Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogs in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.

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. ×yedoensis '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.

Bagworms are commonly known for the well-organized case or bag surrounding them constructed using their silk and plant materials. To understand the genetic basis of these unique characteristics in bagworms, we performed multi-omics analyses of a bagworm species, Eumeta crameri. The genome and transcriptome sequencing of E. crameri were used to construct the nuclear genome with a size of 668.2 Mb, N50 value of 6.6 Mb, and 13,554 coding genes, which was further assembled into 31 pseudochromosomes. The mitochondrial genome had a size of 15.6 Kb. We established the phylogenetic position of E. crameri with respect to 54 other insect species. The comparative analyses of E. crameri with other Lepidopterans revealed the adaptive evolution of genes related to primary metabolic pathways, defense, molting and metamorphosis, and silk formation in the bagworm species. We also showed the ultrafine nature of the E. crameri silk fibers. Further, we performed the gut microbiome sequencing for E. crameri and constructed a gut microbial gene catalog, which revealed the unique composition of the gut microbiome and its significance for host metabolism and defense. Together, the results provide multi-faceted insights into the biological processes that support the well-organized holometabolous metamorphosis inside the bags of E. crameri.

Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes, a useful model organism studied in diverse biological fields. Chromosome-scale genome sequences of the Hd-rR strain of this species were obtained in 2007, and its improved version has facilitated various genome-wide studies. However, despite its widespread utility, omics data for O. latipes are dispersed across various public databases and lack a unified platform. To address this, the medaka section of the National Bioresource Project (NBRP) of Japan established a genome informatics team in 2022 tasked with providing various in silico solutions for bench biologists. This initiative led to the launch of MedakaBase (https://medakabase.nbrp.jp), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides on-demand browsing of diverse genome-wide datasets, including tissue-specific transcriptomes and intraspecific genomic variations, integrated with gene models from different sources. Additionally, the platform offers gene models optimized for single-cell transcriptome analysis, which often requires coverage of the 3' untranslated region (UTR) of transcripts. Currently, MedakaBase provides genome-wide data for seven Oryzias species, including original data for O. mekongensis and O. luzonensis produced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase.

The Red-vented Bulbul (Pycnonotus cafer) of the Pycnonotidae family is one of the most invasive tropical passerine bird species. We accomplished the genome and transcriptome sequencing of P. cafer to explore the genomic basis of invasiveness and assembled the genome size of 1.03 Gb and 15,533 protein-coding genes with an N50 of 3.04 Mb and 97.2% BUSCO completeness. Our study constructed the mitogenome and 18S rRNA marker gene of P. cafer for the first time. Further, we investigated the demographic history and identified recent genetic bottlenecks the species experienced. We established the phylogenetic position of P. cafer and examined the gene family evolution along with orthologous gene clustering to provide clues on the invasive characteristics of P. cafer. Our study thus serves as a significant resource for future studies in invasion genomics and the possible management of this bird species in alien ranges.

Senegalese sole is a promising European aquaculture species whose main challenge is that captive-born males (F1) are unable to reproduce in farms, hindering breeding programs. Chemical communication through the olfactory system is hypothesized to stem this issue. Although significant advancement in genomic resources has been made recently, scarce information exists on the genomic basis of olfaction, a special sensory system for demersal species like flatfish, which could play a prominent role in reproduction, social and environmental interactions. A full-length transcriptome of the olfactory rosettes including females, males, juveniles and adults, of both F1 and wild origins, was generated at the isoform-level by combining Oxford Nanopore long-read and Illumina short-read sequencing. A total of 20,670 transcripts actively expressed were identified: 13,941 known transcripts, 5,758 novel transcripts from known genes, and 971 from novel genes. Given the important role of olfaction in reproductive behaviour, we comparatively examined the expression and functional enrichment of the olfactory receptor gene families (OlfC, OR, ORA and TAAR). Our comprehensive olfactory transcriptome of Senegalese sole provides a foundation for delving into the functional basis of this complex organ in teleost and flatfish. Furthermore, it provides a valuable resource for addressing reproductive management challenges in Senegalese sole aquaculture.

