研究者詳細 - 永野　惇

論文 - 永野　惇

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Simplification of circadian rhythm measurement using species-independent time-indicated genes

Tanigaki Y., Higashi T., Takayama K., Nagano A., Honjo M., Tezuka A., Kamitani M., Fukuda H.

Current Plant Biology （Current Plant Biology） 19 2019年09月

The circadian rhythm varies among species, and the distribution of common circadian rhythm-related genes in plants is not yet clearly understood. In this study, we analyzed the transcriptome data from plants of three different species (Solanum lycopersicum, Arabidopsis thaliana, and Lactuca sativa) and their circadian rhythms. Homology of the gene sequences was analyzed. Thirty genes containing time information were found to be common among the three species studied and were used to measure the circadian rhythm. Because 22 of these 30 genes were associated with photosynthesis, we suggest that light control could be used to regulate the circadian rhythm. Currently, a high-cost transcriptome analysis is required for the measurement of circadian rhythm; however, our results showed that it was possible to reduce the number of target genes to 30 and, hence, to reduce the cost of the analysis. Our findings will enable easier estimation of circadian time, which, in turn, will facilitate environmental control for plant growth through better control of circadian time, thus facilitating better crop management practice.

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Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding

Yamashita H., Katai H., Kawaguchi L., Nagano A.J., Nakamura Y., Morita A., Ikka T.

PLoS ONE （PLoS ONE） 14 （ 8 ） 2019年08月

To obtain genetic information about the germplasm of tea (Camellia sinensis L.) in Japan, 167 accessions including 138 var. sinensis (96 Japanese var. sinensis and 42 exotic var. sinensis) and 29 Assam hybrids were analyzed using single nucleotide polymorphisms (SNPs) markers identified by double-digest restriction-site-associated DNA sequencing (ddRAD-seq) analysis. Approximately 10,000 SNPs were identified by ddRAD-seq and were mapped across the whole genome. The 167 tea accessions were classified into three genetic subgroups: (1) Japanese var. sinensis; (2) Japanese and exotic var. sinensis; (3) Assam hybrids and exotic var. sinensis. Leaf morphology varied widely within each genetic subgroups. The 96 Japanese var. sinensis were classified into four genetic subgroups as follows; two subgroups of Shizuoka (the largest tea production region) landraces, Uji (most ancient tea production region) landraces, and the pedigree of ‘Yabukita’, the leading green tea cultivar in Japan. These results indicated that the SNP markers obtained from ddRAD-seq are a useful tool to investigate the geographical background and breeding history of Japanese tea. This genetic information revealed the ancestral admixture situation of the ‘Yabukita’ pedigree, and showed that the genome structure of ‘Yabukita’ is clearly different from those of other Japanese accessions.

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A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq

Kamitani M., Nagano A.J., Honjo M.N., Kudoh H.

Microbial Ecology （Microbial Ecology） 78 （ 1 ） 113 - 121 2019年07月

ISSN 00953628

Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses.

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Frequent chloroplast capture among Isodon (Lamiaceae) species in Japan revealed by phylogenies based on variation in chloroplast and nuclear DNA

Ogishima M., Horie S., Kimura T., Yamashiro T., Dohzono I., Kawaguchi L., Nagano A.J., Maki M.

Plant Species Biology （Plant Species Biology） 34 （ 3 ） 127 - 137 2019年07月

ISSN 0913557X

A recent phylogenetic study based only on chloroplast DNA (cpDNA) variation revealed that populations of an Isodon species are frequently embedded paraphyletically among other Isodon species. This phylogenetic discrepancy between species taxonomy and molecular phylogeny was considered to have resulted from chloroplast DNA captures and/or incomplete lineage sorting. To elucidate which of these factors was mainly responsible for the observed phylogenetic pattern, we performed phylogenetic analyses of multiple populations of Isodon species in Japan using cpDNA variation, three single-copy nuclear genes, and double-digest restriction-site-associated DNA sequencing (ddRAD-seq). Although a species often shared chlorotypes with other species, our phylogenetical analyses based on variation in the three single-copy nuclear genes and the ddRAD-seq data showed that most populations belonging to the same species were monophyletic at the species level, suggesting that chloroplast capture may have frequently occurred between Isodon species. Some populations of an intraspecific taxon were embedded paraphyletically within the species, regardless of the large amount of phylogenetic information in nuclear DNA; this incongruity may have resulted from incomplete lineage sorting.

