著者

Muhammad Waqar Hameed

出版者

日本遺伝学会

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.14-00057, (Released:2016-03-18)

被引用文献数

2

---

Plants are frequently exposed to limitations in oxygen availability during their lifetime. During evolution, they have developed a number of physiological and morphological adaptations to tolerate oxygen and other stress conditions. These include regulation of growth by gene expression and ATP generation. The regulation of nuclear genes after hypoxia and anoxia is well studied; however, the regulation of mitochondrial genes in response to oxygen stress has not been characterized to date. Therefore, we have established an Arabidopsis mitochondrial genome-specific microarray that accommodates probes for all mitochondrial DNA-encoded genes and conserved open reading frames. Our analysis showed an up-regulation of mitochondrial transcripts in Arabidopsis roots after 48 h of hypoxia. Since no significant difference was detected in the expression of mitochondrial RNA polymerases or the mitochondrial DNA content per cell, we propose a transcriptional mode of induction of mitochondrial gene expression under hypoxia.

著者

Shuzo Iwanishi Shohei Zaitsu Hiroki Shibata Eiji Nitasaka

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.93, no.4, pp.163-167, 2018-08-01 (Released:2018-11-10)

参考文献数

26

被引用文献数

7

---

The Japanese rat snake (Elaphe climacophora) is a common species in Japan and is widely distributed across the Japanese islands. An albino mutant of the Japanese rat snake (“pet trade” albino) has been bred and traded by hobbyists for around two decades because of its remarkable light-yellowish coloration with red eyes, attributable to a lack of melanin. Another albino Japanese rat snake mutant found in a natural population of the Japanese rat snake at high frequency in Iwakuni City, Yamaguchi Prefecture is known as “Iwakuni no Shirohebi”. It has been conserved by the government as a natural monument. The Iwakuni albino also lacks melanin, having light-yellowish body coloration and red eyes. Albino mutants of several organisms have been studied, and mutation of the tyrosinase gene (TYR) is responsible for this phenotype. By determining the sequence of the TYR coding region of the pet trade albino, we identified a nonsense mutation in the second exon. Furthermore, RT-PCR revealed that TYR transcripts were not detected in this snake. These findings suggest that mutation of TYR is responsible for the albino phenotype of the pet trade line of the Japanese rat snake. However, the Iwakuni albino did not share this TYR mutation; thus, these two albino lines differ in their origins.

著者

Kenji Ogaki Kenji Suetsugu Keiju Kishikawa Daisuke Kyogoku Kohtaroh Shutoh Yuji Isagi Shingo Kaneko

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.94, no.5, pp.225-229, 2019-10-01 (Released:2019-12-10)

参考文献数

27

被引用文献数

1 3

---

Gastrodia is the most species-rich genus among mycoheterotrophic plants, and is thus an essential taxon to understand the mechanism of species diversification in mycoheterotrophs. In this study, we developed microsatellite markers with high transferability for four Gastrodia species to examine genetic differentiation and similarity among species, populations and individuals. The 12 microsatellite markers developed from a G. fontinalis library showed high transferability for the ramets that identified G. nipponica, G. kuroshimensis and G. takeshimensis. In addition to the high transferability of these markers, we observed low allele variation within a sampled population of each species and allele differences among the four species. The 12 markers described here will be useful for investigating the genetic differences among and within the Gastrodia species, which evolved by a limitation of gene flow.

著者

Yuki Kimura Masato Nikaido

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.23-00188, (Released:2023-10-17)

参考文献数

28

---

Keratins are intermediate filament proteins that are important for epidermal strength and protection from desiccation. Keratin genes are highly duplicated and have diversified by forming two major clusters in the genomes of terrestrial vertebrates. The keratin genes of lungfishes, the closest fish to tetrapods, have not been studied at the genomic level, despite the importance of lungfishes in terrestrial adaptation. Here, we identified keratin genes in the genomes of two lungfish species and performed syntenic and phylogenetic analyses. Additionally, we identified keratin genes from two gobies and two mudskippers, inhabiting underwater and terrestrial environments. We found that in lungfishes, keratin genes were duplicated and diversified within two major clusters, similar to but independent of terrestrial vertebrates. By contrast, keratin genes were not notably duplicated in mudskippers. The results indicate that keratin gene duplication occurred repeatedly in lineages close to tetrapods, but not in teleost fish, even in species adapted to terrestrial environments.

