著者

Kazutoshi Masuda Hiroaki Setoguchi Koki Nagasawa Shigeru Fukumoto Masae Iwamoto Ishihara Rei-ichi Miura Leiko Mizusawa Ken-ichi Hiratsuka Shota Sakaguchi

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.21-00021, (Released:2021-06-18)

参考文献数

20

被引用文献数

2

---

Arnica mallotopus is a perennial herb endemic to the snowy regions of Japan. At the southern edge of its distribution, in Kyoto Prefecture, overgrazing by sika deer and decreased snowfall have resulted in the rapid decline of A. mallotopus populations. Therefore, there is an urgent need for a conservation genetic analysis of the remaining local populations. In this study, we first developed 13 EST-SSR markers to evaluate genetic variation in A. mallotopus. The average number of alleles per locus was 5.33. Genetic analysis using these markers showed that the investigated samples were classified into two groups corresponding to landscape structure. One group isolated from a tributary of the Yura River showed a strong population bottleneck signal, likely resulting from founder effects and subsequent drifts. On the other hand, the genetic diversity of the second group in the main distribution along the Yura River was higher and less inbred. Overall, our assessment suggested recognizing the two genetic groups as management units in conservation programs for the threatened populations.

著者

Tetsushi Iida Takehiko Kobayashi

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.21-00004, (Released:2021-06-10)

参考文献数

32

---

Many proteins form complexes that function in reaction pathways. Therefore, to understand protein function, it is necessary to reconstitute complexes and pathways in vitro. However, it is not straightforward to achieve full activity in reconstituted systems. To address this problem, we present a yeast system named "in saccharo" analysis, which uses budding yeast for simultaneous expression and analysis of many kinds of non-host proteins, such as human proteins. For this purpose, vectors that can accommodate many genes are required. Here, we describe the construction of a chromosome vector by insertion of unique barcode sequences (BCs) into the ribosomal RNA gene repeat (rDNA). Each unit of the rDNA has a BC that is used as the target for integration of an external gene. Because rDNA is naturally capable of maintaining many repetitive copies, the vector is expected to retain the numerous external genes that may be required for reconstitution of functional protein complexes and reaction pathways. Consistent with this prediction, we were able to clone three human genes that form the RNA silencing pathway, which has no functional equivalent in budding yeast, and to demonstrate functionality in this in saccharo analysis system.

著者

Seiji Masuda Kosuke Nozawa Wataru Matsunaga Yukari Masuta Akira Kawabe 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

vol.91, no.6, pp.293-299, 2016-12-01 (Released:2017-05-13)

参考文献数

34

被引用文献数

4

---

Natural accessions are used for studying intraspecies genetic variation in the model plant Arabidopsis thaliana in order to address fundamental questions of evolution. Transposable elements are responsible for a wide range of mutations and play significant roles in shaping a genome over evolutionary time. In the present study, we aimed to characterize ONSEN, a heat-activated long terminal repeat (LTR) retrotransposon, in natural A. thaliana accessions. Southern blot analysis demonstrated that ONSEN was present in all the studied accessions, but the copy number was diverse. Olympia-1 contained a single ONSEN copy, located in the centromere of Chromosome 3. A premature stop codon in Olympia-1 ONSEN presumably abolishes integrase activity, which in turn presumably renders the retrotransposon non-functional. Hybridization of Col-0 with Olympia-1 showed that several ONSEN copies in Col-0 were activated by heat stress and maintained their transpositional activity in the progeny.

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.95, no.6, pp.Cover, 2020-12-01 (Released:2021-03-23)

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

vol.95, no.6, pp.323-329, 2020-12-01 (Released:2021-03-23)

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

Kotaro Tsukada Ryouhei Yoshihara Shin Hatakeyama Akihiko Ichiishi Shuuitsu Tanaka

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.20-00022, (Released:2021-02-06)

