Biology subjects

Hirabayashi, K.

Publications and source records attributed to Hirabayashi, K..

8 recordsLinked to original sources

bioRxiv2025

A haplotype-phased male genome sequence of the stinging nettle, Urtica dioica ssp. dioica

Stinging nettle (Urtica dioica L.) is a widespread weed of economic significance with a dioecious mating system. Previously, we generated a high-quality genome assembly of a diploid female plant, which showed extreme levels of structural variation between haplotypes. Here, we present a chromosome-level, haplotype-resolved sequence of a diploid male plant; since the male is believed to be the heterogametic sex in Urtica dioica, this assembly represents a first step towards elucidating the control of sex determination in this species. This completely independently assembled genome also allows confirmation of previously reported features of the nettle genome, including (1) a high degree of structural variation between haplotypes, including large inversions, (2) the likely existence of polycentric centromeres, and (3) the presence of urticaceous "pain peptide" sequences. Chromosome 8 stands out for its multiple large, nested inversions and high levels of repetitive sequences, features that are often associated with sex determining regions (SDRs). This chromosome is therefore a candidate for further investigations to characterize the sex determination in nettle.

genomics↗

bioRxiv2024

A high-quality phased genome assembly of stinging nettle, Urtica dioica ssp. dioica

Stinging nettles (Urtica dioica) have a long history of association with human civilization, having been used as a source of textile fibres, food and medicine. Here, we present a chromosome-level, phased genome assembly for a diploid female clone of Urtica dioica from Romania. Using a combination of PacBio HiFi, Oxford Nanopore and Illumina sequencing, and Hi-C long-range interaction data (using a novel Hi-C protocol presented here), we assembled two haplotypes of 574.9 Mbp (contig N50 = 10.9 Mbp, scaffold N50 = 44.0 Mbp) and 521.2 Mbp (contig N50 = 13.5 Mbp, scaffold N50 = 48.0 Mbp), with assembly BUSCO scores of 92.6% and 92.3%. We annotated 20,333 and 20,140 genes for each haplotype, covering over 90% of the complete BUSCO genes and including two copies of a gene putatively encoding the neurotoxic peptide urthionin, which could contribute to nettles characteristic sting. Despite its relatively small size, the nettle genome displays very high levels of repetitiveness, with transposable elements comprising more than 60% of the genome, as well as considerable structural variation. This genome assembly represents an important resource for the nettle community and will enable the investigation of the genetic basis of the many interesting characteristics of this species.

plant biology↗

bioRxiv2024

Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

Kelp forests are declining in many parts of the northeast Pacific1-4. In small populations, genetic drift can reduce adaptive variation and increase fixation of recessive deleterious alleles5-7, but natural selection may purge harmful variants8-10. To understand evolutionary dynamics and inform restoration strategies, we investigated genetic structure and the outcomes of genetic drift and purging by sequencing the genomes of 429 bull kelp (Nereocystis luetkeana) and 211 giant kelp (Macrocystis pyrifera sensu lato11; cf. 12) from the coastlines of British Columbia and Washington. We identified 6-7 geographically and genetically distinct clusters in each species. Low effective population size was associated with low genetic diversity and high inbreeding coefficients (including increased selfing rates), with extreme variation in these genetic health indices among bull kelp populations but more moderate variation in giant kelp. We found no evidence that natural selection is purging putative recessive deleterious alleles in either species. Instead, genetic drift has fixed many such alleles in small populations of bull kelp, leading us to predict (1) reduced within-population inbreeding depression in small populations, which may be associated with an observed shift toward increased selfing rate, and (2) hybrid vigour in crosses between small populations. Our genomic findings imply several strategies for optimal sourcing and crossing of populations for restoration and aquaculture, but which require experimental validation. Overall, our work reveals strong genetic structure and suggests that conservation strategies should consider the multiple health risks faced by small populations whose evolutionary dynamics are dominated by genetic drift.

evolutionary biology↗

bioRxiv2023

Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaea L.) through genome sequencing and assembly of European and North American subspecies

Lingonberry (Vaccinium vitis-idaea L.) produces tiny red berries that are tart and nutty in flavour. It grows widely in the circumpolar region, including Scandinavia, northern parts of Eurasia, Alaska, and Canada. Although cultivation is currently limited, the plant has a long history of cultural use among indigenous communities. Given its potential as a food source, genomic resources for lingonberry are significantly lacking. To advance genomic knowledge, the genomes for two subspecies of lingonberry (V. vitis-idaea ssp. minus and ssp. vitis-idaea var. Red Candy) were sequenced and de novo assembled into contig-level assemblies. The assemblies were scaffolded using the bilberry genome (V. myrtillus) to generate chromosome-anchored reference genome consisting of 12 chromosomes each with total length 548.07 Mbp (contig N50 = 1.17 Mbp, BUSCO (C%) = 96.5%) for ssp. vitis-idaea, and 518.70 Mbp (contig N50 = 1.40 Mbp, BUSCO (C%) = 96.9%) for ssp. minus. RNA sequencing based gene annotation identified 27,243 genes on the ssp. vitis-idaea assembly, and transposable element detection methods found that 45.82% of the genome was repeats. Phylogenetic analysis confirmed that lingonberry is most closely related to bilberry and is more closely related to blueberries than cranberries. Estimates of past effective population size suggested a continuous decline over the past 1-3 MYA, possibly due to the impacts of repeated glacial cycles during Pleistocene leading to frequent population fragmentation. The genomic resource created in this study can be used to identify industry relevant genes (e.g., flavonoid genes), infer phylogeny, and call sequence-level variants (e.g., SNPs) in future research.

