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
1

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

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
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
1

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
6

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 57

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
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
2

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
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
2

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
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 10

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
Uchu Yamakawa Shingo Kaneko Ryosuke Imai Leanne Kay Faulks Koetsu Kon Daisuke Kyogoku Yuji Isagi Yoshiaki Tsuda
出版者
The Genetics Society of Japan
雑誌
Genes & Genetic Systems (ISSN:13417568)
巻号頁・発行日
pp.19-00007, (Released:2019-11-16)
参考文献数
27

The amphidromous sleeper Eleotris oxycephala (Perciformes: Eleotridae) is mainly distributed along the Kuroshio Current in East Asia, and this current is thought to be the main driver of the species' dispersal. Due to anthropogenic environmental changes in rivers, E. oxycephala is ranked as a threatened or near-threatened species in the red lists of 12 prefectures in Japan. Moreover, there is concern that the species' dispersal pattern could be changed due to fluctuations in the Kuroshio Current caused by global warming. In this study, 40 microsatellite markers were developed for E. oxycephala, and their suitability was tested on 43 individuals from two populations of E. oxycephala from Kanagawa and Miyazaki Prefectures. The number of alleles, expected heterozygosity and fixation index at each locus were 2–10 (mean = 5.350), 0.034–0.860 (mean = 0.650) and -0.261–0.448 (mean = 0.065), respectively. Furthermore, there was a lack of genetic difference between the two populations (FST = 0.008, F'ST = 0.024), indicating widespread gene flow via the Kuroshio Current. These markers will be useful to evaluate the genetic structure and infer population demographic history of E. oxycephala populations, which may assist in the conservation of this species.
著者
Kazuki Watanabe Yuki Suzuki Show Inami Hirono Ohashi Takaomi Sakai
出版者
The Genetics Society of Japan
雑誌
Genes & Genetic Systems (ISSN:13417568)
巻号頁・発行日
pp.18-00004, (Released:2018-07-11)
参考文献数
17

In many animal species, females choose potential mating partners according to their own preferences. Thus, female preference-based mate choice affects intraspecific mating success and prevents interspecific mating. To clarify the neuronal basis of female mate choice, it is essential to identify the important relevant sensory cues. In the fruitfly Drosophila melanogaster, the courtship song of males promotes female sexual receptivity. When wild-type virgin females can freely choose one of two types of courting males (winged or wingless males), they prefer to mate with winged males. Here, we report a crucial sensory cue relevant to this female mate choice. In a female choice test, female receptivity toward winged and wingless males was markedly reduced when females had auditory impairments, although females with visual or olfactory impairments showed normal receptivity similar to wild-type females. However, females with visual impairments did not show clear mate preference toward winged males. Thus, these findings suggest that females utilize visual cues in mate choice between winged and wingless males in Drosophila.
著者
Naoyuki Nakahama Azusa Ito Shingo Kaneko Yu Matsuki Yoshihisa Suyama Azusa Hayano Miho Murayama Yuji Isagi
出版者
The Genetics Society of Japan
雑誌
Genes & Genetic Systems (ISSN:13417568)
巻号頁・発行日
pp.17-00021, (Released:2018-01-17)
被引用文献数
2

Microsatellite markers were developed for the endangered orchid Calanthe izu-insularis (Orchidaceae). This species is unique to the Izu Islands in Japan. Unfortunately, its population size has decreased because of excessive collection for horticultural purposes. In addition, although natural hybridization between C. izu-insularis and C. discolor var. discolor has been reported, morphological differences between C. izu-insularis and the hybridized individuals remain unclear. Using next-generation sequencing, 11 polymorphic microsatellite markers were developed. All developed markers could amplify C. aristulifera and nine markers could amplify C. d. var. discolor, two other orchid species that are also endangered in Japan. The number of alleles and expected heterozygosity at each locus were 1–6 (mean, 2.35) and 0.00–0.79 (mean, 0.30), respectively. These microsatellite markers will help conservation geneticists in their investigation of the proportion of pure C. izu-insularis individuals in the Izu Islands.
著者
Manuel Ruiz-García Pablo Orozco-terWengel Armando Castellanos Leonardo Arias
出版者
日本遺伝学会
雑誌
Genes & Genetic Systems (ISSN:13417568)
巻号頁・発行日
vol.80, no.1, pp.57-69, 2005 (Released:2005-04-12)
参考文献数
55
被引用文献数
10 15