著者

Ahmad Luqman-Fatah Tomoichiro Miyoshi

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.22-00038, (Released:2022-11-25)

参考文献数

372

被引用文献数

4

---

Genome sequencing revealed that nearly half of the human genome is comprised of transposable elements. Although most of these elements have been rendered inactive due to mutations, full-length intact long interspersed element-1 (LINE-1 or L1) copies retain the ability to mobilize through RNA intermediates by a so-called "copy-and-paste" mechanism, termed retrotransposition. L1 is the only known autonomous mobile genetic element in the genome, and its retrotransposition contributes to inter- or intra-individual genetic variation within the human population. However, L1 retrotransposition also poses a threat to genome integrity due to gene disruption and chromosomal instability. Moreover, recent studies suggest that aberrant L1 expression can impact human health by causing diseases such as cancer and chronic inflammation that might lead to autoimmune disorders. To counteract these adverse effects, the host cells have evolved multiple layers of defense mechanisms at the epigenetic, RNA and protein levels. Intriguingly, several host factors have also been reported to facilitate L1 retrotransposition, suggesting that there is competition between negative and positive regulation of L1 by host factors. Here, we summarize the known host proteins that regulate L1 activity at different stages of the replication cycle and discuss how these factors modulate disease-associated phenotypes caused by L1.

著者

Masayuki Horie

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.18-00049, (Released:2019-06-29)

参考文献数

89

被引用文献数

6

---

Riboviruses are viruses that have RNA genomes and replicate only via RNA intermediates. Although they do not require a DNA phase for replication and do not encode reverse transcriptase, the presence of DNA forms of riboviral sequences in ribovirus-infected cells has been reported since the 1970s. Additionally, heritable ribovirus-derived sequences, called riboviral endogenous viral elements (EVEs), have been found in the genomes of many eukaryotes. These are now thought to be formed by the reverse transcription machineries of retrotransposons within eukaryotic genomes sometimes referred to as selfish elements. Surprisingly, some reverse-transcribed riboviral DNAs (including EVEs) provide physiological functions for their hosts, suggesting the occurrence of novel interactions among eukaryotic genomes, retrotransposons and riboviruses, and opening the door to new avenues of investigation. Here I review current knowledge on these triangular interactions, and discuss future directions in this field.

著者

Kenji K. Kojima

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.18-00024, (Released:2018-11-09)

参考文献数

172

被引用文献数

84

---

The majority of eukaryotic genomes contain a large fraction of repetitive sequences that primarily originate from transpositional bursts of transposable elements (TEs). Repbase serves as a database for eukaryotic repetitive sequences and has now become the largest collection of eukaryotic TEs. During the development of Repbase, many new superfamilies/lineages of TEs, which include Helitron, Polinton, Ginger and SINEU, were reported. The unique composition of protein domains and DNA motifs in TEs sometimes indicates novel mechanisms of transposition, replication, anti-suppression or proliferation. In this review, our current understanding regarding the diversity of eukaryotic TEs in sequence, protein domain composition and structural hallmarks is introduced and summarized, based on the classification system implemented in Repbase. Autonomous eukaryotic TEs can be divided into two groups: Class I TEs, also called retrotransposons, and Class II TEs, or DNA transposons. Long terminal repeat (LTR) retrotransposons, including endogenous retroviruses, non-LTR retrotransposons, tyrosine recombinase retrotransposons and Penelope-like elements, are well accepted groups of autonomous retrotransposons. They share reverse transcriptase for replication but are distinct in the catalytic components responsible for integration into the host genome. Similarly, at least three transposition machineries have been reported in eukaryotic DNA transposons: DDD/E transposase, tyrosine recombinase and HUH endonuclease combined with helicase. Among these, TEs with DDD/E transposase are dominant and are classified into 21 superfamilies in Repbase. Non-autonomous TEs are either simple derivatives generated by internal deletion, or are composed of several units that originated independently.

