Biology subjects

Kitada, S.

Publications and source records attributed to Kitada, S..

11 recordsLinked to original sources

bioRxiv2026

Evaluating the impact of a sample-matched reference genome on single-cell transcriptomic inferences in Plasmodium falciparum

BackgroundPlasmodium falciparum field isolates exhibit genomic variation, including copy number variation and sequence divergence. In contrast, the P. falciparum 3D7 reference genome (Pf3D7) was derived from a long-term laboratory-adapted strain and does not fully reflect the genomic variation among field isolates. The extent to which the reference genome influences RNA-seq mapping and expression inference in natural infections remains unclear. ResultsWe generated both a reference genome and single cell RNA sequencing (scRNAseq) data from a P. falciparum-infected carrier in Mali. This new ML52 assembly was annotated using Companion with Pf3D7 as the reference. scRNAseq reads from the natural infection isolate were aligned to both the Pf3D7 genome and the isolate-specific ML52 genome, followed by locus-level alignment inspection. For most conserved genes, expression inference was concordant for both references, while genes showing reference-genome-dependent differences were investigated further. Some discrepancies were attributed to mapping artefacts or to reads aligning to unplaced genomic contigs that reflected divergent haplotypes from the co-infecting strains in the naturally infected carrier. While most multigene family loci showed concordant gene expression across both references, var genes exhibited considerable mis-mapping against 3D7 var loci as well as 2/3 of var reads not mapping at all to 3D7. ConclusionscRNAseq expression inference in P. falciparum is robust for conserved genes and most multigene families when comparing to a matched vs unmatched reference genome, but the extremely polymorphic var genes require a matched assembly in order to evaluate expression. These findings highlight the importance of the reference genome for var gene studies and should be considered when interpreting transcriptomic analyses in other organisms possessing highly variable antigenic loci.

bioinformatics↗

bioRxiv2026

Climate-driven fitness decline in Japanese chum salmon reshapes North Pacific chum salmon biogeography

Japanese chum salmon supported by one of the worlds largest hatchery programs have experienced severe declines in marine survival and egg size. To investigate the underlying mechanisms, we analyzed a 21-year time series (1999-2019) of reproductive traits of age-4 chum salmon from 13 rivers together with climate and salmon abundance data using a bootstrap-supported Bayesian network. Here, we assumed that environmental variables can affect the chum salmon populations, but not vice versa, and that there could be maternal effect on reproductive traits, but not the other way around. These constraints enabled us to infer the causal links that shaped the biogeography of North Pacific chum salmon. Global warming caused a decline in Japanese chum salmon abundance, resulting in the increase of the competing Russian chum, which in turn decreased the female body size, fecundity, and egg size of Japanese chum. These findings suggest that climate-driven warming may have exposed genetic effects of hatchery practices, contributing to fitness decline in Japanese chum salmon and the ecological reorganization of chum salmon populations in the North Pacific.

evolutionary biology↗

bioRxiv2026

Body size and egg size trends in Japanese hatchery chum salmon: Links to declines in marine survival and abundance

Variation in life-history traits contributes to fitness and population productivity in salmonids. To investigate long-term changes in egg size and body size of Japanese hatchery chum salmon and their links to declines in return rate and abundance, I analyzed egg size and female fork length (FL) of approximately 21,000 age-4 and age-5 fish from 13 hatchery-enhanced rivers in Japan during 1999-2019. River-specific generalized additive models (GAMs) identified synchronous declines in egg size across most rivers. Hierarchical GAMs adjusting for female FL, age, and river effects revealed a nationwide decline in egg size, whereas adjusted FL showed pronounced interannual variation without a long-term decline. Mean age at return also declined after approximately 2010 because of shifts in age composition. Standardized exponential decay rates were remarkably similar for egg size, return rate, and chum salmon abundance, suggesting common underlying environmental and evolutionary processes. These findings suggest that long-term declines in maternal investment may have contributed to declining return rates and abundance, underscoring the importance of life-history traits in evaluating the long-term consequences of hatchery enhancement programs.

evolutionary biology↗

bioRxiv2025

Generating long deletions across the genome with pooled paired prime editing screens

Engineered deletions are a powerful probe for studying genome architecture, function, and regulation. Yet, the lack of effective methods to create them in large numbers and at multi-kilobase scale has rendered interrogating all the gigabases of human DNA elusive. Prime editing based approaches are promising contenders to fill this gap, but have not been adopted for large-scale pooled screening so far. Here, we performed the first high-throughput paired prime editing deletion screens. To establish the technology, we generated 3,802 deletions of up to 1.2 Mb in a reporter locus in two human cell lines, and identified key determinants of paired prime editing efficiency to be deletion length, predicted pegRNA efficacy, and contact frequency. We used these learnings to generate therapeutically important deletions at rates that are expected to give clinical benefits for retinitis pigmentosa and Duchenne muscular dystrophy. Combining several technological advances, we then performed the first pooled paired prime editing screen to delete over 10,471 sequences of median length 1.1 kb that target 149 genes across the genome. Our screens were high quality, recovering 75% of positive controls. We discovered 462 non-coding regions with fitness effects, and validated deletions with impact as well as tolerated ones in regions with functional annotations. Our screens are the largest pooled characterization of precise deletions to date, demonstrating that prime deletion screens can perturb the genome at scale, and highlighting that most non-coding DNA around essential genes is dispensable for cell growth in one condition.

