BMC Biology最新文献

Background: Stipules are specialized appendages borne at the base of a leaf petiole and may perform a variety of functions including sheltering delicate growing tissues from environmental exposure, facilitating vegetative propagation and dispersal, and providing climbing hooks or protective spines. While stipules are widespread in extant angiosperms and a few fern groups, their origins in geological history remain poorly understood. This study critically reconsiders the absence of stipules in the ancestry of Marattiales.

Results: Based on extraordinary collections from the early Permian Wuda Tuff Flora, we report, for the first time, aphlebia fossils organically attached to psaroniaceous petioles. The psaroniaceous aphlebiae are homologous to marattiaceous stipules, as evidenced by numerous shared characteristics. Functionally, psaroniaceous stipules appear to shelter juvenile fronds and the stem apex, with a continued role in mature fronds. Furthermore, their continued and potentially indeterminate growth, along with their fully laminated structure, suggests a possible role in vegetative propagation after detachment from the parent frond. However, no direct fossil evidence of stipules acting as vegetative propagules is currently available.

Conclusions: Our discovery provides unprecedented view of stipules in psaroniaceous tree ferns. The discovery of psaroniaceous stipules is significant, as it represents the earliest known stipule in the plant kingdom and underscores their multifunctional roles in plant development.

Background: As populations age, the number of people with age-related chronic diseases increases, causing significant social, economic and health problems. Natural variation in lifespan depends on multiple interacting genes and environmental exposures. Its short generation time and many resources make Drosophila melanogaster an advantageous model to uncover the genetic architecture that underlies variation in lifespan.

Results: We performed whole genome sequencing on young and old flies, sexes separately, in an outbred advanced intercross population (AIP) derived from inbred, sequenced lines from the Drosophila Genetic Reference Panel (DGRP). We identified mostly sex-specific variants (extreme Quantitative Trait Loci; xQTLs) at 1,107 genes associated with increased lifespan. We used the same AIP for RNA sequencing of heads, bodies and reproductive tissues for males and females weekly to 10 weeks of age. We identified 2,613 genes with age-related changes, of which 186 had xQTLs. Over half of the significant effects of gene expression with age included sex- and/or tissue-specific context-dependent effects, many of which were antagonistic, indicating complex trade-offs in gene regulation in the context of lifespan. We mapped genes whose expression changes with age onto known gene-gene and protein-protein interactions to construct interaction networks anchored by xQTLs. These networks were enriched for evolutionarily conserved mitochondrial, metabolic, neuronal, immune and developmental genes. Human orthologs of Drosophila genes associated with senescence and lifespan were prevalent indicating the translational potential of results from Drosophila to human populations.

Conclusions: Natural genetic variation in Drosophila identifies sex- and/or tissue-specific genetic variation and networks enriched for evolutionarily conserved genes.

Background: Nutrition during early life often has lasting consequences for adult physiology. However, it remains unclear how developmental diet shapes both the initial energetic state and subsequent change of energy stores. To address this, we systematically varied yeast and sugar concentrations in the developmental diet of Drosophila melanogaster and quantified energy reserves (in joules, derived from fat, glycogen, trehalose, and glucose) at eclosion and after 10 days of adulthood on a standardized diet. Comparing these time points allowed estimation of net change in energy reserves. Additionally, we examined how these effects depend on sex, population, and reproductive status.

Results: Developmental diet strongly influenced initial energy reserves. Higher sugar concentrations increased energy stores at eclosion. However, the subsequent net change in energy was inversely related to these starting conditions. Flies reared on high-sugar larval diets, which emerged with the most energy, exhibited the smallest net change during early adulthood. In contrast, flies from low-sugar diets emerged leaner and subsequently showed the largest net increase. These patterns were modulated by sex and reproductive status. In males, energy stores more closely reflected the larval nutritional background, whereas in females this relationship was weaker-likely due to the energetic demands of oogenesis. Mating was generally associated with lower energy reserves across groups.

Conclusions: Early-life diet affects both the starting point and early-adult change in energy reserves in Drosophila. These findings outline a framework in which developmental history and adult conditions jointly shape energetic trajectories.

Nictation is a dispersal behavior in nematodes, aiding movement and host-finding under stress. This review explores its diversity, genetic and neuronal basis, regulation, and ecological relevance. Nictation involves sensory integration, plasticity, and inter-organismal communication. Though its neural circuitry and molecular pathways remain partly understood, recent findings highlight roles for dauer signaling, neurotransmitters, and neuropeptides. Advances in scoring methods and genetic tools, including of parasitic species, now enable deeper study of its environmental triggers, evolutionary context, and impact on nematode virulence, with key knowledge gaps identified for future research.

