Seeds of exotic plants transported with imported goods pose a risk of alien species invasion in cross-border transportation and logistics. It is critical to develop stringent inspection and quarantine protocols with active management to control the import and export accompanied by exotic seeds. As a result, a method for promptly identifying exotic plant seeds is urgently needed. In this study, we built a database containing 3000 images of seeds of 12 invasive plants and proposed an improved YOLOv5 target detection algorithm that incorporates a channel attention mechanism. Given that certain seeds in the same family and genus are very similar in appearance and are thus difficult to differentiate, we improved the size model of the initial anchor box to converge better; moreover, we introduce three attention modules, SENet, CBAM, and ECA-Net, to enhance the extraction of globally important features while suppressing the weakening of irrelevant features, thereby effectively solving the problem of automated inspection of similar species. Experiments on an invasive alien plant seed data set reveal that the improved network model fused with ECA-Net requires only a small increase in parameters when compared to the original YOLOv5 network model and achieved greater classification and detection accuracy without affecting detection speed.

The genus Convallaria (Asparagaceae) comprises three herbaceous perennial species that are widely distributed in the understory of temperate deciduous forests in the Northern Hemisphere. Although Convallaria species have high medicinal and horticultural values, studies related to the phylogenetic analysis of this genus are few. In the present study, we assembled and reported five complete chloroplast (cp) sequences of three Convallaria species (two of C. keiskei Miq., two of C. majalis L., and one of C. montana Raf.) using Illumina paired-end sequencing data. The cp genomes were highly similar in overall size (161,365–162,972 bp), and all consisted of a pair of inverted repeats (IR) regions (29,140–29,486 bp) separated by a large single-copy (LSC) (85,183–85,521 bp) and a small single-copy (SSC) region (17,877–18,502 bp). Each cp genome contained the same 113 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene content, gene order, AT content and IR/SC boundary structure were nearly identical among all of the Convallaria cp genomes. However, their lengths varied due to contraction/expansion at the IR/LSC borders. Simple sequence repeat (SSR) analyses indicated that the richest SSRs are A/T mononucleotides. Three highly variable regions (petA-psbJ, psbI-trnS and ccsA-ndhD) were identified as valuable molecular markers. Phylogenetic analysis of the family Asparagaceae using 48 cp genome sequences supported the monophyly of Convallaria, which formed a sister clade to the genus Rohdea. Our study provides a robust phylogeny of the Asparagaceae family. The complete cp genome sequences will contribute to further studies in the molecular identification, genetic diversity, and phylogeny of Convallaria.

The classification and phylogenetic relationships within the Phaseoleae tribe (Leguminosae) have consistently posed challenges to botanists. This study addresses these taxonomic intricacies, with a specific focus on the Glycininae subtribe, by conducting a comprehensive analysis of the highly conserved plastome in Amphicarpaea edgeworthii Benth., a critical species within this subtribe. Through meticulous genomic sequencing, we identified a plastome size of 148,650 bp, composed of 128 genes, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Comparative genomic analysis across seven Glycininae species illuminated a universally conserved circular and quadripartite structure, with nine genes exhibiting notable nucleotide diversity, signifying a remarkable genomic variability. Phylogenetic reconstruction of 35 Phaseoleae species underscores the affinity of Amphicarpaea with Glycine, placing Apios as a sister lineage to all other Phaseoleae species, excluding Clitorinae and Diocleinae subtribes. Intriguingly, Apios, Butea, Erythrina, and Spatholobus, traditionally clumped together in the Erythrininae subtribe, display paraphyletic divergence, thereby contesting their taxonomic coherence. The pronounced structural differences in the quadripartite boundary genes among taxa with unresolved subtribal affiliations demand a reevaluation of Erythrininae’s taxonomic classification, potentially refining the phylogenetic contours of the tribe.

Background: The cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.Results: We sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from four Cactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations.Conclusion: Our study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics.