参考文献数

32

---

Photoreactivation is a mechanism in which photolyase directly repairs either cyclobutane pyrimidine dimers (CPDs) or (6-4) photoproducts [(6-4) PPs] caused by ultraviolet (UV) light. In the filamentous fungus Neurospora crassa, some UV-sensitive mutants such as mus-44 have been reported to exhibit a partial photoreactivation defect (PPD) phenotype, but its mechanism has not been elucidated for a long time. In this study, the N. crassa CPD photolyase PHR was overexpressed in the mus-44 strain, but photoreactivation ability was not increased. Furthermore, Escherichia coli CPD photolyase or Arabidopsis thaliana (6-4) PP photolyase was also introduced into mus-44; however, the PPD phenotype was not complemented. These results suggested that the PPD phenotype in N. crassa is not caused by residual unrepaired pyrimidine dimers, which are the main type of DNA damage caused by UV irradiation. Finally, we revealed that mus-44, but not the mus-43 strain, which does not show the PPD phenotype, displayed higher sensitivity with increasing dose rate of UV. Moreover, mus-44 was also sensitive to an interstrand crosslinking agent. This indicates that the high dose of UV in our experimental condition induces DNA damage other than pyrimidine dimers, and that such damage is a likely cause of the PPD phenotype.

著者

Wataru Aoki Maiko Watanabe Masaki Watanabe Naoki Kobayashi Jun Terajima Yoshiko Sugita-Konishi Kazunari Kondo Yukiko Hara-kudo

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.95, no.3, pp.133-139, 2020-06-01 (Released:2020-08-27)

参考文献数

22

被引用文献数

3

---

Entoloma sarcopum is widely known as an edible mushroom but appears morphologically similar to the poisonous mushrooms E. rhodopolium sensu lato (s. l.) and E. sinuatum s. l. Many cases of food poisoning caused by eating these poisonous mushrooms occur each year in Japan. Therefore, they were recently reclassified based on both morphological and molecular characteristics as sensu stricto species. In this study, we analyzed the nucleotide sequences of the rRNA gene (rDNA) cluster region, mainly including the internal transcribed spacer regions and mitochondrial cytochrome oxidase 1 (CO1) gene, in E. sarcopum and its related species, to evaluate performances of these genes as genetic markers for identification and molecular phylogenetic analysis. We found that the CO1 gene contained lineage-specific insertion/deletion sequences, and our CO1 tree yielded phylogenetic information that was not supported by analysis of the rDNA cluster region sequence. Our results suggested that the CO1 gene is a better genetic marker than the rDNA cluster region, which is the most widely used marker for fungal identification and classification, for discrimination between edible and poisonous mushrooms among Japanese E. sarcopum and related species. Our study thus reports a new genetic marker that is useful for detection of Japanese poisonous mushrooms, Entoloma.

著者

Tsuchiya Kimiyuki Suzuki Hitoshi Shinohara Akio HARADA Masashi WAKANA Shigeharu SAKAIZUMI Mitsuru HAN Sang-Hoon LIN Liang-Kong KRYUKOV Alexei P.

出版者

The Genetics Society of Japan

雑誌

Genes & genetic systems (ISSN:13417568)

巻号頁・発行日

vol.75, no.1, pp.17-24, 2000-02

被引用文献数

15 49

---

Taxonomic analysis has previously revealed that the species of moles that inhabit Japan are characterized by exceptional species richness and a high level of endemism. Here, we focused on the evolutionary history of the four Japanese mole species of the genera <i>Euroscapter</i> and <i>Mogera</i>, examining mitochondrial cytochrome <i>b</i> (cyt <i>b</i>) gene sequences and comparing them with those of continental <i>Mogera wogura</i> (Korean and Russian populations), <i>M. insularis</i> from Taiwan, and <i>Talpa europaea</i> and <i>T. altaica</i> from the western and central Eurasian continent, respectively. Our data support the idea that in a radiation center somewhere on the Eurasian continent, a parental stock evolved to modern mole-like morph and radiated several times intermittently during the course of the evolution, spreading its branches to other peripheral geographic domains at each stage of the radiation. Under this hypothesis, the four lineages of Japanese mole species, <i>E. mizura</i>, <i>M. tokudae</i>, <i>M. imaizumii</i>, and <i>M. wogura</i>, could be explained to have immigrated to Japan in this order. <i>Mogera wogura</i> and <i>M. imaizumii</i> showed substantial amounts of geographic variation and somewhat complicated distributions of the cyt <i>b</i> gene types. These intraspecific variations are likely to be associated with the expansion processes of moles in the Japanese Islands during the Pleistocene glacial ages.<br>

