Biology subjects

Tezuka, A.

Publications and source records attributed to Tezuka, A..

9 recordsLinked to original sources

bioRxiv2023

Hybridization and its impact on the ontogenetic allometry of skulls in macaques

The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (M. fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, i.e., the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and non-additive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.

evolutionary biology↗

bioRxiv2021

Fillable and Unfillable Gaps in Rice Transcriptome under Field and Controlled Environments

The differences between plants grown in field and controlled environments have long been recognised; however, few studies have addressed the underlying molecular mechanisms. Here, we show fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments by utilising SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature, and humidity of field environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening; those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature only affects transcriptome dynamics in the morning. We found upregulation of genes related to biotic and abiotic stress, whose expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results accelerate the understanding of plant responses to field environments for both field and laboratory studies.

plant biology↗

bioRxiv2021

Artificial mimicry of seasonal transcriptome dynamics in Arabidopsis thaliana reveals short- and long-term responses to environmental conditions

Plants must respond to various seasonally changing environmental stimuli. In a previous study, seasonally oscillating genes were identified by a massive time-series transcriptome analysis for the wild population of Arabidopsis halleri ssp. gemmifera, a sister species to Arabidopsis thaliana. It was not clear how environmental stimuli shaped the seasonal expression pattern of these seasonally oscillating genes. In this study we show that responses in different time-scales contributed to the formation of seasonal expression patterns for several genes. To analyze the seasonally oscillating genes, we established an experimental system to mimic seasonal expression trends using A. thaliana and a "smart growth chamber mini," a hand-made low-cost small chamber. Arabidopsis thaliana plants were cultured under conditions that mimicked the average monthly temperatures and daylengths under different day-scale incubation. In total, the seasonal trends of 1627 seasonally oscillating genes were mimicked, and they showed varying temporal responses (constant, transient, and incremental) to environmental stimuli. Our results suggest that plants perceive and integrate information regarding environmental stimuli in the field by combining seasonally oscillating genes with different temporal responsiveness.

plant biology↗

bioRxiv2019

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

Recently, increasing attempts have been made to understand how plant genes function in natura studies. To determine whether plant defense genes are activated under multiple biotic stimuli, we combined a high-throughput RNA-Seq with insect survey data on 19 accessions of Arabidopsis thaliana growing on the field site of Switzerland. We found that genes with GO annotations "glucosinolate biosynthetic process" and "response to insects" were the most significantly enriched, exhibiting largely variable expression among plant accessions. Nearly half of the total expression variation in glucosinolate biosynthetic genes, AOPs, ESM1, ESP, and TGG1, was explained by among-accession variance. Combined with the field RNA-Seq data, bioassays confirmed that AOP3 was up-regulated in response to the mustard aphid Lipaphis erysimi. In addition, we also found that the expression of a major cis-jasmone activated gene CYP81D11 was positively correlated with the number of the flea beetles Phyllotreta spp. The combined results from RNA-Seq and insect surveys suggested that plants can activate their defenses even when they are exposed to multiple biotic stimuli in natura.

plant biology↗

bioRxiv2018

High-throughput RNA-Seq analysis on plant response under fluctuating temperature conditions

RNA-Seq is a whole-transcriptome analysis method used to research biological mechanisms and functions; its use in large-scale experiments is limited by costs and labour. In this study, we established a high-throughput and cost effective RNA-Seq library preparation method that did not require mRNA enrichment. The method adds unique index sequences to samples during reverse transcription (RT) that is conducted at a higher temperature ([≥]62{degrees}C) to suppress RT of A-rich sequences in rRNA, and then pools all samples into a single tube. Both single-read and paired end sequencing of libraries is enabled. We found that the pooled RT products contained large amounts of RNA, mainly rRNA, and caused over-estimations of the quantity of DNA, resulting in unstable tagmentation results. Degradation of RNA before tagmentation was necessary for the stable preparation of libraries. We named this protocol low-cost and easy RNA-Seq (Lasy-Seq), and used it to investigate temperature responses in Arabidopsis thaliana. We analysed how sub-ambient temperatures (10-30{degrees}C) affected the plant transcriptomes, using time-courses of RNA-Seq from plants grown in randomly fluctuating temperature conditions. Our results suggest that there are diverse mechanisms behind plant temperature responses at different time scales.

plant biology↗

bioRxiv2018

The ability of ddRAD-Seq to estimate genetic diversity and genetic introgression in endangered native livestock