genomics↗

bioRxiv2023

Effects of climate, release practices, predation, and competition on declining hatchery-enhanced chum salmon

We investigated variations in the marine survival of Japanese hatchery chum salmon (Oncorhynchus keta) during 25 years of climate change (1998-2023). Japan is the worlds largest producer of hatchery salmon, and is located near the global southern distribution limit of chum salmon. Our goal was to identify local and context-specific metrics related to the observed coastwide decline in salmon marine survival over the past two decades. We hypothesized multiple metrics in three categories of stressors: hatchery carryovers, ocean conditions, and predators and competitors. The hatchery carryovers are stressors related to hatchery rearing that affect survival at a different life stage. We collected, processed, and collated large publicly available datasets into a comprehensive open-access database encompassing the life cycle of Japanese chum salmon, from eggs to adult spawners. Multivariate regression models showed associations between stressors and adult salmon return rate (marine survival) varied by coastal management region, salmon life stage, and seasonal high-seas distribution area. In the early marine life history stage, parental egg size and fry size-at-release had the largest positive model effects on marine survival. The sea surface temperature (SST) at time of fry release and a predator of fry had significant negative effects. In the offshore and high-seas life stages, summer SST had negative effects, while winter SST had positive effects. Russian chum and/or pink salmon abundance had negative effects, while no effect was found for North American pink and chum salmon abundance. Generalized additive models (GAMs) identified a nationwide decline in egg size and fry size-at-release. Our study highlights the need for an experimental approach to hatchery practices, including monitoring and analyses with updated information, leading to effective management decisions and policies for future sustainability and conservation of salmon resources.

evolutionary biology↗

bioRxiv2021

The effects of long-term translocation on population genetic structure of Ayu in Japan: Management implications for a recreationally fished iconic species

Ayu (Plecoglossus altivelis altivelis) is an important freshwater fisheries resource and popular recreational fishing species in Japan, lives for only one year, and has a single breeding season. To supplement increased recreational fishing demand for this species, huge numbers of wild-born landlocked juveniles have been translocated from Lake Biwa into most Japanese rivers for more than 100 generations. Hatchery-reared juveniles born from captive-reared parents for more than 30 generations have also been extensively released. Previous studies have reported that landlocked and amphidromous forms of Ayu easily hybridise, but survival of landlocked larvae could be very low in seawater, leading to a general consensus among scientists, hatchery managers, and commercial and recreational fishers that the reproductive success of landlocked Ayu is very low, or even 0 in translocated rivers. Despite this, limited information exists regarding the reproductive success of landlocked Ayu in translocated rivers, and no study has evaluated the effects of translocation on population structure. Demonstrating that hybridisation occurs between the two forms is central to future management and conservation of this specie. To address this issue, a comprehensive literature search was undertaken, and three published genetic data sets are analysed. Analyses provide strong evidence for very high gene flow between populations, but population structure has been retained in several regions, and several populations are nested. Allele frequencies are similar in amphidromous and landlocked forms. Genetic diversity is homogeneous in amphidromous populations. Bayesian admixture analysis infers widespread introgression in Japanese rivers, with a mean introgression proportion of 24 {+/-} 8%. Maximum likelihood admixture graphs detect two migration events from Lake Biwa to anadromous populations. Analyses consistently indicate that hybridisation between translocated landlocked juveniles and native amphidromous Ayu occurs throughout Japanese rivers.

evolutionary biology↗

bioRxiv2021

Genome-wide association study reveals putative bacterial risk factors for cavitary Mycobacterium avium complex lung disease

Mycobacterium avium complex (MAC) lung disease is a slowly progressive disease, and its increasing incidence has garnered increased research interests. Cavitary MAC lung disease is associated with a higher mortality rate. Though genetic studies have unraveled the human risk factors, the role of microbial factors on pathogenesis behind the disease remains elusive. In this study, M. avium isolates were collected from sputum specimens of 109 distinct Japanese patients with or without a cavity (60 with a cavity and 49 without cavity) in a hospital located in Osaka prefecture. M. avium genomes were sequenced and searched for DNA motifs associated with cavity formation using a bacterial GWAS. Excluding known macrolide resistance mutations; cavity formation was found to be primarily associated with variants of cytochrome P450 of the CYP139 family, type I polyketide synthase Pks13, and the promoter region of an operon encoding membrane-anchored protease FtsH and folate synthesis pathway enzymes. Cavity risk variants at these three loci were frequent in the MahEastAsia2 lineage among the six lineages detected in M. avium global populations. Furthermore, the study demonstrated a correlation between the cavity risk promoter variant and increased sulfamethoxazole/trimethoprim resistance. Together, these findings suggest that natural variation in the biosynthesis and maintenance processes of M. avium membrane components influences the disease type of MAC lung disease. Although further validation is needed, the bacterial genetic markers listed in the present study could contribute to prognosis prediction based on bacterial genotyping and help develop treatment strategies in the future. IMPORTANCENontuberculous mycobacterial lung disease is of great concern in countries with an increasingly aging population. The disease types can largely be classified into non-cavitary nodular bronchiectasis and cavitary diseases (fibrocavitary, nodular bronchiectasis with cavity) that require different treatment strategies depending on the causal agents. Several studies have reported human risk factors for the disease; however, little efforts were made to investigate the risk factors in nontuberculous mycobacteria. Moreover, molecular genetics experiments have been difficult to search for virulence factors in M. avium, which the population genomics approaches could overcome. Here, the GWAS results suggested variants in three chromosomal loci associated with mycobacterial membrane components as risk factors for cavitary MAC lung disease. These findings could help develop treatment strategies for MAC lung disease in the future.