著者

Tetsuji Hosoda Hitoshi Suzuki Masashi Harada Kimiyuki Tsuchiya Sang-Hoon Han Ya-ping Zhang Alexei P. Kryukov Liang-Kong Lin

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.75, no.5, pp.259-267, 2000 (Released:2002-09-19)

参考文献数

39

被引用文献数

55 67

---

We compared partial sequences (402 bp) of the mitochondrial cytochrome b gene in 68 individuals of martens (Martes), weasels (Mustela) and their relatives from the Northern Hemisphere to identify the modes of geographic differentiation in each species. We then compared complete sequences (1140 bp) of the gene in 17 species of the family Mustelidae to know the spatial and temporal modes of speciation, constructing linearized trees with transversional substitutions for deeper lineage divergences and with transversions and transitions for younger lineages. Our data suggested that these lineages of Martes and Mustela differentiated in a stepwise fashion with five radiation stages from the generic divergences (stage I) to the intraspecific divergences (stage V), during the last 10 or 20 million years as the fossil evidence suggests. In the lineage of Martes, the first offshoots are of Martes flavigula, M. pennanti, and Gulo gulo (stage II), the second is M. foina (stage III), and the third are M. americana, M. martes, M. melampus, and M. zibellina (stage IV). The divergence of the lineages of Mustela is likely to have taken place concurrently with the radiations of the Martes. These divergence processes are attributable in part to the geographic allocation along the two continents, North America and Eurasia, as well as among peripheral insular domains, such as Taiwan and the Japanese Islands. In addition, the Eurasian continent itself was shown to have been involved in the species diversification in the martens and weasels.

著者

Baojun Zhao Shuyu Xue Wanchao Zhu TianShu Lv Qinguo Wei Shuai Shang Honghai Zhang

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.18-00018, (Released:2018-12-19)

参考文献数

20

被引用文献数

1 1

---

The Siberian weasel (Mustela sibirica) is widely distributed in mainland Asia, but its introduction into Japan and subsequent expansion have affected the Japanese weasel (M. itatsi). To provide a useful tool for population genetic studies and control of M. sibirica, we developed 10 polymorphic microsatellite markers. Among 40 individuals of M. sibirica collected in Hubei Province, China, the number of alleles per locus varied from 2 to 19, with the observed heterozygosity ranging from 0.050 to 1.000 and the expected heterozygosity ranging from 0.049 to 0.920. None of the loci deviated from Hardy–Weinberg equilibrium. These markers will be useful in further studies investigating the population structure and natural history of M. sibirica, and may thus provide new insights for the efficient management of this species.

著者

Tomoya Suzuki Akira S. Hirao Masaki Takenaka Koki Yano Koji Tojo

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.20-00033, (Released:2021-01-24)

参考文献数

27

被引用文献数

3

---

We developed microsatellite markers for Appasus japonicus (Heteroptera: Belostomatidae). This belostomatid bug is distributed in East Asia (Japanese Archipelago, Korean Peninsula and mainland China) and often listed as an endangered species in the Red List or the Red Data Book at the national and local level in Japan. Here, we describe twenty novel polymorphic microsatellite loci developed for A. japonicus, and marker suitability was evaluated using 56 individuals from four A. japonicus populations (Nagano, Hiroshima and Yamaguchi prefectures, Japan, and Chungcheongnam-do, Korea). The number of alleles per locus ranged from 1 to 12 (mean = 2.5), and the average observed and expected heterozygosity and fixation index per locus were 0.270, 0.323 and 0.153, respectively. In addition, a population structure analysis was conducted using the software STRUCTURE, and its result suggested that the 20 markers described here will be useful for investigating the genetic structure of A. japonicus populations, which should contribute to population genetics studies of this species.

著者

So Nakagawa Toshiaki Katayama Lihua Jin Jiaqi Wu Kirill Kryukov Rise Oyachi Junko S Takeuchi Takatomo Fujisawa Satomi Asano Momoka Komatsu Jun-ichi Onami Takashi Abe Masanori Arita

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.23-00085, (Released:2023-10-14)

参考文献数

53

---

Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.

