND6 and Cytb shared seven, one, seven, and one nucleotides, respectively. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one, while the termination codons TAA, TAG, TA, and T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.06%. From a phylogenetic analysis, the loss of wing color polymorphism in monomorphic sympatric populations is likely to occur with the coexistence of two Mnais species.
- Published
- 2020
37. Complete mitochondrial DNA sequence of the parasitic honey bee mite Varroa destructor (Mesostigmata : Varroidae)
- Author
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Jun-ichi Takahashi, Manabu Kato, Masato Yoshioka, Stephen J. Martin, Reona Harada, and Hisashi Okuyama
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Beekeeping ,Mitochondrial DNA ,biology ,Honey bee ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Heavy strand ,Varroa destructor ,Varroa ,Destructor ,Molecular Biology ,Apis cerana - Abstract
Varroa destructor is a parasite mite of the eastern honey bee Apis cerana, which is native to Asia. The European honey bee Apis mellifera was imported to Asia from Europe and the USA for apiculture in the 19th century. In a short period of time, V. destructor parasitized the artificially introduced honey bees. Varroa destructor was estimated to have spread around the world with A. mellifera when it was exported from Asia to locations worldwide about 50 years ago. The mitochondrial DNA of the parasitic honey bee mite V. destructor was analyzed using next-generation sequencing. The complete mitochondrial genome of V. destructor was identified as a 16,476-bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The heavy strand was predicted to have nine PCGs and 13 tRNA genes, whereas the light strand was predicted to contain four PCGs, nine tRNA genes, and two rRNA genes. All PCGs began with ATA as the start codon, except COIII and CytB, which had ATG as the start codon. Stop codons were of two types: TAA for eight genes and TAG for five genes. Molecular phylogenetic analysis revealed that V. destructor from Japan was genetically distant from that of France. A high base substitution rate of 2.82% was also confirmed between the complete mitochondrial DNA sequences of V. destructor from Japan and the USA, suggesting that one Varroa mite strain found in the USA is not from Japan.
- Published
- 2020
38. Analysis of the complete mitochondrial genomes of two dwarf honeybee species,Apis floreaandApis andreniformis(Insecta: Hymenoptera: Apidae), in Thailand
- Author
-
Sureerat Deowanish, Jun-ichi Takahashi, and Hisashi Okuyama
- Subjects
0106 biological sciences ,0301 basic medicine ,biology ,Apidae ,Zoology ,Dwarf honeybee ,North africa ,Hymenoptera ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Genome ,03 medical and health sciences ,Honey Bees ,030104 developmental biology ,Genetics ,Apis andreniformis ,Molecular Biology ,Apis florea - Abstract
The dwarf honeybees Apis florea and Apis andreniformis inhabit the bush and forests of continental Asia and north Africa and some islands of Sundaland and the Philippines. We analysed, for the firs...
- Published
- 2018
39. Complete mitochondrial genome sequence of the broad-winged damselfly, Mnais pruinosa Selys, 1853 (Odonata: Calopterygidae)
- Author
-
Takuya Kiyoshi, Jun-ichi Takahashi, Yoshitaka Tsubaki, and Hisashi Okuyama
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,biology ,damselfly ,Odonata ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Mnais pruinosa ,03 medical and health sciences ,030104 developmental biology ,Calopterygidae ,Damselfly ,Evolutionary biology ,Genetics ,Saga Prefecture ,Next generation sequence ,dark-brown-winged morphs ,Molecular Biology ,Mitogenome Announcement ,Sequence (medicine) ,Research Article - Abstract
In this study, we analyzed the complete mitochondrial genome of the Mnais pruinosa Selys, 1853 from Saga Prefecture, Japan. The mitochondrial genome of M. pruinosa was identified as a circular molecule of 15,494 bp, and was found to be similar to that of other damselfly species. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, as well as one A + T-rich control region. The genes ATP8 and ATP6 shared seven nucleotides, ATP6 and COIII shared one nucleotide, ND4 and ND4L shared seven nucleotides, and ND6 and Cytb shared one nucleotide. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one; the termination codons TAA, TAG, incomplete TA, and single T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.18%.