著者

Takahiko Kubo Yoshiyuki Yamagata Maki Eguchi Atsushi Yoshimura

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.83, no.6, pp.443-453, 2008 (Released:2009-03-12)

参考文献数

41

被引用文献数

32 41

---

Postzygotic reproductive isolation (RI) often arises in inter-subspecific crosses as well as inter-specific crosses of rice (Oryza sativa L.). To further understand the genetic architecture of the postzygotic RI, we analyzed genes causing hybrid sterility and hybrid breakdown in a rice inter-subspecific cross. Here we report hybrid male sterility caused by epistatic interaction between two novel genes, S24 and S35, which were identified on rice chromosomes 5 and 1, respectively. Genetic analysis using near-isogenic lines (NILs) carrying IR24 (ssp. indica) segments with Asominori (ssp. japonica) genetic background revealed a complicated aspect of the epistasis. Allelic interaction at the S24 locus in the heterozygous plants caused abortion of male gametes carrying the Asominori allele (S24-as) independent of the S35 genotype. On the other hand, male gametes carrying the Asominori allele at the S35 locus (S35-as) showed abortion only when the IR24 allele at the S24 locus (S24-ir) was concurrently introgressed into the S35 heterozygous plants, indicating that the sterility phenotype due to S35 was dependent on the S24 genotype through negative epistasis between S24-ir and S35-as alleles. Due to the interaction between S24 and S35, self-pollination of the double heterozygous plants produced pollen-sterile progeny carrying the S24-ir/S24-ir S35-as/S35-ir genotype in addition to the S24 heterozygous plants. This result suggests that the S35 gene might function as a modifier of S24. This study presents strong evidence for the importance of epistatic interaction as a part of the genetic architecture of hybrid sterility in rice. In addition, it suggests that diverse systems have been developed as postzygotic RI mechanisms within the rice.

著者

Takatomi Okaura Nguyen Duc Quang Masatoshi Ubukata Ko Harada

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.82, no.6, pp.465-477, 2007 (Released:2008-02-09)

参考文献数

49

被引用文献数

61 79

---

Generally, oaks dominate the broadleaf deciduous forests in Japan. The genetic variation in 6 cpDNA regions (trnT-trnL, trnL-trnF, atpB-rbcL, and trnH-psbA speacers, trnL intron, and matK gene) with regard to the Japanese oak (Quercus mongolica var. crispula) and 3 related species in the section Prinus (Q. serrata, Q. dentata and Q. aliena) was investigated in 598 trees belonging to 44 populations distributed throughout the Japanese archipelago. Additional samples were collected from Korea, China, and Russia (Sakhalin). Thirteen haplotypes (I to XIII) were identified on the bases of 15 nucleotide substitutions and 3 indels. Haplotypes I and II were discovered in northeastern Japan, whereas haplotypes III to IX were distributed in southwestern Japan. The boundary distinguishing these 2 groups was located in central Japan coincident with the Itoigawa-Shzuoka tectonic line. Haplotype I was also found in Sakhalin, whereas haplotypes VI, VII, VIII, X, XI, XII, and XIII were found in Korea and China. Four oak species in the same location shared identical haplotypes, suggesting cpDNA introgression by occasional hybridization. Both the values of total haplotype diversity (HT) and haplotype diversity within populations (HS) in Q. mongolica var. crispula were higher in the southwestern populations than in the northeastern populations. A haplotype network indicated that haplotype VI is the ancestral haplotype. The presence of identical haplotypes in Korea, China, and Japan suggested that the haplotypes diversified on the Eurasian continent before the last glacial period. The difference in genetic structure between the northeastern and southwestern regions indicates a difference in the history of migration and recolonization in Japan during the last glacial period.