Background: The black soldier fly (BSF, Hermetia illucens) is widely used for waste bioconversion and sustainable protein production. However, domestication and prolonged captive rearing can rapidly alter genetic diversity and population structure. This study investigated how selective breeding, genetic drift, and relaxed selection have shaped genomic variation and effective population size in multiple BSF populations. Using genome-wide restriction site-associated DNA sequencing, we analysed population structure, heterozygosity, and selection signatures across 11 BSF populations, including 1 long-term domesticated line, 5 selectively bred lines (Line A to Line E), 3 wild-derived populations, and 2 commercial strains.

Results: Despite shared origins, lines LA to LE diverged rapidly within 6 years. Principal component analysis and ADMIXTURE clustering (K = 11) revealed that LC to LE retained close genetic affinity, while LA and LB diverged markedly from each other and LC-LE. Demographic reconstructions using Stairway Plot showed that effective population sizes increased during the initial homogenized selective breeding phase (2018-2019) but declined after 2022, consistent with bottlenecks and relaxed selection. Wild-derived populations maintained higher heterozygosity and lower inbreeding coefficients than domesticated lines. Finally, genome-wide analyses identified 133 candidate genes under selection, including signatures of balancing selection and selective sweeps, reflecting divergent evolution under domestication.

Conclusions: These findings demonstrate that genetic differentiation occurs rapidly in BSF populations under domestication, driven by artificial selection, relaxation, genetic drift, and environmental adaptation. These results highlight the need for genetic monitoring in breeding programmes, including maintenance of large founder populations, periodic genetic assessment, and genetic rescue to preserve adaptive potential and reduce inbreeding risks.

Background: Anthropogenic forces have resulted in staggering losses of biodiversity and population declines in many species over the past two centuries. Associated with these declines are potential adverse effects linked to small population sizes, including loss of genetic diversity and increased levels of inbreeding. Here, we leverage DNA sequencing from museum specimens to examine genetic variation between historic and contemporary populations of four species of warblers (Aves, Setophaga) that vary with respect to degree of population changes over this period. To explore the genetic impacts of varying population declines, we gathered polymorphism data at 157 PCR-amplified loci in 341 individuals sampled in two time periods-historic (1789-1955) vs contemporary (2001-2020).

Results: For all four species, we observed decreases in nucleotide diversity and heterozygosity in contemporary data sets compared to historic data sets. In three species, this loss was accompanied by a corresponding increase in inbreeding coefficient F_IS. We find that these genetic diversity declines correspond to declining contemporary effective population sizes (Ne) over deeper time scales, as well as fluctuations in contemporary estimates of Ne.

Conclusion: Our findings suggest that loss of genetic diversity resulting from historic population declines persists over time (50-100 years), even when population trajectories later stabilize. Our results highlight the utility of long-term genetic temporal comparisons to reveal hidden genetic diversity loss and reveal important considerations for managing genetic diversity loss.

Background: Organelle genome fragmentation is a drastic large-scale chromosomal mutation. Why and how organelle genomes become fragmented is still poorly understood. Two previous studies based on whole genome comparison between human louse and fruit fly proposed that the loss of mtSSB gene (for mitochondrial single-stranded DNA-binding protein) might be associated with mitochondrial (mt) genome fragmentation. Whether this association is valid has not been investigated due to the lack of mt genome fragmentation data.

Results: We investigated this association by exploring the genomic and transcriptomic data of 198 species of parasitic lice, book lice, bark lice, and other closely related hemipteroid insects accumulated in the past few decades. We show that the loss of mtSSB gene is correlated significantly with mt genome fragmentation in bark lice, book lice, and parasitic lice (Psocodea). The absence of mtSSB is more frequent than expected in the species with fragmented mt genomes whereas the presence of mtSSB is more frequent than expected in the species with single-chromosome mt genome organization. Nevertheless, our results reject a cause-and-effect relationship between the loss of mtSSB and mt genome fragmentation because mtSSB is present in 11 species of parasitic lice and one book louse species that have fragmented mt genomes.

Conclusions: The loss of mtSSB gene is correlated with mt genome fragmentation but is not the cause of mt genome fragmentation. Rather, it is plausible that fragmented mt genomes with multiple small-sized minichromosomes may make mtSSB gene and mtSSB protein less critical or unnecessary, leading to their loss eventually in the species with fragmented mt genomes.