- Published
- 2019
40. Analysis of the complete mitochondrial genome of the giant honeybee, Apis dorsata, (Hymenoptera: Apidae) in Thailand
- Author
-
Jun-ichi Takahashi, Hisashi Okuyama, and Sureerat Deowanish
- Subjects
0301 basic medicine ,Genetics ,Mitochondrial DNA ,Apis dorsata ,Biology ,Ribosomal RNA ,biology.organism_classification ,Genome ,Stop codon ,DNA sequencing ,03 medical and health sciences ,030104 developmental biology ,Transfer RNA ,Gene ,Ecology, Evolution, Behavior and Systematics - Abstract
The giant honeybee, Apis dorsata, is a species native to the East Asian continent and some islands of Sundaland and the Philippines. We analyzed, for the first time, the complete mitochondrial genome of A. dorsata from Thailand using next generation sequencing. The mitochondrial genome was found to be a circular molecule of 15,279 bp in length, which consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and an AT rich region. Start codons ATA, ATG and ATT were found in two, three and ten genes, respectively, while stop codons TAA and TAG were observed in 12 and 1 gene, respectively. All tRNA genes formed typical cloverleaf secondary structures, except for His (H) and Tyr (Y). The heavy (H)-strand was found to have nine PCGs and 14 tRNA genes, while the light (L)-strand was found to contain four protein-coding, eight tRNA, and two rRNA genes.
- Published
- 2017
41. Analysis of the complete mitochondrial genome of Apis nigrocincta (Insecta: Hymenoptera: Apidae) on Sangihe Island in Indonesia
- Author
-
H. Randall Hepburn, Soesilowati Hadisoesilo, Jun-ichi Takahashi, and Hisashi Okuyama
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,Ecology ,Ribosomal RNA ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Genome ,Stop codon ,03 medical and health sciences ,030104 developmental biology ,Genetic distance ,Evolutionary biology ,Phylogenetics ,Genetics ,Apis nigrocincta ,Gene ,Ecology, Evolution, Behavior and Systematics - Abstract
The cavity-nesting honeybee, Apis nigrocincta, only inhabits the tropical forests of Sulawesi, Sangihe and Mindanao Islands, which are designated as biodiversity hotspots and one of the important areas for biological conservation. In the present study, for the first time, we analyzed the complete mitochondrial genome of A. nigrocincta from two regions in Sangihe Island, Indonesia. The mitochondrial genome of A. nigrocincta consists of a circular molecule of approximately 1.5 kb that includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and one AT-rich control region. Two A. nigrocincta had AT mitochondrial genome contents of approximately 84.57 and 84.23%. Start codons ATT, ATG and ATA were found in 13 PCGs. Stop codons TAA and TAG were observed in 12 PCGs and the ND2 gene, respectively. The heavy (H)-strand was predicted to have 9 PCGs and 14 tRNA genes, while the light (L)-strand was predicted to contain 4 PCGs, 8 tRNA, and 2 rRNA genes. All tRNA genes formed typical cloverleaf secondary structures, except for tRNA-Ser(AGN) and tRNA-His. The 104 mutation sites that differed between the A. nigrocincta from two regions in Sangihe Island, Indonesia were evenly distributed throughout the mitochondrial genome. The phylogenetic relationship, inferred using 13 PCGs (based on the maximum likelihood), was consistent with that reported in previous studies that predicted a sister relationship between A. nigrocincta and A. cerana. We discovered that the genetic distance between the A. nigrocincta varieties on Sangihe Island is 0.0067, indicating that they maintained a high genetic diversity on this island.
