Biology subjects

Biswa, B. B.

Publications and source records attributed to Biswa, B. B..

4 recordsLinked to original sources

bioRxiv2025

Chromosome-scale genomes of two wild flowering cherrys (Cerasus itosakura and C. jamasakura) provide insights into structural evolution in Prunus

Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. xyedoensis Somei-yoshino, and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of Somei-yoshino. Comparison with the phased genome of Somei-yoshino revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.

genomics↗

bioRxiv2024

Tameness selection pressure affects gut virome diversity in mice

The gut microbiome, a complex ecosystem comprising bacteria, viruses, archaea, fungi, and other microorganisms, plays a pivotal role in host health, immunity, and behaviour. Among its components, bacteriophages and viruses that infect bacteria significantly influence microbial community dynamics by affecting bacterial diversity, function, and evolution. Despite extensive research on bacterial components, the viral metagenome (virome) remains relatively unexplored. This study investigated the effect of selective breeding for tameness on the gut virome of wild heterogeneous stock (WHS) mice. WHS mice were selectively bred for active tameness, resulting in four groups: S1 and S2 (selected for tameness), and C1 and C2 (non-selected). In previous study, we observed an increased abundance of Limosilactobacillus reuteri in tame groups compared to non-selected groups, as well as a tameness-promoting effect of L. reuteri with long-term administration. Given the regulatory role of phages in bacterial populations, this study focused on analysing the gut virome using shotgun metagenome sequencing data. From the 84 samples, we generated 6078 non-redundant viral operational taxonomic units (vOTUs) and identified the hosts of 3,065 of these vOTUs. Significant differences in gut virome beta diversity were observed between the selectively bred and control groups, suggesting that tameness selection exerts distinct pressure on the virome. Additionally, phage-host interaction analysis revealed strong correlations between specific phages and their bacterial hosts, indicating a co-occurrence that influences host behaviour. Overall, this study provides novel insights into the role of the gut virome in shaping host behaviour and highlights the broader implications of microbial contributions to domestication and selective breeding outcomes.

microbiology↗

bioRxiv2024

Decoding the Centromeric Region with a Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa

The Oshima cherry (Cerasus speciosa), which is endemic to Japan, has significant cultural and horticultural value. In this study, we present a near complete telomere-to-telomere genome assembly for C. speciosa, derived from the old growth "Sakurakkabu" tree on Izu Oshima Island. Using Illumina short-read, PacBio long-read, and Hi-C sequencing, we constructed a 269.3 Mbp genome assembly with a contig N50 of 32.0 Mbp. We examined the distribution of repetitive sequences in the assembled genome and identified regions that appeared to be centromeric. Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. This high-quality reference genome provides a crucial tool for studying the genetic diversity and evolutionary history of Cerasus species, facilitating advancements in horticultural research and the preservation of this iconic species.

genomics↗

bioRxiv2024

Enhanced tameness by Limosilactobacillus reuteri from gut microbiota of selectively bred mice

Domestication alters animal behaviour, primarily their tameness. In this study, we examine the effect of gut bacteria on mouse tameness. We previously conducted selective breeding for active tameness, defined as the motivation to approach a human hand, using genetically heterogeneous mice derived from eight wild inbred strains. We examined gut microbiota in the selectively bred mice by analysing faecal samples from 80 mice through shotgun metagenomic analysis. In the current study, we found that the selectively bred mice exhibit higher levels of active tameness as well as higher levels of blood oxytocin, which plays a key role in social behaviours. Selection for tameness did not substantially alter the taxonomic or functional diversity of the gut microbiota. However, we observed an increased abundance of Limosilactobacillus reuteri in the selected groups and higher pyruvate levels in their plasma. We isolated L. reuteri strains secreting extracellular pyruvate from mice faeces and administrated the cultured bacteria through drinking water. Mice treated with L. reuteri showed higher colonization of the bacteria in the gut, as well as higher levels of active tameness behaviour and blood oxytocin. Additionally, we generated 374 high-quality metagenome-assembled genomes (MAGs) of bacteria across 11 phyla. This collection includes 27 novel species level bacterial MAGs not previously known to exist in the mouse gut. This study elucidates the potential role of L. reuteri in the animal domestication process and explores the underlying mechanisms that may influence this process.

microbiology↗