著者

Eli Kaminuma Yukino Baba Masahiro Mochizuki Hirotaka Matsumoto Haruka Ozaki Toshitsugu Okayama Takuya Kato Shinya Oki Takatomo Fujisawa Yasukazu Nakamura Masanori Arita Osamu Ogasawara Hisashi Kashima Toshihisa Takagi

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.19-00034, (Released:2020-03-26)

参考文献数

37

被引用文献数

3

---

Recently, the prospect of applying machine learning tools for automating the process of annotation analysis of large-scale sequences from next-generation sequencers has raised the interest of researchers. However, finding research collaborators with knowledge of machine learning techniques is difficult for many experimental life scientists. One solution to this problem is to utilise the power of crowdsourcing. In this report, we describe how we investigated the potential of crowdsourced modelling for a life science task by conducting a machine learning competition, the DNA Data Bank of Japan (DDBJ) Data Analysis Challenge. In the challenge, participants predicted chromatin feature annotations from DNA sequences with competing models. The challenge engaged 38 participants, with a cumulative total of 360 model submissions. The performance of the top model resulted in an area under the curve (AUC) score of 0.95. Over the course of the competition, the overall performance of the submitted models improved by an AUC score of 0.30 from the first submitted model. Furthermore, the 1st- and 2nd-ranking models utilised external data such as genomic location and gene annotation information with specific domain knowledge. The effect of incorporating this domain knowledge led to improvements of approximately 5%–9%, as measured by the AUC scores. This report suggests that machine learning competitions will lead to the development of highly accurate machine learning models for use by experimental scientists unfamiliar with the complexities of data science.

著者

Masashi Tsuchida Takehiro Fukushima Shuhei Nasuda Ali Masoudi-Nejad Goro Ishikawa Toshiki Nakamura Takashi R. Endo

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.83, no.1, pp.43-53, 2008 (Released:2008-03-28)

参考文献数

41

被引用文献数

22 28

---

Rye chromosome 1R contains many agronomically useful genes. Physical dissection of chromosome 1R into segments would be useful in mapping 1R-specific DNA markers and in assembling DNA clones into contig maps. We applied the gametocidal system to produce rearranged 1R chromosomes of Imperial rye (1Ri) added to common wheat. We identified rearranged 1Ri chromosomes and established 55 1Ri dissection lines of common wheat carrying a single rearranged 1Ri chromosome. Fifty-two of the rearranged 1Ri chromosomes had single breakpoints and three had double breakpoints. The 58 breakpoints were distributed in the short arm excluding the satellite (12 breakpoints), in the satellite (4), in the long arm (28), and in the centromere (14). Out of the 55 lines, nine were homozygous for the rearranged 1Ri chromosomes, and the remaining lines were hemizygous. We developed 26 PCR-based EST markers that were specific to the 1Ri chromosome, and nine of them amplified 1Ri arm-specific PCR products without restriction-enzyme digestion. Using the nine EST markers and two previously reported 1R-specific markers, we characterized the 55 1Ri dissection lines, and also proved that we can select critical progeny plants carrying specific rearranged 1Ri chromosomes by PCR, without cytological screening, in 48 out of the 55 hemizygous dissection lines.

著者

Hidenori Nishihara

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.94, no.6, pp.269-281, 2019-12-01 (Released:2020-01-30)

参考文献数

123

被引用文献数

32

---

In the current era, as a growing number of genome sequence assemblies have been reported in animals, an in-depth analysis of transposable elements (TEs) is one of the most fundamental and essential studies for evolutionary genomics. Although TEs have, in general, been regarded as non-functional junk/selfish DNA, parasitic elements or harmful mutagens, studies have revealed that TEs have had a substantial and sometimes beneficial impact on host genomes in several ways. First, TEs are themselves diverse and thus provide lineage-specific characteristics to the genomes. Second, because TEs constitute a substantial fraction of animal genomes, they are a major contributing factor to evolutionary changes in genome size and composition. Third, host organisms have co-opted many repetitive sequences as genes, cis-regulatory elements and chromatin domain boundaries, which alter gene regulatory networks and in addition are partly involved in morphological evolution, as has been well documented in mammals. Here, I review the impact of TEs on various aspects of the genome, such as genome size and diversity in animals, as well as the evolution of gene networks and genome architecture in mammals. Given that a number of TE families probably remain to be discovered in many non-model organisms, unknown TEs may have contributed to gene networks in a much wider variety of animals than considered previously.