Unplanned crossbreeding between a native livestock and a specific productive breed was one of the main reasons that caused the loss of valuable genetic resources in native livestock. To avoid further loss and damage of genetic resources in the native livestock, introgressed individuals should be distinguished to eliminate them by preventing any further employment in future mating plans. In general, the genetic diversity of native livestock had already decreased and mass elimination of introgressed individuals from the population endangers their existence. To solve this problem, high-resolution markers are required to discriminate between introgressed variation and native variation. Here, we applied ddRAD-Seq markers for native Japanese horse \"Taishu\" that has undergone recent genetic introgression. Genome-wide ddRAD-Seq markers can distinguish five breeds of native Japanese horses and Anglo-Arabian introgressed breeds. We found the signatures of genetic introgression of Anglo-Arabian at only two chromosomes; however, the signatures were separated in their genome suggesting that it might not be the cause of recent introgression. The genetic diversity of Taishu was less than other Japanese breeds and the decreasing genetic diversity is an urgent issue compared to genetic introgression. Although few signatures of recent introgression were detected, a lot of shared SNPs (10% of all SNPs in Taishu) were detected between Taishu and Anglo-Arabian. To avoid misestimation of the presence and degree of introgression in native livestock, information regarding shared SNPs and population genetic approaches need to be assessed by using the large number of genome-wide markers such as ddRAD-Seq.

genomics↗

bioRxiv2018

Prediction of environmental response in field-grown rice using expression-dynamics-QTL

How genetic variations affect gene expression dynamics of field-grown plants remains unclear. Using statistical analysis of large-scale time-series RNA-sequencing of field-grown rice from chromosome segment substitution lines (CSSLs), we identified 1675 expression dynamics quantitative trait loci (edQTLs) leading to polymorphisms in expression dynamics under field conditions. Based on the edQTL and environmental information, we successfully predicted gene expression under environments different from training environments, and in rice cultivars with more complex genotypes than the CSSLs. Overall, edQTL identification helped understanding the genetic architecture of expression dynamics under field conditions, which is difficult to assess with laboratory experiments1.The prediction of expression based on edQTL and environmental information will contribute to crop breeding by increasing the accuracy of trait prediction under diverse conditions.

bioinformatics↗

bioRxiv2018

Genetic basis of transgressive segregation in rice heading phenotypes

Transgressive segregation produces hybrid progeny phenotypes that exceed parental phenotypes. Unlike heterosis, extreme phenotypes caused by transgressive segregation are heritably stable. We examined transgressive phenotypes of flowering time in rice. Our previous study examined days to flowering (heading; DTH) in six F2 populations for which the parents had distal DTH, and found very few transgressive phenotypes. Here, we demonstrate that transgressive segregation in F2 populations occurred between parents with proximal DTH. DTH phenotypes of the A58 x Kitaake F2 progenies frequently exceeded those of both parents. Both A58 and Kitaake are japonica rice cultivars adapted to Hokkaido, Japan, which is a high-latitude region, and have short DTH. Among the four known loci required for short DTH, three loci had common alleles in A58 and Kitaake, and only the one locus had different alleles. This result indicates that there is a similar genetic basis for DTH between the two varieties. We identified five new quantitative trait loci (QTLs) associated with transgressive DTH phenotypes by genome-wide single nucleotide polymorphism (SNP) analysis. Each of these QTLs showed different degrees of additive effects on DTH, and two QTLs had epistatic effect on each other. These results demonstrated that genome-wide SNP analysis facilitated detection of genetic loci associated with the extreme phenotypes and revealed that the transgressive phenotypes were produced by exchanging complementary alleles of a few minor QTLs in the similar parental genotypes.

genetics↗

bioRxiv2017

Gauss-power mixing distributions comprehensively describe stochastic variations in RNA-seq data

MotivationGene 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 remain unclear.\n\nResultsIn this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent distribution profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, the distribution profiles could be described by a Gauss-power mixing distribution derived from a simple model of a stochastic transcriptional network containing a feedback loop. The distribution profiles of gene expression levels were roughly classified as Gaussian, power law-like containing a long tail, and mixed. The fitting function predicted that gene expression levels with long-tailed distributions would be strongly influenced by feedback regulation. Thus, the features of gene expression levels are correlated with their functions, with the levels of essential genes tending to follow a Gaussian distribution and those of genes encoding nucleic acid-binding proteins and transcription factors exhibiting long-tailed distributions.\n\nAvailabilityFastq files of RNA-seq experiments were deposited into the DNA Data Bank of Japan Sequence Read Archive as accession no. DRA005887. Quantified expression data are available in supplementary information.\n\nContactawa@hiroshima-u.ac.jp\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