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Construction of a high-density linkage map for bronze loquat using RAD-Seq

Fukuda S., Nagano Y., Matsuguma K., Ishimoto K., Hiehata N., Nagano A., Tezuka A., Yamamoto T.

Scientia Horticulturae （Scientia Horticulturae） 251 59 - 64 2019年06月

ISSN 03044238

We constructed a high-density genetic linkage map of bronze loquat (Eriobotrya deflexa) for a three-way cross of loquat (Eriobotrya japonica) × (loquat × bronze loquat) by using single nucleotide polymorphism (SNP) markers generated by RAD-Seq, with the combination of simple sequence repeat (SSR) markers, which have been used in the previous study. The map of bronze loquat (‘Taiwan loquat No. 1’) consisted of 960 loci including 793 SNPs, 166 SSRs (98 apple, 8 loquat and 60 pear SSRs), and the loquat canker resistance gene Pse-a. This map covered 17 linkage groups over a total length of 1707.4 cM with an average distance of 1.78 cM between markers. The number of linkage groups corresponded to the basic chromosome number (n = 17). The analysis of the markers that can be anchored to apple draft genome showed that almost all loquat linkage groups were aligned to the apple draft genome. The constructed map will enable us to determine the location of quantitative trait loci and genes of interest, and to analyze genome synteny in the tribe Pyreae, subfamily Spiraeoideae of the family Rosaceae.

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A key metabolic gene for recurrent freshwater colonization and radiation in fishes

Ishikawa A., Kabeya N., Ikeya K., Kakioka R., Cech J.N., Osada N., Leal M.C., Inoue J., Kume M., Toyoda A., Tezuka A., Nagano A.J., Yamasaki Y.Y., Suzuki Y., Kokita T., Takahashi H., Lucek K., Marques D., Takehana Y., Naruse K., Mori S., Monroig O., Ladd N., Schubert C.J., Matthews B., Peichel C.L., Seehausen O., Yoshizaki G., Kitano J.

Science （Science） 364 （ 6443 ） 886 - 889 2019年05月

ISSN 00368075

Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential w-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.

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Genetic properties responsible for the transgressive segregation of days to heading in rice

Koide Y., Sakaguchi S., Uchiyama T., Ota Y., Tezuka A., Nagano A., Ishiguro S., Takamure I., Kishima Y.

G3: Genes, Genomes, Genetics （G3: Genes, Genomes, Genetics） 9 （ 5 ） 1655 - 1662 2019年05月

Transgressive segregation produces hybrid progeny phenotypes that exceed the parental phenotypes. Unlike heterosis, extreme phenotypes caused by transgressive segregation are heritably stable. We examined transgressive phenotypes of flowering time in rice, and revealed transgressive segregation in F2 populations derived from a cross between parents with similar (proximal) days to heading (DTH). The DTH phenotypes of the A58 · Kitaake F2 progenies were frequently more extreme than those of either parent. These transgressive phenotypes were maintained in the F3 and F4 populations. Both A58 and Kitaake are japonica rice cultivars adapted to Hokkaido, Japan, which is a high-latitude region, and have a short DTH. Among the four known loci required for a short DTH, three loci had common alleles in A58 and Kitaake, implying there is a similar genetic basis for DTH between the two varieties. A genome-wide single nucleotide polymorphism (SNP) analysis based on the F4 population identified five new quantitative trait loci (QTL) associated with transgressive DTH phenotypes. Each of these QTL had different degrees of additive effects on DTH, and two QTL had an epistatic effect on each other. Thus, a genome-wide SNP analysis facilitated the detection of genetic loci associated with extreme DTH phenotypes, and revealed that the transgressive phenotypes were produced by exchanging the complementary alleles of a few minor QTL in the similar parental phenotypes.