DNA samples of the spectacled bear (Tremarctos ornatus) from five Andean countries, Venezuela, Colombia, Ecuador, Peru and Bolivia, were analyzed for nine microsatellite loci. Seven of them were polymorphic, which led us to investigate several population-genetic parameters. Private alleles and significant differences in gene frequencies were found among the populations studied, which demonstrated the extent of genetic differentiation among the spectacled bear populations. The levels of gene diversity measured with these microsatellites were rather modest in this species. Hardy-Weinberg disequilibrium was especially found for the overall and the Ecuadorian samples, and might be due to the Wahl-und effect or consanguinity. Significant genetic heterogeneity was mainly observed among the Colombian and the Ecuadorian populations. Markov chain Monte Carlo simulations clearly showed that two different gene pools were present, one present in the Venezuelan-Colombian bears and other in the Ecuadorian ones.
著者
Masaru Murakami Chikako Matsuba Hideo Fujitani
出版者
日本遺伝学会
雑誌
Genes & Genetic Systems (ISSN:13417568)
巻号頁・発行日
vol.76, no.1, pp.25-32, 2001 (Released:2002-05-31)
参考文献数
23
被引用文献数
32 37

The hyper-variable segments (323∼327 bp) of the mitochondrial D-loop for 169 Carassius auratus fishes in Japan were amplified by the polymerase chain reaction and the amplified products were sequenced directly and compared. A dendrogram showing three major clusters was generated with the sequence data for 37 haplotypes at 66 polymorphic sites. One cluster (cluster I) exclusively consisted of the gengorobuna, which was regarded as an independent (sub) species. The triploid ginbuna belonged to two remaining clusters, mainly in the diploid ginbuna cluster (cluster III) and partially in the goldfish cluster (cluster II). This finding suggests that the triploid ginbuna has been derived from two different maternal lineages. The triploid ginbuna was considered to have come into existence during the last ice age on the basis of this phylogenetic data. No geographic differentiation was observed with respect to the triploid ginbuna sampled at three different localities in Japan; the Shibuta River in Kanagawa, Lake Imba in Chiba and Lake Biwa in Shiga. The phylogenetic tree also demonstrated a monophyletic relationship amongst the nigorobuna, the nagabuna and the ginbuna, sharing cluster III. The nigorobuna and nagabuna populations have most likely arisen from geographic and temporal variations within the ginbuna populations. We also discuss the evolutionary origin of the triploid in view of its paternal ancestors.
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
vol.94, no.6, pp.253-267, 2019-12-01 (Released:2020-01-30)
参考文献数
89
被引用文献数
1 1

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
Jun Kitano Seiichi Mori
出版者
The Genetics Society of Japan
雑誌
Genes & Genetic Systems (ISSN:13417568)
巻号頁・発行日
vol.91, no.2, pp.77-84, 2016-04-01 (Released:2016-10-13)
参考文献数
78
被引用文献数
5