Background: Accurate prediction of anticancer drug responses remains a significant challenge due to the intricate interplay between genomic features and pharmacological mechanisms. We present Matrix Completion with Low-rank Regularization and Principal Component Analysis (MCLRP), a multimodal framework that synergistically integrates low-rank matrix completion with transcriptomic principal component analysis through dual-stream feature interaction. This innovative architecture not only leverages the similarities among drugs and mutation patterns in cell lines via matrix completion but also preserves gene-level interpretability of response patterns by incorporating gene expression data into the model.

Results: Benchmarked against seven computational paradigms (including matrix completion, ridge regression, SRMF, and their hybrid variants) across the Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE) repositories, MCLRP demonstrated superior predictive performance for 75% of drug responses, alongside enhanced biological plausibility. Notably, the model identified imatinib as a potential therapeutic alternative for M14 melanoma cell lines through cross-drug response extrapolation, suggesting innovative strategies for overcoming doxorubicin resistance. Interestingly, our mutation-response mapping revealed that BRAF-mutated lineages exhibited a 4.7-fold increase in sensitivity (p < 1e-5) to AZ628 compared to wild-type lineages, with synergistic amplification (8.1-fold, p < 1e-7) observed in BRAF/PIK3CA co-mutants.

Conclusions: These findings establish MCLRP as a dual-purpose predictive-analytical tool that not only enhances drug response forecasting but also uncovers mutation-specific pharmacological vulnerabilities through systems-level pattern recognition.

Background: The interconnectedness of human, animal, and environmental health drives emerging threats, such as antimicrobial-resistant pathogens. The widespread use of the same antimicrobials in both human and livestock may play a role in interspecies bacterial transmission by disrupting natural microbial communities and creating an environment favouring resistant bacteria. Pigs and poultry receive high levels of antimicrobials and are reservoirs of multidrug-resistant bacteria, including Streptococcus suis, a zoonotic pig pathogen. S. suis detection in non-porcine hosts, particularly poultry, raises a critical question: is this due to transient spillover or does it represent sustained host jumps and adaptation?

Results: Analysing over 3000 S. suis genomes from a diverse range of hosts-including pigs, wild boar, humans, cats, dogs, cattle, fish, otter, and birds-we identify a multidrug-resistant lineage, distinct from the lineage responsible for most zoonoses, that has undergone multiple host jump events into birds. Unlike transmission to humans, which is exclusively derived through contacts with pigs, we find evidence of S. suis adaptation to birds. This includes phylogenetic persistence, independent acquisition of bird-specific mobile genomic islands, enhanced survival in chicken versus pig blood, and subsequent transmission from poultry to wild birds.

Conclusions: While chickens may not be a source of zoonotic S. suis infections, shared antibiotic usage in pigs and poultry may have promoted host jumps of multidrug-resistant S. suis, leading to onward transmission to wild bird populations. Our results suggest that antibiotic use in livestock production may promote transmission of antimicrobial-resistant bacteria to other hosts, thereby expanding the ecological range of bacterial pathogens.

Background: Based on the climate change and more extreme temperature events in the past 30 years, heat stress (HS) has become one of the most detrimental abiotic stresses that affect crop growth and development, limit their geographical distribution, and reduce yield. As a typical chimonophilous crop, wheat is very sensitive to high temperature. Deciphering the molecular mechanism of the wheat response to high temperature will help in the development of cultivars that perform better under HS.

Results: In this study, we identified a wheat Kelch-type F-box gene, TaFBK34. Overexpression of TaFBK34 wheat plants (TaFBK34-OE) showed stronger heat tolerance compared to the wild type, while plants with attenuated TaFBK34 (TaFBK34-RNAi) exhibited the phenotype of heat sensitivity. Increased expression of antioxidant-related genes and a heat-shock protein gene was observed in TaFBK34-OE plants compared with the wild type, coinciding with higher activities of the antioxidant enzymes, accumulation of proline and soluble sugar, reduced malondialdehyde and reactive oxygen species content. The opposite trends were observed in TaFBK34-RNAi lines. TaFBK34 interacts with the ADP-ribosylation factor, TaARL2. Compared to the wild type, more TaARL2 protein accumulated in TaFBK34-RNAi lines after HS treatment; moreover, TaARL2 continued to increase after MG132 (a proteasome inhibitor) injection for 12 h + 37 °C for 12 h, indicating that TaARL2 is involved in the response to HS and is degraded by the 26S proteasome.

Conclusions: These findings show that TaFBK34 improves wheat tolerance to HS, at least in part through an interaction with the TaARL2 protein, and provides potential applications of these genes for the improvement of wheat.