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Genomic reconstruction of 100 000-year grassland history in a forested country: Population dynamics of specialist forbs

Yamaura Y., Narita A., Kusumoto Y., Nagano A.J., Tezuka A., Okamoto T., Takahara H., Nakamura F., Isagi Y., Lindenmayer D.

Biology Letters （Biology Letters） 15 （ 5 ） 2019年05月

ISSN 17449561

Grassland ecosystems worldwide have been extensively converted to other land uses and are globally imperiled. Because many grasslands have been maintained by human activities, understanding their origin and history is fundamentally important to better contemporary management. However, existing methods to reconstruct past vegetation can produce contrasting views on grassland history. Here, we inferred demographic histories of 40 populations of four grassland forb species throughout Japan using high-resolution genome sequences and model-flexible demographic simulation based on the site frequency spectrum. Although two species showed a slight decline in population size between 100 000 - 10 000 years ago, our results suggest that population sizes of studied species have been maintained within the range of 0.5 - 2.0 times the most recent estimates for at least 100 000 years across Japan. Our results suggest that greater than 90% declines in Japanese grasslands and subsequent losses of grassland species in the last 100 years are geologically and biologically important and will have substantial consequences for Japanese biota and culture. People have had critical roles in maintaining disturbance-dependent grassland ecosystems and biota in this warm and wet forested country. In these contexts, disturbances associated with forest harvesting and traditional extensive farming have the potential to maintain grassland ecosystems and can provide important opportunities to reconcile resource production and conservation of grassland biodiversity.

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Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana

Sato Y., Shimizu-Inatsugi R., Yamazaki M., Shimizu K.K., Nagano A.J.

BMC Plant Biology （BMC Plant Biology） 19 （ 1 ） 2019年04月

Background: Genetic variation in plants alters insect abundance and community structure in the field; however, little is known about the importance of a single gene among diverse plant genotypes. In this context, Arabidopsis trichomes provide an excellent system to discern the roles of natural variation and a key gene, GLABRA1, in shaping insect communities. In this study, we transplanted two independent glabrous mutants (gl1-1 and gl1-2) and 17 natural accessions of Arabidopsis thaliana to two localities in Switzerland and Japan. Results: Fifteen insect species inhabited the plant accessions, with the insect community composition significantly attributed to variations among plant accessions. The total abundance of leaf-chewing herbivores was negatively correlated with trichome density at both field sites, while glucosinolates had variable effects on leaf chewers between the sites. Interestingly, there was a parallel tendency for the abundance of leaf chewers to be higher on gl1-1 and gl1-2 than on their different parental accessions, Ler-1 and Col-0, respectively. Furthermore, the loss of function in the GLABRA1 gene significantly decreased the resistance of plants to the two predominant chewers; flea beetles and turnip sawflies. Conclusions: Overall, our results indicate that insect community composition significantly varies among A. thaliana accessions across two distant field sites, with GLABRA1 playing a key role in altering the abundance of leaf-chewing herbivores. Given that such a trichome variation is widely observed in Brassicaceae plants, the present study exemplifies the community-wide effect of a single plant gene on crucifer-feeding insects in the field.

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Quantitative trait loci mapping for the shear force value in breast muscle of F<inf>2</inf> chickens

Ono T., Kouguchi T., Ishikawa A., Nagano A.J., Takenouchi A., Igawa T., Tsudzuki M.