microbiology↗

bioRxiv2020

Population-specific FST and Pairwise FST: History and Environmental Pressure

Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a populations history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to seashores with abundant rainfall, and to the south with dry summers. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable process times and are useful in population genomics studies. The R codes for our method and simulations are available in the Supplemental Material.

evolutionary biology↗

bioRxiv2019

Fitness decline in hatchery-enhanced salmon populations is manifested by global warming

Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single nucleotide polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region and NADH-3 combined) from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the highest level of genetic drift towards Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The highest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was highest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. By regressing the SNP population structures on those of the microsatellites, we estimated the selection on the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites according to geographical information and performed regression analyses of SNP allele frequencies on the two coordinates of multi-dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise FST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis found a differentiation of Japanese/Korean populations. The top five outlier SNPs were mtDNA3 (combined locus of the control region and NADH-3), U502241 (unknown), GnRH373, ras1362, and TCP178, which were consistently identified by principal component analysis. We summarized the functions of the 53 nuclear SNPs and mtDNA3 locus by referring to a gene database system and discussed the functions of the outlier SNPs and fitness of chum salmon.

evolutionary biology↗

bioRxiv2019

Consequences of hatchery stocking: Lessons from Japan

More than 26 billion juveniles of 180 marine species are released annually into the wild in over 20 countries, but the usefulness of this strategy remains unclear. Here, I analyse the effects of stocking by Japanese marine and salmon stock-enhancement programmes and evaluate their efficacy through a Bayesian meta-analysis of new and previously considered cases. The posterior mean recapture rate ({+/-} SD) was 8.3 {+/-} 4.7%. Without considering personnel costs and negative impacts on wild populations, the mean economic efficiency was 2.8 {+/-} 6.1, with many cases having values of 1 to 2. On the macro-scale, the proportion of released seeds to total catch was 76 {+/-} 20% for Japanese scallop, 28 {+/-} 10% for abalone, 20 {+/-} 5% for swimming crab, 13 {+/-} 5% for kuruma prawn, 11 {+/-} 4% for Japanese flounder, and 7 {+/-} 2% for red sea bream; according to these percentages, stocking effects were generally small, and population dynamics were unaffected by releases but dependent on the carrying capacity of the nursery habitat. All cases of Japanese releases, except for Japanese scallop, were probably economically unprofitable. Captive breeding reduces the fitness of hatchery fish in the wild. In addition, long-term releases replace wild genes and may cause fitness decline in the recipient population when the proportion of hatchery fish is very high. Short-term hatchery stocking can be useful, particularly for conservation purposes, but large-scale programmes may harm the sustainability of populations. Nursery habitat recovery and fishing pressure reduction often outperform hatcheries in the long run.

ecology↗

bioRxiv2018

Comprehensive understanding of population structure and adaptation through graphical representation of gene-environment-trait associations

During the history of range expansion, the populations encounter with variety of environments. They respond to the local environments by modifying the mutually interacting traits. Therefore, to understand the whole life history of the populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to infer the coadaptation of the multiple traits. Toward this end, we provide an exploratory analysis based on the features of populations: site frequency spectra of populations, population-specific FST, association between genes and environments, positive selections on traits mapped on the admixture graph, and GWAS results. Correspondence analysis of genes, environments, and traits provides a birds-eye view of the history of population differentiation and range expansion and various types of environmental selections at the times. Principal component analysis of the estimated trait-specific polygenic adaptations mapped on the admixture graph enables to understand the coadaptation of multiple traits. The potential usefulness was confirmed by analyzing a public dataset of wild poplar in northwestern America. In response to the northern cold temperature and longer daylength, the populations increased the photosynthetic activity and nutrient use efficiency at the expense of the risk of pathogen invasion, and in response to warm temperature, they increased the growth. At higher altitude, they shifted the maximum activity to earlier period in spring to reduce the activity in dry summer. The R codes for our representation method and simulations of population colonization used in this study are available as supplementary script.

bioinformatics↗