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

vol.94, no.6, pp.233-252, 2019-12-01 (Released:2020-01-30)

参考文献数

172

被引用文献数

81

---

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

Takashi Yura

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.19-00005, (Released:2019-07-08)

参考文献数

51

被引用文献数

32

---

The heat shock response mediated by transcription factor σ32 is a major stress response to cope with heat and other stresses in Escherichia coli. Although much attention has been paid to the role of highly conserved heat shock proteins such as chaperones and proteases in sustaining cellular protein homeostasis under stress, relatively little is known about the dynamic nature of underlying regulatory mechanisms. When cells are suddenly exposed to high temperature, synthesis of σ32 is rapidly induced by activated translation of rpoH mRNA, which encodes σ32, through disruption of mRNA secondary structure. The increased synthesis of σ32 is accompanied by stabilization of σ32, which is normally very unstable and rapidly degraded by the membrane-localized FtsH protease. It was recently found that σ32 must be localized to the inner membrane by the SRP-dependent pathway to work properly for regulation, but the roles played by membrane and other components of the cell remained unknown. Random transposon mutagenesis of the strongly deregulated I54N-σ32 mutant has now started to unravel the complex regulatory circuit, involving membrane protein(s), other cellular components or σ32-interfering polypeptides, for dynamic fine-tuning of σ32 activity that could be of vital importance for cell survival.

著者

Masato Nikaido

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.19-00009, (Released:2019-09-02)

参考文献数

60

被引用文献数

10

---

The vomeronasal organ (VNO) plays a key role in sensing pheromonal cues, which elicit innate responses and induce social and sexual behaviors. The vomeronasal receptor 1 genes, V1Rs, encode members of a pheromone receptor family that are mainly expressed in the VNO. Previous studies have revealed that the V1R family shows extraordinary variety among mammalian species owing to successive gene gains and losses. Because species-specific pheromonal interaction may facilitate species-specific reproductive behaviors, understanding the evolution of V1Rs in terms of their origin, repertoire and phylogeny should provide insight into the mechanisms of animal diversification. Here I summarize recent studies about the V1R family from its initial discovery in the rat genome to extensive comparative analyses among vertebrates. I further introduce our recent findings for V1Rs in a broad range of vertebrates, which reveal unexpected diversity as well as shared features common among lineages.

著者

Atsuo Iida Zi Wang Atsuko Sehara-Fujisawa

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.19-00033, (Released:2019-10-01)

参考文献数

15

被引用文献数

2

---

Integrins, transmembrane molecules that facilitate cell-to-cell and cell-to-extracellular matrix interactions, are heterodimers that consist of an α- and β-subunit. The integrin α4 gene (itgα4) is expressed in various type of cells and tissues. Its biochemical functions and physiological roles have been revealed using cultured cell assays. In contrast, the primary effect caused by itgα4 deletion on vertebrate development is poorly understood, because knockout mice exhibit multiple defects that can lead to embryonic lethality in the uterus. Zebrafish are a convenient vertebrate model to investigate morphogenesis during embryogenesis, because of their external fertilization and subsequent development outside the female's body. Here, we generated a zebrafish mutant line named itgα4 ko108 using the CRISPR/Cas9 genome editing system; the mutant genome harbored an approximately 2.0-kb deletion in the itgα4 locus. A truncated transcript was detected in itgα4 (+/-) or (-/-) fish but not in (+/+) fish. The mutant transcript was hypothesized to encode a truncated Itgα4 protein due to a premature stop codon. itgα4 (-/-) embryos obtained from the mating of heterozygous parents exhibited no apparent phenotype during development at 24 hours post-fertilization (hpf). However, approximately half of them exhibited cephalic hemorrhage at 48 hpf. The incidence ratio was significantly higher than that in (+/+) or (+/-) embryos. Embryonic hemorrhage has also been reported previously in Itgα4 knockout mice. In contrast, embryonic lethality with the other defects reported in the knockout mice was not observed in our zebrafish model. Therefore, the mutant line itgα4 ko108 should be a useful model to investigate a physiological function for Itgα4 in the blood circulation system.