Poultry Science （Poultry Science） 98 （ 3 ） 1096 - 1101 2019年03月

ISSN 00325791

The shear force value is one of the major traits that determine meat quality. In the present study, we performed QTL analysis for chicken breast muscle shear force value at 7 wk of age using 545 single nucleotide polymorphism (SNP) markers developed via restriction-site associated DNA sequencing (RAD-seq). An F2 resource family was generated by mating Oh-Shamo, a native Japanese chicken breed, and the White Plymouth Rock chicken breed. A total of 215 F2 birds were produced. Simple interval mapping revealed one significant main-effect QTL between 6.28 and 8.10 Mb SNPs on the chromosome Z with a logarithm of odds score of 5.53 at the genome-wide 5% level. At this QTL, the confidence interval, phenotypic variance explained, and additive effect were 26 cM, 12.24%, and -0.31 in males and -0.34 in females, respectively. No QTL with epistatic interaction effects were detected. To our knowledge, this is the first report on a QTL affecting the shear force value in the chicken breast muscle, using SNP markers derived from RAD-seq.

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Classification of tea (Camellia sinensis) landraces and cultivars in Kyoto, Japan and other regions, based on simple sequence repeat markers and restriction site-associated DNA sequencing analysis

Kubo N., Mimura Y., Matsuda T., Nagano A.J., Hirai N., Higashimoto S., Yoshida H., Uemura N., Fujii T.

Genetic Resources and Crop Evolution （Genetic Resources and Crop Evolution） 66 （ 2 ） 441 - 451 2019年02月

ISSN 09259864

The tea plant (Camellia sinensis (L.) Kuntze) of Japan is now thought to have originated in China. Actual cultivation of tea plants presumably started in Kyoto, and then spread to other regions of Japan. Tea gardens used to be composed of heterogenic, seed-derived populations—landraces—selected for climatic preferences and cultivation methods. Cultivars were bred from landraces in the modern era. A number of landraces remain in Kyoto Prefecture. However, little is known about their genetic characteristics compared with other landraces. We investigated the relationships of tea landraces and cultivars from Kyoto Prefecture and other regions. A neighbor-joining phylogram was constructed from 113 lines including 68 landraces, 44 cultivars, and one wild relative, based on simple sequence repeat markers. The lines could be classified into four groups (I–IV). In group I, most of the Kyoto landraces were close to other Japanese landraces, supporting the idea of the spread of tea plants from Kyoto to other regions in the country. The remaining lines were included into groups III and IV, apart from group II, which contained Shizuoka lines. Similar results were observed by restriction site-associated DNA sequencing analysis using 44 cultivars. Our data provide valuable information for the classification of tea lines, especially for the relationships of Kyoto lines among Japanese tea varieties.

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Annual transcriptome dynamics in natural environments reveals plant seasonal adaptation

Nagano A.J., Kawagoe T., Sugisaka J., Honjo M.N., Iwayama K., Kudoh H.

Nature Plants （Nature Plants） 5 （ 1 ） 74 - 83 2019年01月

As most organisms have evolved in seasonal environments, their environmental responses should be adapted to seasonal transitions. Here we show that the combination of temperature and day length shapes the seasonal dynamics of the transcriptome and adaptation to seasonal environments in a natural habitat of a perennial plant Arabidopsis halleri subsp. gemmifera. Weekly transcriptomes for two years and bihourly diurnal transcriptomes on the four equinoxes/solstices, identified 2,879 and 7,185 seasonally- and diurnally-oscillating genes, respectively. Dominance of annual temperature changes for defining seasonal oscillations of gene expressions was indicated by controlled environment experiments manipulating the natural 1.5-month lag of temperature behind day length. We found that plants have higher fitness in ‘natural’ chambers than in ‘unnatural’ chambers simulating in-phase and anti-phase oscillations between temperature and day length. Seasonal temperature responses were disturbed in unnatural chambers. Our results demonstrate how plants use multiple types of environmental information to adapt to seasonal environments.

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Mutation in the putative ketoacyl-ACP reductase CaKR1 induces loss of pungency in Capsicum

Koeda S., Sato K., Saito H., Nagano A.J., Yasugi M., Kudoh H., Tanaka Y.

