Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternative to antibiotic growth promoters. Altered intestinal microbiota play important roles in growth promotion, but the underlying mechanism remains unknown. We generated 1.64 terabases of metagenomic data from 495 chicken intestinal digesta samples and constructed a comprehensive chicken gut microbial gene catalog (9.04 million genes), which is also the first gene catalog of an animal’s gut microbiome that covers all intestinal compartments. Then, we identified the distinctive characteristics and temporal changes in the foregut and hindgut microbiota. Next, we assessed the impact of MCE on chickens and gut microbiota. Chickens fed with MCE had improved growth performance, and major microbial changes were confined to the foregut, with the predominant role of Lactobacillus being enhanced, and the amino acids, vitamins, and secondary bile acids biosynthesis pathways being upregulated, but lacked the accumulation of antibiotic-resistance genes. In comparison, treatment with chlortetracycline similarly enriched some biosynthesis pathways of nutrients in the foregut microbiota, but elicited an increase in antibiotic-producing bacteria and antibiotic-resistance genes. The reference gene catalog of the chicken gut microbiome is an important supplement to animal gut metagenomes. Metagenomic analysis provides insights into the growth-promoting mechanism of MCE, and underscored the importance of utilizing safe and effective growth promoters.

Background: Ethylene-responsive factors (ERFs) play important roles in plant growth and development and the response to adverse environmental factors, including abiotic and biotic stresses. Results: In the present study, we identified 160 soybean ERF genes distributed across 20 chromosomes that could be clustered into eight groups based on phylogenetic relationships. A highly ABA-responsive ERF gene, GmERF75, belonging to Group VII was further characterized. Subcellular localization analysis showed that the GmERF75 protein is localized in the nucleus, and qRT-PCR results showed that GmERF75 is responsive to multiple abiotic stresses and exogenous hormones. GmERF75-overexpressing Arabidopsis lines showed higher chlorophyll content compared to WT and mutants under osmotic stress. Two independent Arabidopsis mutations of AtERF71, a gene homologous to GmERF75, displayed shorter hypocotyls, and overexpression of GmERF75 in these mutants could rescue the short hypocotyl phenotypes. Overexpressing GmERF75 in soybean hairy roots improved root growth under exogenous ABA and salt stress. Conclusions: These results suggested that GmERF75 is an important plant transcription factor that plays a critical role in enhancing osmotic tolerance in both Arabidopsis and soybean.

Amid growing challenges to global food security, high-throughput crop phenotyping has become an essential tool, playing a critical role in genetic improvement, biomass estimation, and disease prevention. Unlike controlled laboratory environments, field-based phenotypic data collection is highly vulnerable to unpredictable factors, significantly complicating the data acquisition process. As a result, the choice of appropriate data collection equipment and processing methods has become a central focus of research. Currently, three key technologies for extracting crop phenotypic parameters are Light Detection and Ranging (LiDAR), Multi-View Stereo (MVS), and depth camera systems. LiDAR is valued for its rapid data acquisition and high-quality point cloud output, despite its substantial cost. MVS offers the potential to combine low-cost deployment with high-resolution point cloud generation, though challenges remain in the complexity and efficiency of point cloud processing. Depth cameras strike a favorable balance between processing speed, accuracy, and cost-effectiveness, yet their performance can be influenced by ambient conditions such as lighting. Data processing techniques primarily involve point cloud denoising, registration, segmentation, and reconstruction. This review summarizes advances over the past five years in 3D reconstruction technologies—focusing on both hardware and point cloud processing methods—with the aim of supporting efficient and accurate 3D phenotype acquisition in high-throughput crop research.

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), is the primary vector of Candidatus Liberibacter asiaticus, the causal agent of huanglongbing, the most devastating disease of citrus worldwide. Understanding its population structure and developing lineage-specific markers are important for surveillance, quarantine and pest management. Here, 133 complete mitochondrial genomes were analyzed, comprising 77 previously published sequences, 13 newly assembled genomes and 43 metagenome-assembled mitogenomes. Phylogenetic analysis revealed two highly differentiated mitochondrial lineages—an Asian lineage (n = 91, including the Uruguay sample) and an American lineage (n = 42, including the Pakistan sample) (FST = 0.560, p < 0.001)—separated by 32 fixed variants (132 genomes, excluding the reference sequence MF426268.1). Within the Asian lineage, the Yunnan–Guizhou Plateau population showed significant differentiation from lowland populations (FST = 0.130, p < 0.05), reduced nucleotide diversity and moderately supported monophyletic clustering consistent with long-term isolation, while demographic analyses suggested that Southeast China may have acted as a post-colonization expansion center. Candidate lineage-specific markers, including variants in trnG and rrn16, provide molecular resources for population-origin assignment, quarantine surveillance and pest monitoring; these candidates require validation across broader geographic sampling.