Biology subjects

Fujichika, T.

Publications and source records attributed to Fujichika, T..

3 recordsLinked to original sources

bioRxiv2025

Geographic divergence and the genomic basis of reproductive diapause in Drosophila triauraria

Adjusting reproduction timing to environmental cues is essential for lifetime fitness. In many insects, reproductive diapause shows clinal variation along environmental gradients such as photoperiod and temperature. How such continuous trait variation may be encoded at the molecular level and maintained in the presence of gene flow remains largely elusive. The fruit fly Drosophila triauraria is distributed across a wide latitudinal range of the Japanese archipelago. Northern strains exhibit a strong photoperiodic reproductive diapause in females, whereas southern strains fail to arrest ovarian development even under short-day conditions at low temperatures. These distinct phenotypes and the presumable clinal variation in between, provide an ideal opportunity to examine the molecular basis of latitudinal divergence. We first investigated diapause induction in both females and males from previously reported and newly tested strains collected from the regions spanning [~]26-43{degrees}N along the Japanese archipelago. The assessment revealed continuous geographic variation in sensitivity to photoperiod and temperature. We then analyzed the whole-genome sequences of 21 strains, including 14 newly sequenced, to identify genomic regions underlying this divergence. In addition to the conventional FST analysis, we applied a "monophyletic window" approach suitable for limited sample sizes. The analysis identified a candidate region containing putative E-box and TER-box sequence motifs of the timeless (tim) gene, which has been previously implicated in diapause regulation in multiple insect species. The quantitative PCR analysis further supported a partial association between the tim expression and the incidence of female diapause. These findings reinforce the growing evidence for a role of circadian clock genes in the adaptive regulation of reproductive diapause and demonstrate the utility of tree-based approaches for detecting genomic regions of geographic divergence.

genetics↗

bioRxiv2025

BubR1 and Mad2 regulate adult midgut remodeling in Drosophila diapause

Diapause is a survival strategy in which growth and aging are temporarily suspended, enabling animals to withstand unfavorable environments. Various insects, including the fruit fly Drosophila, enter reproductive diapause, or dormancy, in response to colder temperatures and/or shorter day lengths. During reproductive diapause, ovarian development halts, and non-reproductive organs also undergo remodeling at both morphological and metabolic levels: however, the mechanisms underlying this remodeling and its physiological impact remain largely unclear. Here, we show that the Drosophila adult midgut undergoes extensive remodeling in diapause, marked by a sustained suspension of growth due to the cell cycle arrest of intestinal stem cells (ISCs) that revert to normal upon returning to recovery conditions. During dormancy, BubR1 and Mad2, key regulators of mitosis, are highly expressed and localized in the cytoplasm of ISCs rather than at the kinetochore, and both BubR1 and Mad2 are essential for diapause-specific midgut remodeling. Furthermore, disruption of midgut growth arrest during diapause reduces the resistance to starvation in adult flies. Together, our findings identify a novel role for BubR1 and Mad2 in ISCs-promoting proper midgut remodeling during dormancy-and highlight the importance of this process for survival under adverse environments.

developmental biology↗

bioRxiv2023

Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

evolutionary biology↗