Stickleback fishes have been established as a leading model system for studying the genetic mechanisms that underlie naturally occurring phenotypic diversification. Because of the tremendous diversification achieved by stickleback species in various environments, different geographical populations have unique phenotypes and genotypes, which provide us with unique opportunities for evolutionary genetic research. Among sticklebacks, Japanese species have several unique characteristics that have not been found in other populations. The sympatric marine threespine stickleback species Gasterosteus aculeatus and G. nipponicus (Japan Sea stickleback) are a good system for speciation research. Gasterosteus nipponicus also has several unique characteristics, such as neo-sex chromosomes and courtship behaviors, that differ from those of G. aculeatus. Several freshwater populations derived from G. aculeatus (Hariyo threespine stickleback) inhabit spring-fed ponds and streams in central Honshu and exhibit year-round reproduction, which has never been observed in other stickleback populations. Four species of ninespine stickleback, including Pungitius tymensis and the freshwater, brackish water and Omono types of the P. pungitius-P. sinensis complex, are also excellent model systems for speciation research. Anthropogenic alteration of environments, however, has exposed several Japanese stickleback populations to the risk of extinction and has actually led to extinction of several populations and species. Pungitius kaibarae, which is endemic to East Asia, used to inhabit Kyoto and Hyogo prefectures, but is now extinct. Causes of extinction include depletion of spring water, landfill of habitats, and construction of river-mouth weirs. Here, we review the importance of Japanese sticklebacks as genetic resources, the status of several endangered stickleback populations and species, and the factors putting these populations at risk.
著者
Satoshi Ishishita Yoichi Matsuda
出版者
日本遺伝学会
雑誌
Genes & Genetic Systems (ISSN:13417568)
巻号頁・発行日
pp.16-00022, (Released:2016-09-15)
被引用文献数
1

Hybrid incompatibility is important in speciation as it prevents gene flow between closely related populations. Reduced fitness from hybrid incompatibility may also reinforce prezygotic reproductive isolation between sympatric populations. However, the genetic and developmental basis of hybrid incompatibility in higher vertebrates remains poorly understood. Mammals and birds, both amniotes, have similar developmental processes, but marked differences in development such as the XY/ZW sex determination systems and the presence or absence of genomic imprinting. Here, we review the sterile phenotype of hybrids between the Phodopus dwarf hamsters P. campbelli and P. sungorus, and the inviable phenotype of hybrids between two birds of the family Phasianidae, chicken (Gallus gallus domesticus) and Japanese quail (Coturnix japonica). We propose hypotheses for developmental defects that are associated with these hybrid incompatibilities. In addition, we discuss the genetic and developmental basis for these defects in conjunction with recent findings from mouse and avian models of genetics, reproductive biology and genomics. We suggest that these hybrids are ideal animal models for studying the genetic and developmental basis of hybrid incompatibility in amniotes.
著者
Xin Liu Hua Wang Guang Li Hui-Zhe Huang Yi-Quan Wang
出版者
日本遺伝学会
雑誌
Genes & Genetic Systems (ISSN:13417568)
巻号頁・発行日
vol.88, no.4, pp.261-269, 2013 (Released:2014-01-25)
参考文献数
25
被引用文献数
2 4

Vertebrate Pax1 gene is a member of Pax gene family and encodes a transcription factor associated with crucial roles in the development of pharyngeal pouch, scletrotome and limb bud. In zebrafish, the genome contains two Pax1 paralogs, DrPax1a and DrPax1b, which share high sequence similarity with other Pax1 genes. To elucidate the function of zebrafish DrPax1b gene, we first examined the gene expression pattern and found that it was mainly expressed in the endodermal pharyngeal pouch, caudal somites, notochord, and fin bud. Then, we performed knockdown experiments using antisense morpholino oligonucleotides, which lead to the defects in the vertebral column, tail, pharyngeal skeleton, and pectoral fin. Additionally, we also found that the mouse MmPax1 mRNA, but not the amphioxus AmphiPax1/9 mRNA, could rescue the MO-induced defects. Furthermore, sequence alignment revealed that the N-terminal region of vertebrate Pax1 and amphioxus Pax1/9 were highly conserved, whereas their C-terminal regions were relatively divergent. However, the chimeric Am(N)Dr(C)Pax1, Mm(N)Dr(C)Pax1 and Dr(N)Mm(C)Pax1 mRNA could partially rescue the defects, while the Dr(N)Am(C)Pax1 mRNA could not. In conclusion, our data demonstrate a conserved function of DrPax1b in the development of the vertebral column, pectoral fin and pharyngeal skeleton formation in zebrafish and also provide critical insight into the functional evolution of Pax1 gene by changing its C-terminal sequence.
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

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

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 26

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.