Theoretical and Applied Genetics （Theoretical and Applied Genetics） 132 （ 1 ） 65 - 80 2019年01月

ISSN 00405752

Key message: A putative ketoacyl-ACP reductase (CaKR1) that was not previously known to be associated with pungency of Capsicum was identified from map-based cloning and functional characterization. Abstract: The pungency of chili pepper fruits is due to the presence of capsaicinoids, which are synthesized through the convergence of the phenylpropanoid and branched-chain fatty acid pathways. The extensive, global use of pungent and non-pungent peppers underlines the importance of understanding the genetic mechanism underlying capsaicinoid biosynthesis for breeding pepper cultivars. Although Capsicum is one of the earliest domesticated plant genera, the only reported genetic causes of its loss of pungency are mutations in acyltransferase (Pun1) and putative aminotransferase (pAMT). In this study, a single recessive gene responsible for the non-pungency of pepper No.3341 (C. chinense) was identified on chromosome 10 using an F 2 population derived from a cross between Habanero and No.3341. Five candidate genes were identified in the target region, within a distance of 220 kb. A candidate gene, a putative ketoacyl-ACP reductase (CaKR1), of No.3341 had an insertion of a 4.5-kb transposable element (TE) sequence in the first intron, resulting in the production of a truncated transcript missing the region coding the catalytic domain. Virus-induced gene silencing of CaKR1 in pungent peppers resulted in the decreased accumulation of capsaicinoids, a phenotype consistent with No.3341. Moreover, GC–MS analysis of 8-methyl-6-nonenoic acid, which is predicted to be synthesized during the elongation cycle of branched-chain fatty acid biosynthesis, revealed that its deficiency in No.3341. Genetic, genomic, transcriptional, silencing, and biochemical precursor analyses performed in combination provide a solid ground for the conclusion that CaKR1 is involved in capsaicinoid biosynthesis and that its disruption results in a loss of pungency.

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Genetic analysis of Taishu horses on and off Tsushima Island: Implications for conservation

Tezuka A., Takasu M., Tozaki T., Nagano A.J.

Journal of Equine Science （Journal of Equine Science） 30 （ 2 ） 33 - 40 2019年

ISSN 13403516

Taishu horses are a native Japanese breed, of which only 41 individuals remained on Tsushima Island in 2018. Their genetic diversity is considered lower than that of other Japanese native horse breeds; thus, it needs to be investigated for sustainable conservation of this breed. Historical records revealed that several Taishu individuals were released areas off-Tsushima Island in mid-1980s. At present, Taishu horses living outside of Tsushima Island, hereafter referred to as Non-Tsushima Taishus (NTTs), are tagged. However, the genetic structure of the NTT individuals remains unclear, and such individuals are not included in the current mating plans for Taishu horses. Herein, we examined the genetic structure of 18 NTT individuals by comparing their genomic (SNP) information with that of individuals on Tsushima Island (TT), four other native Japanese breeds, and one Anglo- Arabian breed by using ddRAD-seq. We found that all individuals related to the Taishu can be grouped in one cluster, which was separated from other horse breeds. Patterns of specific and shared SNPs in NTT individuals closely resembled those of TT individuals, suggesting very minor genetic differences. Meanwhile, the heterozygosity of NTT individuals was slightly higher than that of TT individuals, and many NTT individuals were of fertile age, suggesting that the pedigree of NTT individuals would be useful in breed conservation plans for Taishu horses. Based on their genomic information, we also reconstructed the pedigree structures of four NTT individuals with no family information. The inclusion of NTT individuals in future mating plans on Tsushima Island may be an effective and feasible method for conserving the Taishu horse breed in Japan.

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Mapping of quantitative trait loci for growth and carcass-related traits in chickens using a restriction-site associated dna sequencing method

Ono T., Ohara K., Ishikawa A., Kouguchi T., Nagano A.J., Takenouchi A., Igawa T., Tsudzuki M.