genomics↗

bioRxiv2023

Isoxanthohumol improves obesity and glucose metabolism via inhibiting intestinal lipid absorption with a bloom of Akkermansia muciniphila in mice

AimsDysbiosis is an important factor that leads to metabolic disorders by disrupting energy balance and insulin sensitivity. A decrease in Akkermansia muciniphila is a phenotype of obesity-induced dysbiosis. Although interventions to increase A. muciniphila are expected to improve glucose metabolism, the underlying mechanism has not been fully understood. MethodsIsoxanthohumol (IX), a prenylated flavonoid found in beer hops was administered to high fat diet-fed mice. We analyzed glucose metabolism, gene expression profiles and histology of liver, epididymal adipose tissue and colon. Lipase activity, fecal lipid profiles and plasma metabolomic analysis were assessed. Fecal 16s rRNA sequencing was obtained and selected bacterial species were used for in vitro studies. Fecal microbiota transplantation and monocolonization were conducted to antibiotic-treated or germ-free (GF) mice. ResultsThe administration of IX lowered weight gain, decreased steatohepatitis and improved glucose metabolism. Mechanistically, IX inhibited pancreatic lipase activity and lipid absorption by decreasing the expression of the fatty acid transporter CD36 in the small intestine, which was confirmed by increased lipid excretion in feces. IX administration improved the gut barrier function and reduced metabolic endotoxemia. In contrast, the effects of IX were nullified by antibiotics. As revealed using 16S rRNA sequencing, the microbial community structure changed with a significant increase in the abundance of A. muciniphila in the IX-treated group. An anaerobic chamber study showed that IX selectively promoted the growth of A. muciniphila while exhibiting antimicrobial activity against some Bacteroides and Clostridium species. To further explore the direct effect of A. muciniphila on lipid and glucose metabolism, we monocolonized either A. muciniphila or Bacteroides thetaiotaomicron to GF mice. A. muciniphila monocolonization decreased CD36 expression in the jejunum and improved glucose metabolism, with decreased levels of multiple classes of fatty acids determined using plasma metabolomic analysis. ConclusionOur study confirmed a direct role of A. muciniphila in energy metabolism, which was induced by microbial actions of IX. These highlight new treatment strategies for preventing metabolic syndrome by boosting the gut microbiota with food components.

microbiology↗

bioRxiv2022

Inositol pyrophosphate profiling reveals regulatory roles of IP6K2-dependent enhanced IP7 metabolism in enteric nervous system

Inositol pyrophosphates (PP-IPs) regulate diverse physiological processes; to better understand their functional roles, assessing their tissue-specific distribution is important. Here, we profiled PP-IP levels in mammalian organs using a novel HILIC-MS/MS protocol and discovered that the gastrointestinal tract (GIT) contained the highest levels of IP7 and its precursor IP6. Although their absolute levels in the GIT is diet-dependent, elevated IP7 metabolism still exists under dietary regimes devoid of exogenous IP7. Of the major GIT cells, enteric neurons selectively express the IP7-synthesizing enzyme IP6K2. IP6K2-knockout mice exhibited significantly impaired IP7 metabolism in the various organs including the proximal GIT. Additionally, HILIC-MS/MS analysis displayed that genetic ablation of IP6K2 significantly impaired IP7 metabolism in the gut and duodenal muscularis externa containing myenteric plexus. Whole transcriptome analysis of duodenal muscularis externa further suggested that IP6K2 inhibition induced the gene sets associated with mature neurons such as inhibitory, GABAergic and dopaminergic neurons, concomitantly with suppression of those for neural progenitor/stem cells and glial cells. In addition, IP6K2 inhibition explicitly affected transcript levels of certain genes modulating neuronal differentiation and functioning, implying critical roles of IP6K2-IP7 axis in developmental and functional regulation of enteric nervous system. These results collectively reveal an unexpected role of mammalian IP7--a highly active IP6K2-IP7 pathway is conducive to enteric nervous system.

molecular biology↗

bioRxiv2022

The rate of inversion fixation in plant genomes is highly variable.

AO_SCPLOWBSTRACTC_SCPLOWChromosomal inversions are theorized to play an important role in adaptation by preventing recombination, but testing this hypothesis requires an understanding of the rate of inversion fixation. Here we use chromosome-level whole genome assemblies for 32 genera of plants to ask how fast inversions accumulate and what factors affect this rate. We find that on average species accumulate 4 to 28 inversions per million generations, but this rate is highly variable, and we find no correlation between sequence divergence or repeat content and the number of inversions and only a small correlation with chromosome size. We also find that inversion regions are depleted for genes and enriched for TEs compared to the genomic background. This suggests that idiosyncratic forces, like natural selection and demography, are controlling how fast inversions fix.

evolutionary biology↗

bioRxiv2018

Triazole ureas covalently bind to strigolactone receptors and regulate signaling

Strigolactones (SLs), a class of plant hormones with multiple functions, mediate plant-plant and plant-microorganism communications in the rhizosphere. In this study, we developed potent strigolactone antagonists, which covalently bind to the strigolactone receptor D14, by preparing an array of triazole urea compounds. Using yeast two-hybrid assays and rice tillering assays, we identified a triazole urea compound KK094 as a potent inhibitor of strigolactone receptors. The LC-MS/MS analysis and X-ray crystallography concluded that KK094 was hydrolyzed by D14, and that a reaction product of this degradation covalently binds to the Ser residue of the catalytic triad of D14. We also identified KK052 and KK073, whose effects on D14-D53/D14-SLR1 complex formation were opposite due to a trifluoromethyl group on its benzene ring. These results demonstrate that triazole urea compounds are potentially powerful tools for agricultural application and may be useful for the elucidation of the complicated mechanism underlying SL-perception.

plant biology↗