Background: Paenibacillus polymyxais a typical plant growth-promoting rhizobacterium (PGPR), and synthesis of indole-3-acetic acid (IAA) is one of the reasons for its growth-promoting capacity. The synthetic pathways of IAA inP. polymyxamust be identified and modified.Results: P. polymyxaSC2 and its spontaneous mutant SC2-M1 could promote plant growth by directly secreting IAA. Through metabonomic and genomic analysis, the genespatA,ilvB3, andfusEin the native IPyA pathway of IAA synthesis in strain SC2-M1 were predicted. A novel strong promoterP₀₄₄₂₀was rationally selected, synthetically analyzed, and then evaluated on its ability to express IAA synthetic genes.Co-expression of three genes,patA,ilvB3, andfusE, increased IAA yield by 60% in strain SC2-M1. Furthermore, the heterogeneous geneiaamof the IAM pathway and two heterogeneous IPyA pathways of IAA synthesis were selected to improve the IAA yield of strain SC2-M1.The genesELJP6_14505,ipdC,andELJP6_00725of the entire IPyA pathway fromEnterobacter ludwigiiJP6 were expressed well by promoterP₀₄₄₂₀in strain SC2-M1 and increased IAA yield in the engineered strain SC2-M1 from 13 to 31 μg/mL, which was an increase of 138%.Conclusions: The results of our study help reveal and enhance the IAA synthesis pathways ofP. polymyxaand its future application.

Rice is one of the main food crops and several studies have examined the molecular mechanism of the exposure of the rice plant stigma. The improvement in the exposure of the stigma in female parent hybrid combinations can enhance the efficiency of hybrid breeding. In the present study, a mutant plant with low exposed stigma (lesr) was discovered among the descendants of the indica thermo-sensitive sterile line 115S. The ES% rate of the mutant decreased by 70.64% compared with the wild type variety. The F₂ population was established by genetic analysis considering the mutant as the female parent and the restorer line 93S as the male parent. The results indicated a normal F₁ population, while a clear division was noted for the high and low exposed stigma groups, respectively. This process was possible only by a ES of 25% in the F₂ population. This was in agreement with the ratio of 3:1, which indicated that the mutant was controlled by a recessive main-effect QTL locus, temporarily named as LESR. Genome-wide comparison of the SNP profiles between the early, high and low production bulks were constructed from F₂ plants using bulked segregant analysis in combination with high-throughput sequencing technology. The results demonstrated that the candidate loci was located on the chromosome 10 of the rice. Following screening of the recombinant rice plants with newly developed molecular markers, the genetic region was narrowed down to 0.25 Mb. This region was flanked by InDel-2 and InDel-2 at the physical location from 13.69 to 13.94 Mb. Within this region, 7 genes indicated base differences between parents. A total of 2 genes exhibited differences at the coding region and upstream of the coding region, respectively. The present study aimed to further clone the LESR gene, verify its function and identify the stigma variation.

Callicarpa americana L. is a member of the Lamiaceae family with important ornamental and medicinal value. Although the chloroplast genome of Lamiaceae has been extensively studied, its mitochondrial genome remains unreported, limiting a comprehensive understanding of the phylogeny and genome evolution of Lamiaceae. In this study, the complete mitochondrial genome of C. americana was successfully assembled for the first time. The genome is 499,565 bp in length, showing a complex multi-branched closed-loop structure that contains 37 protein-coding genes, 23 tRNA genes, and 4 rRNA genes. The difference in mitochondrial genome size is relatively large compared to Orobanchaceae species, but the difference in GC content is not obvious. The expansion of genome size was mainly due to the accumulation of non-coding regions and repetitive sequences. Meanwhile, two pairs of long repetitive sequences (LR3 and LR5) mediated homologous recombination. The mitogenome was also identified; there were a total of 494 C-to-U RNA editing sites in protein-coding genes. In addition, 42 mitochondrial plastid DNA fragments (MTPTs) were detected, with a total length of 21,464 bp, accounting for 4.30% of the genome. Repeat sequence analysis showed that tetranucleotide SSR was the most abundant repeat type in the mitochondria of Lamiaceae. Phylogenetic analysis based on the alignment of 32 protein-coding gene sequences showed that Callicarpa is sister to the other eight species of Lamiaceae. This work fills an important gap by presenting the first complete mitochondrial genome of C. americana, providing an important data resource for further understanding the structural evolution, dynamic recombination mechanism, and phylogeny of the mitochondrial genome of Lamiaceae.

Introduction: Cultivar background may influence antioxidant-related non-volatile metabolite composition of black tea even under identical manufacturing conditions, but the compositional basis and its relationship to assay-specific antioxidant readouts remain unclear. Methods: We conducted a controlled comparison of black teas produced from Gougunao No. 2 (G2R) and the traditional Gougunao group small-leaf cultivar (BDZ) using the same processing protocol. Untargeted metabolomics was performed using ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (UPLC-HRMS) in positive and negative ion modes, followed by differential-metabolite analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment based on the differential-metabolite list. Antioxidant-related properties were evaluated using ferric-reducing antioxidant power (FRAP), hydroxyl-radical (·OH) scavenging, ABTS radical-cation (ABTS ^•+ ) scavenging, and DPPH radical (DPPH•) scavenging, together with total phenolic content and total flavonoid content. Results: Multivariate analyses showed clear cultivar-dependent separation of global metabolite fingerprints. Positive-ion data highlighted enrichment of amino-acid-related pathways, consistent with higher abundance of 10 annotated amino acids in G2R, whereas negative-ion data emphasized secondary-metabolism pathways centered on flavonoid and phenylpropanoid biosynthesis, accompanied by cultivar-dependent phenolic/flavonoid-related metabolic features. Functionally, G2R exhibited higher FRAP and stronger ·OH scavenging activity than BDZ, together with 10–30% higher total phenolics and total flavonoids, while ABTS ^•+ showed only a small, non-significant difference and DPPH• activities were comparable between cultivars. Conclusion: Under the tested conditions, cultivar background is associated with coordinated amino-acid- and phenolic/flavonoid-related metabolic differences and with assay-specific antioxidant indices, suggesting that integrated metabolomics-antioxidant profiling may be useful for quality-oriented cultivar evaluation within the scope of this two-cultivar study.