Journal of Poultry Science （Journal of Poultry Science） 56 （ 3 ） 166 - 176 2019年

ISSN 13467395

In the present study, quantitative trait loci (QTLs) analysis was performed to identify the chromosomal positions of growth andcarcass-relatedtrait QTLs using 319 F2 chickens obtainedfrom intercrosses of an Oh-Shamo male and four White Plymouth Rock females. Body weight was measured weekly until the birds were 7 weeks old. Carcassrelatedtraits were also measuredat this timepoint. A genetic linkage map was constructedusing 545 single nucleotide polymorphism (SNP) markers that were developedusing a restriction-site associatedDNA sequencing method. The linkage map includedthe 23 autosomes andthe Z chromosome. Using simple interval QTL mapping, we were able to identify 10 significant andsuggestive main-effect QTLs for growth andcarcass-relatedtraits present on chromosomes 1, 2, 3, 5, 8, 19, 24, andZ. These loci explained 5.60 -16.52% of the phenotypic variances. The chromosomal positions of the 10 QTLs overlappedwith those of previously reportedQTLs, whereas the targetedtraits varied. Our QTLs will aidfuture breeding programs in improving growth andmeat yieldof chickens (e.g., via marker-assisted selection), particularly in the Japanese brandchicken industry.

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Transcriptional variation in glucosinolate biosynthetic genes and inducible responses to aphid herbivory on field-grown Arabidopsis thaliana

Sato Y., Tezuka A., Kashima M., Deguchi A., Shimizu-Inatsugi R., Yamazaki M., Shimizu K.K., Nagano A.J.

Frontiers in Genetics （Frontiers in Genetics） 10 （ JUL ） 2019年

Recently, increasing attempts have been made to understand how plant genes function in natura. In this context, transcriptional profiles represent plant physiological status in response to environmental stimuli. Herein, we combined high-throughput RNA-Seq with insect survey data on 19 accessions of Arabidopsis thaliana grown at a field site in Switzerland. We found that genes with the gene ontology (GO) annotations of “glucosinolate biosynthetic process” and “response to insects” were most significantly enriched, and the expression of these was highly variable among plant accessions. Nearly half of the total expression variation in the glucosinolate biosynthetic genes (AOPs, ESM1, ESP, and TGG1) was explained by among-accession variation. Of these genes, the expression level of AOP3 differed among Col-0 accession individuals depending on the abundance of the mustard aphid (Lipaphis erysimi). We also found that the expression of the major cis-jasmone activated gene CYP81D11 was positively correlated with the number of flea beetles (Phyllotreta striolata and Phyllotreta atra). Combined with the field RNA-Seq data, bioassays confirmed that AOP3 was up-regulated in response to attack by mustard aphids. The combined results from RNA-Seq and our ecological survey illustrate the feasibility of using field transcriptomics to detect an inducible defense, providing a first step towards an in natura understanding of biotic interactions involving phenotypic plasticity.

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New taxa of Rhododendron tschonoskii alliance (Ericaceae) from East Asia

Yoichi W., Minamitani T., Oh S.H., Nagano A.J., Abe H., Yukawa T.

PhytoKeys （PhytoKeys） 134 （ 2019 ） 97 - 114 2019年

ISSN 13142011

Three new taxa, Rhododendron sohayakiense Y.Watan. & T.Yukawa (Ericaceae), and its two varieties, var. kiusianum Y.Watan., T.Yukawa & T.Minamitani and var. koreanum Y.Watan. & T.Yukawa are described and illustrated from Japan and South Korea. They can be distinguished from each other and from the other members of the R. tschonoskii alliance, i.e. R. tschonoskii, R. tetramerum, R. trinerve and R. tsusiophyllum, through their combination of leaf size, leaf morphologies including lateral nerves on abaxial leaf surface, corolla morphologies including number of corolla lobes, style length and anther form. Phylogenetic inferences based on chloroplast DNA and genome-wide sequences revealed that each of the three new taxa is monophyletic and they further form a clade. Distributions of the three taxa are also clearly separated from each other and also from the other members of the R. tschonoskii alliance.