Amaranthus, a genus in Amaranthaceae, is divided into three subgenera—Amaranthus, Acnida, and Albersia—and contains approximately 70 to 80 species. Understanding its phylogenetic relationships is essential for species classification, genetic diversity assessment, and evolutionary studies. This knowledge is vital for improving Amaranthus utilization in crop improvement and managing the ecological impacts of invasive weeds. In this study, we analyzed the chloroplast genomes of 27 Amaranthus species across all three subgenera to characterize their genomic features and construct a comprehensive phylogenetic tree. Our aim was to elucidate the phylogenetic relationships within the genus and evaluate interspecific affinities among the subgenera. We also addressed the taxonomic ambiguity surrounding A. bouchonii and A. powellii to determine their distinct species within the genus. Chloroplast genome sizes ranged from 149,949 to 150,818 bp, with GC content varying between 36.52% and 36.63%. Comparative structural analyses confirmed highly conserved quadripartite structures, gene content, and organization, comprising 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat and codon usage analyses revealed conserved repeat patterns and a preference for codons ending in A or U. Selection pressure analysis indicated a predominantly purifying selection, with matK showing signs of positive selection, particularly in A. spinosus. Phylogenetic analysis of 80 protein-coding genes confirmed the monophyly of subgenus Amaranthus but found Alberisa and Acnida to be paraphyletic. Despite their morphological similarity, A. bouchonii and A. powellii were placed in separate clades within subgenus Amaranthus, with A. bouchonii clustering with A. retroflexus, and A. powellii aligning with the A. hybridus complex. Additionally, we identified 16 variable regions as potential molecular markers for species identification. Our study provides the most comprehensive Amaranthus chloroplast genome dataset to date, offering new insights into its evolutionary relationships and valuable genomic resources for taxonomy, germplasm management, and invasive risk assessment.

Introduction: Leonurus japonicus (Chinese motherwort) is a medicinal Lamiaceae species renowned for its pharmacological compounds, yet its mitochondrial genome remains unexplored. Elucidating mitogenomic structure and evolution can inform plant genetics, phylogenetics, and molecular breeding.Methods: We assembled the complete mitochondrial genome of L. japonicus using a combination of Oxford Nanopore long reads and Illumina short reads. Three assembly strategies—de novo assembly with PMAT and Flye, and hybrid assembly with Unicycler—were integrated and validated via read mapping and comparison to reference mitogenomes (Salvia miltiorrhiza, Arabidopsis thaliana, Liriodendron tulipifera). Annotation employed GeSeq, tRNAscan-SE, and manual curation. Repeat elements (SSR, tandem, dispersed) were identified with MISA, TRF, and REPuter; plastid‐to‐mitochondrion transfers (MTPTs) were detected by BLASTN against the assembled plastome; and RNA editing sites were predicted using Deepred-mt. Phylogenetic and synteny analyses were conducted with IQ-TREE, MAFFT alignments of 24 conserved PCGs, and NGenomeSyn visualization.Results: The circular mitogenome spanned 384,199 bp (45.1% GC) and encoded 35 protein-coding genes, 11 tRNAs, and 3 rRNAs. We detected 241 SSRs, 13 tandem repeats, and 90 dispersed repeats, indicating extensive recombination potential. Thirty-one MTPTs totaling 24,818 bp (6.46% of the mitogenome) were identified. Comparative analyses revealed strong purifying selection (Ka/Ks < 1) across most PCGs, with selective signatures in atp4 and ccmB. Phylogenetic inference placed L. japonicus among Lamiales, closely allied to Scutellaria tsinyunensis and Rotheca serrata. Synteny maps demonstrated frequent genome rearrangements. Deepred-mt predicted 408 C-to-U RNA editing sites, notably in nad4 and ccmB, including novel start and stop codons. Discussion: The L. japonicus mitogenome exhibits marked structural plasticity, reflecting dynamic repeats and organelle‐to‐organelle DNA transfers. Extensive RNA editing underscores post-transcriptional regulation in mitochondrial function. These findings enrich genomic resources for Leonurus, support phylogenetic and evolutionary studies in Lamiaceae, and lay groundwork for molecular breeding and conservation strategies targeting mitochondrial traits.