Repetitive DNA sequences, as transposable elements (TEs) and satellite DNA (satDNA) spread and diversify within host genomes, impacting genome biology in numerous ways. In the first part of this review, we emphasize the evolutionary importance of satDNAs and TEs, providing a short summary of their roles and the mechanisms by which they influence the structure and function of genomes. We also discuss the broad, complex, and extensive relationships between TEs and satDNAs. Following that, we bring together different mechanisms on the generation of satDNA from TE, as it has been demonstrated that almost any part of any type of TE can undergo tandemization and produce novel satDNAs. Importantly, we here present a hypothesis that would explain the existence of particular types of monomers, namely composite satDNA monomers which display multiple subsequent stretches of similarity to various TEs, for which the explanation was lacking so far. We propose that even highly shuffled and degraded TE remnants residing in heterochromatin "TE graveyards" can give rise to new satDNA sequence monomers, transforming these genomic loci into DNA "recycling yards." Furthermore, we emphasize important evolutionary questions regarding the causes, mechanisms, and frequency of these occurrences.

In molecular evolution analyses, genomic DNA sequence information is usually represented in the form of 4 bases (ATGC). However, research since the turn of the century has revealed the importance of epigenetic genome modifications, such as DNA base methylation, which can now be decoded using advanced sequence technologies. Here we provide an integrated framework for analyzing molecular evolution of nucleotide substitution, methylation, and demethylation using an expanded nucleotide code that incorporates different types of methylated bases. As a first attempt, we analyzed substitution rates between bases, both unmethylated and methylated ones. As the model methylomes, we chose those of Helicobacter pylori, an unicellular bacterium with the largest known repertoire of sequence-specific DNA methyltransferases. We found that the demethylation rates are remarkably high while the methylation rates are comparable with the substitution rates between unmethylated bases. We found that the ribosomal proteins known for sequence conservation showed high methylation and demethylation frequencies, whereas the genes for DNA methyltransferases themselves showed low methylation and demethylation frequencies compared to base substitution. This work represents the first step towards molecular evolutionary epigenomics, which, we expect, would contribute to understanding epigenome evolution.

Salmonella enterica serovar I 4, [5],12:i:- (serovar I 4, [5],12:i:-) is one of the most frequent multidrug-resistant (MDR) Salmonella serovars associated with food-animal production globally, and strains often contain Salmonella genomic island-4 (SGI-4), an integrative conjugative element (ICE) encoding metal tolerance for copper, silver, and arsenic. Horizontal gene transfer (HGT) of SGI-4 from serovar I 4, [5],12:i:- to recipient bacteria results in enhanced metal tolerance for the transconjugants; however, the origin of transfer (oriT) for SGI-4 mobilization is unknown. In this study, the oriT within SGI-4 of MDR serovar I 4, [5],12:i:- strain USDA15WA-1 was identified by: a) cloning an internal region of SGI-4 into a non-mobilizable plasmid and demonstrating HGT to a bacterial recipient, and b) deleting the predicted oriT region of SGI-4 from strain USDA15WA-1 and abolishing SGI-4 transfer. Sequence similarity to oriTSGI-4 was identified in other Enterobacteriaceae, and conjugation of SGI-4 occurred from USDA15WA-1 to Salmonella serovars from serogroups C-E as well as Escherichia coli and Citrobacter. Localization of the SGI-4 oriT enhances our understanding of a DNA region involved in HGT of an ICE in a frequent MDR Salmonella serovar, thereby providing a model to investigate HGT of SGI-4 and dissemination of metal tolerance genes in the food-animal production environment.

Understanding the molecular causes of complex diseases remains one of the most pressing challenges in biomedicine. Despite large-scale genome-wide association studies mapping thousands of risk loci, identifying which genetic variants truly drive disease remains difficult. Traditional statistical genetics has laid a strong foundation for variant discovery, but it often struggles to capture non-linear interactions and cannot fully integrate the breadth of the interconnected multi-omics data. In recent years, deep learning approaches have shown promise in bridging these gaps: modeling high-order genetic interactions, uncovering latent biological structure, and enabling multi-layered data integration. However, most current deep learning models for genomics remain exploratory in nature, and issues such as susceptibility to overfitting, difficulties in interpretability, and the general lack of standardized evaluation frameworks have limited their widespread adoption for genomics research. In this review, we explore how traditional statistical and deep learning methods can be applied to uncover causal mechanisms in complex disease. We critically compare these two frameworks for their advantages and limitations in detecting genetic associations and prioritizing causal associations. Toward the end, we propose a future direction centered around hybrid models that blend the scalability of deep learning with the inferential power of statistical genetics. Our goal is to guide researchers in developing next-generation computational tools to uncover the molecular basis of complex diseases and accelerate the translation of genetic findings into effective treatments.