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Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data

Awazu A., Tanabe T., Kamitani M., Tezuka A., Nagano A.J.

Scientific Reports （Scientific Reports） 8 （ 1 ） 2018年12月

Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution, although the physiological basis of this assumption remains unclear. In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent empirical probability density function (ePDF) profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, various types of ePDF of gene expression levels were obtained that were classified as Gaussian, power law-like containing a long tail, or intermediate. These ePDF profiles were well fitted with a Gauss-power mixing distribution function derived from a simple model of a stochastic transcriptional network containing a feedback loop. The fitting function suggested that gene expression levels with long-tailed ePDFs would be strongly influenced by feedback regulation. Furthermore, the features of gene expression levels are correlated with their functions, with the levels of essential genes tending to follow a Gaussian-like ePDF while those of genes encoding nucleic acid-binding proteins and transcription factors exhibit long-tailed ePDF.

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ddRAD-seq based phylogeographic study of Sargassum thunbergii (Phaeophyceae, Heterokonta) around Japanese coast

Kobayashi H., Haino Y., Iwasaki T., Tezuka A., Nagano A.J., Shimada S.

Marine Environmental Research （Marine Environmental Research） 140 104 - 113 2018年09月

ISSN 01411136

Using genome-wide SNP data obtained from high-throughput techniques based on double digest restriction site-associated DNA sequencing (ddRAD-seq), we elucidated the migration history and genetic diversity of the Japanese population of the ecologically important brown seaweed Sargassum thunbergii (Mertens ex Roth) Kuntze. STRUCTURE and NeighborNet analyses showed a clear genetic differentiation among populations of four geographic regions: Kyushu (POP1); Sea of Japan (POP2); Hokkaido and Tohoku (POP3); and Pacific coast from Kyushu to Kanto (POP4). Approximate Bayesian Computation (ABC) analysis indicated that POP4 diverged first, followed by the separation between POP2 (the largest effective population size) and POP3; POP1 was the last to form, shaped by the mixture of POP2 (73%) and POP4 (27%). High genetic diversity was detected in POP1 and POP2, whereas low genetic diversity was detected in POP3 and POP4. These results indicated that S. thunbergii populations of Kyushu and the Sea of Japan might have been maintained as large and stable populations gathered different lineages from China, Korea and/or Japan.

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Assessment of genetic diversity in Coho salmon (Oncorhynchus kisutch) populations with no family records using ddRAD-seq

Hosoya S., Kikuchi K., Nagashima H., Onodera J., Sugimoto K., Satoh K., Matsuzaki K., Yasugi M., Nagano A.J., Kumagayi A., Ueda K., Kurokawa T.

BMC Research Notes （BMC Research Notes） 11 （ 1 ） 2018年08月

Objective: Selective breeding for desirable traits is becoming popular in aquaculture. In Miyagi prefecture, Japan, a selectively bred population of Coho salmon (Oncorhynchus kisutch) has been established with the original, randomly breeding population maintained separately. Since they have been bred without family records, the genetic diversity within these populations remains unknown. In this study, we estimated the genetic diversity and key quantitative genetic parameters such as heritability and genomic breeding value for body size traits by means of genomic best linear unbiased prediction to assess the genetic health of these populations. Results: Ninety-nine and 83 females from the selective and random groups, respectively, were genotyped at 2350 putative SNPs by means of double digest restriction associated DNA sequencing. The genetic diversity in the selectively bred group was low, as were the estimated heritability and prediction accuracy for length and weight (h 2 = 0.26-0.28; accuracy = 0.34), compared to the randomly bred group (h 2 = 0.50-0.60; accuracy = 0.51-0.54). Although the tested sample size was small, these results suggest that further selection is difficult for the selectively bred population, while there is some potential for the randomly bred group, especially with the aid of genomic information.

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論文 - 永野　惇