著者

Masahiro Furuyama Haruna Nagaoka Tadashi Sato Mitsuru Sakaizumi

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.19-00013, (Released:2019-08-10)

参考文献数

27

被引用文献数

1

---

Gene-centromere (G-C) mapping provides insight into vertebrate genome composition, structure and evolution. Although medaka fish are important experimental animals, no genome-wide G-C map of medaka has been constructed. In this study, we used 112 interspecific triploid hybrids and 152 DNA markers to make G-C maps of all 24 linkage groups (LGs). Under the assumption of 50% interference, 24 centromeres were localized onto all corresponding medaka LGs. Comparison with 21 centromere positions deduced from putative centromeric repeats revealed that 19 were localized inside the centromeric regions of the G-C maps, whereas two were not. Based on the centromere positions indicated in the G-C maps and those of centromeric repeats on each LG, we classified chromosomes as either biarmed or monoarmed; n = 24 = 10 metacentrics/submetacentrics + 14 subtelocentrics/acrocentrics, which is consistent with the results of previous karyological reports. This study helps to elucidate genome evolution mechanisms, and integrates physical and genetic maps with karyological information of medaka.

著者

Koki R. Katsuhara Naoyuki Nakahama Taketo Komura Masaya Kato Yuko Miyazaki Yuji Isagi Motomi Ito Atushi Ushimaru

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.18-00058, (Released:2019-06-29)

参考文献数

19

---

Commelina communis f. ciliata (Commelinaceae), a newly distinguished taxon, is an annual andromonoecious herb exhibiting a mixed mating system, the details of which remain unclear. We developed microsatellite markers for use in exploring the evolution of andromonoecy and mixed mating in the species. Fifteen microsatellite loci were developed using next-generation sequencing. The primer sets were used to evaluate 65 C. communis f. ciliata individuals from three populations in Japan; we found 1–13 alleles per locus and the expected heterozygosity ranged from 0.00 to 0.76. The markers are potentially useful to examine intra- and interspecies genetic structure and the mixed mating strategy of Commelina species via paternity analysis.

著者

Tao Tian Yajie Lu Jun Yao Xin Cao Qinjun Wei Qi Li

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.18-00006, (Released:2018-08-31)

参考文献数

27

被引用文献数

7

---

Autosomal dominant non-syndromic hearing loss (ADNSHL) is characterized by postlingual progressive onset. Due to its high genetic heterogeneity, it is difficult to perform a molecular diagnosis for most patients with ADNSHL. In our study, whole-exome sequencing (WES) was used to screen pathogenic gene candidates by analyzing genomic DNA samples from a large Chinese family (JSNY-067), including the proband and her father, who suffered from non-syndromic hearing loss. The pathogenicity of candidate nonsynonymous variants in ADNSHL genes was evaluated by co-segregation analysis in family members by direct PCR and Sanger sequencing. Furthermore, multiple in silico analyses (SIFT, Polyphen2, PROVEAN and MutationTaster) and molecular dynamics simulation were used to assess the potential pathogenicity of the candidate mutations. We identified a novel causative mutation, c.622A>G in MYO6 (DFNA22), that resulted in a p.K208E substitution. This mutation co-segregated with the hearing loss phenotype in extended family members, and was predicted to be pathogenic by SIFT, PolyPhen2, PROVEAN and MutationTaster. Furthermore, molecular dynamics simulation analysis revealed that the p.K208E substitution had a limited influence on the whole protein structure and stability, but that it could affect the locations of the sidechains of nearby hydrophilic residues, which in turn resulted in the sidechains of Asn186 and Glu190 being exposed more frequently at the surface of the protein. WES has thus been shown to be a useful molecular diagnostic tool in screening uncommon gene mutations associated with hereditary hearing loss.