- Published
- 2017
42. The complete mitochondrial genome and genetic distinction of the Taiwanese honeybee, Apis cerana (Hymenoptera: Apidae)
- Author
-
Tatsuhiko Kadowaki, Jun-ichi Takahashi, Takuya Kiyoshi, Hisashi Okuyama, Chung Ping Lin, and Yuri Shinmura
- Subjects
0301 basic medicine ,Genetics ,education.field_of_study ,Mitochondrial DNA ,Phylogenetic tree ,Population ,Biology ,biology.organism_classification ,Genome ,03 medical and health sciences ,030104 developmental biology ,Heavy strand ,Genetic distance ,education ,Gene ,Ecology, Evolution, Behavior and Systematics ,Apis cerana - Abstract
The Asian cavity-nesting honeybee, Apis cerana is widely distributed across Asia and nearby islands, showing interesting patterns of genetic differences caused by repeated isolation and re-unification of populations owing to repeated changes in sea levels. In the present study, we analyzed the complete mitochondrial genome of A. cerana from Taiwan and eastern China for the first time. The mitochondrial genomes of these honeybee populations were circular 15,251- and 15,332-bp molecules, respectively, and included 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content in mitochondrial genome of Taiwanese and Chinese honeybees was 83.50 and 83.54%, respectively. The heavy strand encoded nine PCGs and 14 tRNA genes and the light strand encoded four PCGs, eight tRNA genes, and two rRNA genes. The ATP6 and ATP8 genes shared 19 nucleotides. Eight PCGs of the A. cerana mitochondrial genome started with ATT, ATP6, COIII, and Cytb genes with ATG, ATP8 gene with ATC, and ND4 gene with ATA. All tRNA genes formed typical cloverleaf secondary structures, except for tRNA-Ser (AGN). The phylogenetic analysis inferred from the 13 mitochondrial PCGs, based on maximum likelihood, indicated that the Taiwanese and eastern Chinese populations of A. cerana are closely related taxa. The 272 sites that differed between A. cerana from Taiwan and eastern China were evenly distributed throughout the mitochondrial genome. We found that the genetic distance between the two population was 0.025, indicating that they are genetically different enough to be considered different subspecies or local populations.
- Published
- 2017
43. Characterization of the complete mitochondrial genome of the giant black Himalayan honeybee (Apis laboriosa) from Nepal
- Author
-
Hisashi Okuyama, Jimi Rai, Takeshi Wakamiya, and Jun-ichi Takahashi
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Mitochondrial DNA ,Phylogenetic tree ,biology ,Apis dorsata ,Ribosomal RNA ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Stop codon ,03 medical and health sciences ,030104 developmental biology ,Heavy strand ,Transfer RNA ,Gene ,Ecology, Evolution, Behavior and Systematics - Abstract
The giant black honeybee, Apis laboriosa, has been applied to the highlands of Southeast Asia, where the number of nests has been drastically decreasing. In this study, we first analyzed the complete mitochondrial genome of A. laboriosa from Nepal using Next sequencing technology. The mitochondrial genome is a circular molecule of approximately 1.5 kb, and includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content of the A. laboriosa mitochondrial genome is 84.7%. Start codons ATG and ATT were found in three and ten genes, respectively, while stop codons TAA and TAG were observed in 12 and 1 gene, respectively. All tRNA genes formed typical cloverleaf secondary structures, except for Ser (AGN) and Gln (Q). The heavy strand (H-strand) was predicted to have 9 PCGs and 14 tRNA genes, while the light strand (L-strand) was predicted to contain four protein-coding, eight tRNA, and two rRNA genes. The 1858 mutation sites that differ between A. laboriosa and Apis dorsata were evenly distributed throughout the mitochondrial genome. The phylogenetic relationship, inferred using 13 PCGs (based on maximum likelihood) was consistent with several previous studies that predicted a sister relationship between A. laboriosa and A. dorsata. A phylogenetic analysis inferred from the 13 mitochondrial PCGs, based on maximum likelihood, indicates that A. laboriosa and A. dorsata are very closely related. We found that the genetic distance between A. laboriosa and A. dorsata is 0.197, indicating that, while they are genetically similar enough to be considered sister species, they are indeed two distinct species.
- Published
- 2017
44. Complete mitochondrial genome of the honeybee Apis cerana native to two remote islands in Japan
- Author
-
Takeshi Wakamiya, Jun-ichi Takahashi, Izumi Washitani, Hisashi Okuyama, and Ayumi Fujiwara
- Subjects
0106 biological sciences ,0301 basic medicine ,Conservation genetics ,Mitochondrial DNA ,biology ,Subspecies ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Japonica ,03 medical and health sciences ,030104 developmental biology ,Genetic distance ,Evolutionary biology ,Botany ,Genetic variation ,Genetics ,Gene ,Ecology, Evolution, Behavior and Systematics ,Apis cerana - Abstract
The honeybee species native to two remote islands (Amami-Oshima and Tsushima) in Japan were previously reported to be morphologically distinct from the Japanese honeybee Apis cerana japonica. To our knowledge, this is the first study to analyze the complete mitochondrial genome of the honeybee species from the two islands. The mitochondrial genome was a circular and approximately 1.5 kbp molecule that included 13 protein-cording genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 AT-rich control region. The average AT content of the mitochondrial genome was 84%. The genetic distance suggested that the honeybee species from the two remote islands were more closely related to A. cerana japonica, among the A. cerana subspecies. Although the mitochondrial genome of the honeybee species from the two remote islands showed genetic variation distinct from those found in the A. cerana group, they were classified as the Japanese honeybee A. cerana japonica.
