Shuji Shigenobu

The paper investigates how host-derived lipids sustain membrane biogenesis in the obligate endosymbiont Buchnera aphidicola, showing host lipid metabolism is critical for symbiont survival.

The paper presents a chromosome-level genome assembly and transcriptome resource for the medicinal leech Hirudo verbana using PacBio and Hi-C data.

The paper predicts structures of rapidly evolving aphid effector proteins using Alphafold2 with custom multiple sequence alignments, revealing saposin-like folds and structural diversity.

This paper demonstrates that EC-isHCR retains the features of conventional isHCR and introduces an automated probe design tool to enhance its applicability across diverse samples.

This study investigates the phylogenetic origin and pigment patterns of mushifugu, finding it to be a distinct species with evidence of past hybridization with komonfugu.

The paper identifies the candidate gene SUGI_0493010 for MS2-type male sterility in Japanese cedar using linkage mapping and transcriptomic data.

The paper shows that disrupting the tryptophanase gene in bacteria enables mutualism with stinkbugs, suggesting this gene loss facilitated the evolution of insect-bacterium mutualism.

This study examines symbiont replacement in aphids, showing how new and resident symbionts adapt, with insights into genome erosion and co-evolution.

The paper traces individual PGC clones in mice to show early stochastic bottlenecks shape clonal contributions and reproductive success.

This study uses CRISPR/Cas9 to knockout Laccase2 in pea aphids, revealing its essential role in eggshell pigmentation, hardening, and survival during overwintering diapause.

MedakaBase provides a centralized platform for genomic resources and analysis tools for medaka fish, including gene models and omics data for multiple Oryzias species.

This study shows Wolbachia in aphids bypasses the germ line by directly transmitting from maternal bacteriocytes to embryos, using the obligate symbiont transfer system.

This study examines how symbiotic bacteria in aphids change across their complex life cycles, finding that Buchnera is absent in sexual males and less abundant in gall-forming generations.

This paper develops mouse-Geneformer, a deep learning model for mouse single-cell transcriptomes, showing cross-species utility for human data and disease modeling.

This study identifies Chlamydomonas γ-tubulin mutations that cause partial loss of protofilaments in centriolar microtubules, highlighting γ-tubulin's role in maintaining triplet microtubule stability.

This study identifies a novel role for Hox13 in regulating newt hindlimb bud outgrowth by interacting with Fgf10 and Tbx4 during development.

The paper presents a chromosome-level genome assembly for the Japanese cedar, using long-read and Hi-C sequencing to achieve high contiguity and accuracy.

This study shows that colonization by a compatible orchid mycorrhizal fungus primes induced systemic resistance in Bletilla striata against a necrotrophic pathogen by modulating jasmonate and ethylene pathways, similar to arbuscular mycorrhizal plants.

The paper identifies Fem, a W-linked piRNA precursor in Bombyx mori, as a chimeric sequence derived from transposons, challenging previous hypotheses about its origin.

The paper examines pyloric sphincter formation in Xenopus laevis during metamorphosis, finding that it forms during metamorphic climax and involves gene expression changes similar to amniotes.

This study compares gonadal transcriptomes of turtles and alligators during temperature-sensitive periods to identify conserved molecular cues for temperature-dependent sex determination.

The paper identifies two distinct stem cell lineages in Hydra, germline and somatic, and finds shared stemness genes with origins in unicellular eukaryotes.

The paper identifies genes whose overexpression is adaptive under stress in budding yeast, revealing cellular requirements influenced by genetic background and environment.

This study presents six new draft genomes of Cuban Anolis lizards and analyzes genetic variations and transposon accumulation during their diversification.

This study presents long-read genome assemblies of 12 Vigna species, revealing new WOX transcription factors and transcriptional changes linked to stress tolerance.

The paper identifies genes and genomic regions responsible for PPIX production in the uterus of Japanese quail, linking them to eggshell pigmentation.

This study shows that hox13 paralogs are functionally conserved in limb development and regeneration in newts.

This study analyzes the genome, transcriptome, and methylome of Reticulitermes speratus, showing gene duplication contributes to caste-specific functions and social evolution.