著者

Mikihiro Kase Takayuki Shimizu Keita Kamino Kazuo Umetsu Hideki Sugiyama Takashi Kitano

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.17-00004, (Released:2017-06-30)

被引用文献数

5

---

The brown hagfish (Eptatretus atami) is one of several known hagfish species occurring in Japanese coastal waters. To date, there has been no research studying genetic polymorphisms in the species. In the present study, we analyzed differences in nucleotide sequences between two populations: one from Suruga Bay on the Pacific coast of Honshu, Japan, and the other from the Sea of Japan, off Akita on the northwest coast of Honshu. We sequenced part of the cytochrome oxidase subunit 1 gene (COX1) from the mitochondrial genome, and three G protein-coupled receptor genes from the nuclear genome. Phylogenetic networks of all four genes showed divergence between the two populations. Further, comparison of the COX1 data using a phylogenetic tree for a range of hagfish species indicated clear differences between the populations, suggesting that they differ at the species level. The numbers of their teeth, in particular of fused cusps (anterior/posterior multicusps), also supported these findings. Individuals of the Suruga Bay population had 3/3 fused cusps, as described for E. atami, whereas individuals of the Akita population had 3/2 fused cusps. These results suggest that the brown hagfish from the Sea of Japan, off the northwest coast of Honshu, is a distinct species from E. atami.

著者

Seigo Yamamoto Mitsuhiko Murase Manabu Miyazaki Sakura Hayashi Akihiko Koga

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.20-00047, (Released:2021-03-06)

参考文献数

7

---

Albino mutants (white coat and red eyes) of tanuki (Nyctereutes procyonoides viverrinus) have been repeatedly found in the Central Alps area of Japan. We recently reported that an albino tanuki from Iida, a city in this area, lacks the third exon of the TYR gene encoding tyrosinase, which is essential for melanin synthesis. The absence of this exon was due to the chromosomal deletion of a complex structure. In the present study, we analyzed TYR of another albino tanuki that was found in Matsusaka, a city located outside the mountainous area. In this animal, the third exon was also lost, and the loss was due to a deletion in which the structure was identical to that of the Iida mutant. Our results indicate, in consideration of the complex structure of the deletion, that the two albino animals inherited a single deletion that arose in their common ancestor. Iida and Matsusaka are approximately 170 km apart. This is, to our knowledge, the first report of an albino mutant gene that is widely distributed in mammalian natural populations. As the origin of this mutation is not known, the distance covered by the mutant gene remains unclear. If we assume that the mutation occurred halfway between Iida and Matsusaka, we can predict the migration distance to be approximately 85 km; however, if the mutation occurred at any other place, a longer distance would be predicted. Natural selection against albino tanuki may be relaxed because of a recent increase in food resources and refuge in urban areas.

著者

Ryota Yasui Ayaka Washizaki Yuko Furihata Tetsuro Yonesaki Yuichi Otsuka

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.89, no.2, pp.51-60, 2014-04-01 (Released:2014-09-13)

参考文献数

54

被引用文献数

1 10

---

Bacteria have a variety of resistance mechanisms for surviving bacteriophage infections. Here, we describe a novel anti-phage mechanism in Escherichia coli. Cells harboring a plasmid with the genes abpA and abpB, formerly yfjL and yfjK, blocked the propagation of bacteriophages belonging to three families: T4, T2, T7 and λ phages. Both genes were necessary for the inhibition of phage propagation, and deletion of either chromosomal gene resulted in a 20% increase of progeny compared to wild-type cells. Neither overexpression nor deficiency of AbpA and AbpB had any apparent effect on E. coli growth. We isolated seven suppressor mutants of T4 phage that grew weakly on cells overexpressing AbpA and AbpB, and found that their mutations were all located in gene 41, which encodes a replicative DNA helicase that is essential for DNA replication. Furthermore, we demonstrated that AbpA and AbpB inhibited DNA replication and late gene expression of T4 phage. Similarly, DNA replication of T7 and λ phages was also inhibited by AbpA and AbpB. These results strongly suggest that E. coli AbpA and AbpB target DNA replication of phages to block their propagation.