- Published
- 2017
45. Complete mitochondrial DNA sequence of the paper wasp Polistes riparius (Hymenoptera: Vespidae)
- Author
-
Masato Yoshioka, Jun-ichi Takahashi, Kazuhisa Yamasaki, Hisashi Okuyama, Kanae Nakahama, Tomoki Oishi, and Katsuhiko Sayama
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,Hymenoptera ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Polistinae ,Genetics ,Next generation sequence ,Molecular Biology ,Mitogenome Announcement ,Sequence (medicine) ,Paper wasp ,Vespidae ,paper wasp ,Polistes riparius ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,Research Article - Abstract
The paper wasp Polistes riparius is distributed in cold regions of northern East Asia to Russia. P. riparius are characterized by having longer cells than those of the closely related P. chinensis, which has a similar life history, as an adaptation to cold regions. The phylogenetic relationships of paper wasps have recently been studied; however, the genetic diversity and population structure of P. riparius has not been determined. The present study is the first to analyze the complete mitochondrial genome using next generation sequencing of P. riparius collected from Sapporo, Hokkaido Prefecture, Japan. The genome consisted of a closed loop that was 16,383 bp-long and included 13 protein coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.54%. The heavy (H)-strand was predicted to have 12 PCGs and 14 tRNA genes, while the light (L)-strand was predicted to contain one PCGs, eight tRNA genes, and two rRNA genes. All PCGs started with ATG. Stop codons were of two types: TAA for 11 genes (ND1, ND2, ND3, ND4L, ND5, ND6, COXI, COXII, COXIII, COB, ATP6 and ATP8) and TAG for two genes (ND3 and ND4). The molecular phylogenetic relationship based on the maximum likelihood method using 13 PCGs was consistent with some previous studies in which a closely relationship between P. riparius and P. jokahamae.
- Published
- 2020
46. Complete mitochondrial DNA sequence of the giant water bug Kirkaldyia deyrolli (Hemiptera: Belostomatidae)
- Author
-
Shin-ya Ohba, Hisashi Okuyama, Juiki Nakasako, and Jun-ichi Takahashi
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,biology ,Lethocerus ,Aquatic ecosystem ,Endangered species ,Zoology ,Subtropics ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Hemiptera ,Belostomatidae ,03 medical and health sciences ,030104 developmental biology ,Genus ,Genetics ,Molecular Biology - Abstract
Giant water bugs (genus Kirkaldyia and Lethocerus) are well known species from aquatic habitats throughout the world’s subtropical and tropical areas. Only one species of the Kirkaldyia deyrolli is...
- Published
- 2020
47. Complete mitochondrial DNA sequence of the alien hornet Vespa velutina (Insecta: Hymenoptera) invading Kyushu Island, Japan
- Author
-
Yûsuke N. Minoshima, Hisashi Okuyama, Ryoichi Takahashi, and Jun-ichi Takahashi
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,Zoology ,alien species ,010603 evolutionary biology ,01 natural sciences ,Genome ,03 medical and health sciences ,origin ,Genetics ,Molecular Biology ,Gene ,Mitogenome Announcement ,Asian hornet ,Kyushu Island ,genetic distance ,Phylogenetic tree ,Vespidae ,biology ,Velutina ,Ribosomal RNA ,biology.organism_classification ,030104 developmental biology ,Genetic distance ,Research Article - Abstract
We analyzed the complete mitochondrial genome of the invasive Asian hornet Vespa velutina from Kyushu Island, Japan. The mitochondrial genome of V. velutina was identified as a circular molecule of 16,388 bp. We predicted that the genome contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with one A + T-rich control region. The average AT content is 81.68%. Molecular phylogenetic analysis using the 13 mitochondrial PCGs from 11 closely related taxa of Vespidae indicated that the V. velutina invading the Japanese Islands of Kyushu and Tsushima have a common origin.