著者

Timothy A. Jinam Hideaki Kanzawa-Kiriyama Naruya Saitou

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.90, no.3, pp.147-152, 2015-06-01 (Released:2015-10-27)

参考文献数

49

被引用文献数

9 27

---

The Japanese Archipelago stretches approximately 3,000 kilometers from Hokkaido in the north to the Ryukyu Islands in the south, and has seen human activity since at least 30 thousand years ago (KYA). The Jomon period from 16 to 3 KYA is associated with cord-marked pottery and the people at that time, who were hunter-gatherers, occupied a range of locations across the Japanese Archipelago. The Yayoi period from 3 to 1.7 KYA saw the introduction of migrants from the Asian Continent who brought rice agriculture to the archipelago. The dual-structure model, which is based on craniofacial measurements, proposes that admixture between the Jomon and Yayoi people resulted in current-day Japanese. Subsequent genetic studies using uniparental and autosomal markers in current-day and ancient human samples are widely in support of the dual-structure model. These genetic data have also unveiled the uniqueness of the indigenous Ainu and Ryukyuan people while further demonstrating the genetic substructure within the Mainland Japanese.

著者

Mikihiro Kase Takayuki Shimizu Keita Kamino Kazuo Umetsu Hideki Sugiyama Takashi Kitano

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.92, no.4, pp.197-203, 2017-08-01 (Released:2018-02-10)

参考文献数

29

被引用文献数

5

---

The brown hagfish (Eptatretus atami) is one of several known hagfish species occurring in Japanese coastal waters. To date, there has been no research studying genetic polymorphisms in the species. In the present study, we analyzed differences in nucleotide sequences between two populations: one from Suruga Bay on the Pacific coast of Honshu, Japan, and the other from the Sea of Japan, off Akita on the northwest coast of Honshu. We sequenced part of the cytochrome oxidase subunit 1 gene (COX1) from the mitochondrial genome, and three G protein-coupled receptor genes from the nuclear genome. Phylogenetic networks of all four genes showed divergence between the two populations. Further, comparison of the COX1 data using a phylogenetic tree for a range of hagfish species indicated clear differences between the populations, suggesting that they differ at the species level. The numbers of their teeth, in particular of fused cusps (anterior/posterior multicusps), also supported these findings. Individuals of the Suruga Bay population had 3/3 fused cusps, as described for E. atami, whereas individuals of the Akita population had 3/2 fused cusps. These results suggest that the brown hagfish from the Sea of Japan, off the northwest coast of Honshu, is a distinct species from E. atami.

著者

Kazuki Fukushima Toko Kanomata Aoi Kon Hiromi Masuko-Suzuki Kana Ito Sadayoshi Ogata Yoshinobu Takada Yukihiro Komatsubara Tsuyoshi Nakamura Takumi Watanabe Saori Koizumi Hitoshi Sanuki Jong-In Park Satoshi Niikura Keita Suwabe Sota Fujii Kohji Murase Seiji Takayama Go Suzuki Masao Watanabe

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.20-00066, (Released:2021-06-18)

参考文献数

62

被引用文献数

1

---

In various coastal areas of Japan, naturalized radish populations are observed. Radish is a cruciferous plant and exhibits self-incompatibility, involving a system controlled by a single locus with multiple S alleles. Although the S allele diversity of radish cultivars and wild radishes has been characterized, the S allele distribution in naturalized populations has not yet been analyzed in relation to the positions of the plants in situ. Here, we show the S allele distribution in naturalized radish populations of Yakushima, a small island in the East China Sea, with positions of the plants. Radish plants were sampled in coastal areas in Yakushima, and their S alleles were detected and characterized. Most of the S alleles had been previously identified in radish cultivars. However, four novel S alleles, which may be unique to Yakushima, were also found. Moreover, seeds in siliques from plants growing in the study areas were sampled, and S allele determination in DNA extracted from these seeds suggested that the plants had exchanged their pollen among their close neighbors. There was also a problem in that the PCR amplification of some SRK alleles was difficult because of their sequence diversity in the naturalized populations, as occurs in cultivars. Our results suggest that the exchange of S alleles between cultivars and naturalized populations occurs and that S alleles in naturalized populations are highly diverse. The methodology established in our study should be applicable to other self-incompatible species to dissect the diversity of S allele distribution in naturalized populations.

著者

Morteza M. Saber Marziyeh Karimiavargani Takanori Uzawa Nilmini Hettiarachchi Michiaki Hamada Yoshihiro Ito Naruya Saitou

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.20-00012, (Released:2021-03-24)

参考文献数

56

被引用文献数

4

---

Down syndrome in humans is caused by trisomy of chromosome 21. DSCR4 (Down syndrome critical region 4) is a de novo-originated protein-coding gene present only in human chromosome 21 and its homologous chromosomes in apes. Despite being located in a medically critical genomic region and an abundance of evidence indicating its functionality, the roles of DSCR4 in human cells are unknown. We used a bioinformatic approach to infer the biological importance and cellular roles of this gene. Our analysis indicates that DSCR4 is likely involved in the regulation of interconnected biological pathways related to cell migration, coagulation and the immune system. We also showed that these predicted biological functions are consistent with tissue-specific expression of DSCR4 in migratory immune system leukocyte cells and neural crest cells (NCCs) that shape facial morphology in the human embryo. The immune system and NCCs are known to be affected in Down syndrome individuals, who suffer from DSCR4 misregulation, which further supports our findings. Providing evidence for the critical roles of DSCR4 in human cells, our findings establish the basis for further experimental investigations that will be necessary to confirm the roles of DSCR4 in the etiology of Down syndrome.

著者

Fumio Yamada Mika Takaki Hitoshi Suzuki

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.77, no.2, pp.107-116, 2002 (Released:2002-06-06)

参考文献数

57

被引用文献数

38 50

---

We determined mitochondrial 12S ribosomal RNA (rRNA) and cytochrome b (cyt b) gene sequences in three leporid species of Japan, the Amami rabbit Pentalagus furnessi from the Ryukyu Islands, the Japanese hare Lepus brachyurus from Honshu, and a Japanese form of the mountain hare Lepus timidus ainu from Hokkaido. We compared the sequences with those of other taxa of leporids available in databases. Phylogenetic trees of the 12S rRNA gene sequences indicated that the lineage of P. furnessi diversified during the generic radiation of the leporids at an ancient time, which was estimated to have been the middle Miocene. Cyt-b gene trees revealed that the lineage of L. brachyurus branched off at an early stage in the speciation of Lepus, probably at the beginning of the Pliocene. The cyt b sequences of L. t. ainu were somewhat distinct from those of continental conspecific populations; this lineage divergence is likely to have occurred during the middle or late Pleistocene. The results show that the three regions of the Japanese archipelago, Ryukyu, Honshu-Shikoku-Kyushu, and Hokkaido, now preserve their own leporid taxa, each with a different extent of genetic endemicity. It is possible that the zoogeographic traits of the Japanese leporids are a consequence of the evolutionary dynamics of leporids in East Asia, in that the radiation centers of leporids are likely to have shifted from tropical, through temperate, to arctic zones.

著者

Patwira Boonjing Yukari Masuta Kosuke Nozawa Atsushi Kato Hidetaka Ito

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.19-00046, (Released:2020-08-03)

参考文献数

34

被引用文献数

10

---

The Ty1/copia-like retrotransposon ONSEN is conserved among Brassica species, as well as in beans, including adzuki bean (Vigna angularis (Willd.) Ohwi & Ohashi), which is one of the economically important crops in Japan. ONSEN has acquired a heat-responsive element that is recognized by plant heat stress defense factors, resulting in its transcription and the production of full-length extrachromosomal DNA under conditions with elevated temperatures. DNA methylation plays an important role in regulating the activation of this transposon in plants. Therefore, chemical inhibition of DNA methyltransferases has been utilized to study the effect of DNA methylation on transposon activation. To understand the effect of DNA methylation on ONSEN activation, Arabidopsis thaliana and adzuki bean seedlings were treated with zebularine, which is known to be an effective chemical demethylation agent. The results showed that ONSEN transcription levels were upregulated in zebularine-treated plants. Extrachromosomal DNA of ONSEN also accumulated in the treated plants.