- Published
- 2018
48. Origins of Vespa velutina hornets that recently invaded Iki Island, Japan and Jersey Island, UK
- Author
-
Jun-ichi Takahashi, Takuya Kiyoshi, T Takeuchi, Hisashi Okuyama, and Stephen J. Martin
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,Population ,Wasps ,Zoology ,010603 evolutionary biology ,01 natural sciences ,DNA, Mitochondrial ,Invasive species ,03 medical and health sciences ,Japan ,Genetics ,Animals ,East Asia ,China ,education ,Molecular Biology ,Vespa velutina ,Islands ,education.field_of_study ,biology ,Velutina ,Haplotype ,biology.organism_classification ,United Kingdom ,030104 developmental biology ,Haplotypes ,Animal Migration - Abstract
The native distribution of the yellow-legged hornet, Vespa velutina, is throughout East Asia. Around 15 years ago this species was accidentally introduced into South Korea and France, where it became established and then spread into neighbouring countries. Previous mitochondrial DNA studies showed that the South Korean, Japanese, and French populations all originated from Eastern China. Recently, the hornet has invaded Iki Island, Japan and Jersey Island, UK. In this study, we analyze the complete mitochondrial DNA sequence of V. velutina to trace the origin of these two populations. The mitochondrial DNA haplotypes (COI, Cytb, and 16S rRNA) of V. velutina in Iki Island matched the unique haplotype present in China, South Korea, and Japan, while the haplotype from Jersey Island matched that of V. velutina found in France and China. These findings were supported by data from the complete mitochondrial DNA sequence of V. velutina from Iki Island, which was consistent with the sequence from South Korea and Tsushima, whereas V. velutina in Jersey was most similar to the French population.
- Published
- 2019
- Full Text
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49. A comparison of complete mitochondrial DNA sequences of Mnais costalis Selys, 1869 (Odonata: Calopterygidae) from three different populations (one allopatric and two sympatric)
- Author
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Jun-ichi Takahashi, Yoshitaka Tsubaki, Takuya Kiyoshi, and Hisashi Okuyama
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,biology ,Phylogenetic tree ,Allopatric speciation ,Odonata ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Genome ,03 medical and health sciences ,030104 developmental biology ,Damselfly ,Calopterygidae ,Evolutionary biology ,Sympatric speciation ,Genetics ,Molecular Biology - Abstract
In Japan, two closely-related damselflies, Mnais costalis Selys, 1869 (Odonata: Calopterygidae) and M. pruinosa Selys-Longchamps (Odonata: Calopterygidae), 1853, coexist, and they exhibit geographic variations in wing color, body size, and habitat preference. In this study, we analyzed the complete mitochondrial genome of M. costalis from Saga Prefecture, Japan (sympatric populations that exhibit wing color polymorphism), and compared the genome with M. costalis that exhibit monomorphic orange wing color. The mitochondrial genome of M. costalis from Saga Prefecture was identified as a circular molecule of 15,488 bp, similar to that found in other M. costalis populations. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, along with one A + T-rich control region. Among the PCGs, ATP8 and ATP6, ATP6 and COIII, ND4 and ND4L, and ND6 and Cytb shared seven, one, seven, and one nucleotides, respectively. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one, while the termination codons TAA, TAG, TA, and T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.06%. From a phylogenetic analysis, the loss of wing color polymorphism in monomorphic sympatric populations is likely to occur with the coexistence of two Mnais species.
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- 2019
50. Complete mitochondrial DNA sequence of the three-keeled pond turtle Mauremys reevesii (Reptilia: Testudines)
- Author
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Jun-ichi Takahashi, Mari Asami, and Hisashi Okuyama
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,biology ,Mauremys reevesii ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,DNA sequencing ,law.invention ,03 medical and health sciences ,030104 developmental biology ,law ,Evolutionary biology ,Genetics ,Turtle (robot) ,Alien species ,Molecular Biology ,Sequence (medicine) - Abstract
The complete mitochondrial genome of the three-keeled pond turtle Mauremys reevesii from Japan was analyzed using next-generation sequencing. The mitochondrial genome of M. reevesii was observed to...
- Published
- 2019
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