Shoufu Gong

TGA (TGACG motif-binding factor) proteins are plant-specific group D basic leucine zipper (bZIP) transcription factors that bind as-1/TGACG elements. TGA proteins regulate salicylic acid (SA)-dependent transcription and have context-dependent roles in jasmonic acid (JA)-related defense, growth, development and stress responses. Tea (Camellia sinensis) and oil tea (Camellia oleifera) are Theaceae crops grown for beverages and edible oil, and anthracnose, drought and chilling reduce their yield and quality. Although tea bZIP genes, including group D TGA members, have been cataloged, a comparative, family-wide analysis of TGA genes across representative Theaceae genomes and their cultivar-dependent responses to anthracnose has not been reported. We therefore identified TGA genes genome-wide in six representative Theaceae species: Camellia chekiangoleosa, C. oleifera, C. sinensis, Camellia crapnelliana, Camellia japonica and Stewartia sinensis. Arabidopsis thaliana was included as a reference species. We then examined their phylogeny, gene structure and conserved motifs, codon usage, duplication and collinearity, and promoter cis-elements. Public expression data for 32 TGA genes from C. sinensis, C. oleifera and C. chekiangoleosa were analyzed across tissues and under salt, drought and cold treatments, and a pericarp transcriptome dataset from the resistant ‘MY53’ and susceptible ‘MY01’ C. oleifera genotypes was reanalyzed after inoculation with Colletotrichum fructicola. The survey identified 68 non-redundant TGA genes (10–13 per species), each with intact bZIP and DOG1 domains and predicted nuclear localization. Phylogenetic analysis resolved five groups, and Theaceae members clustered mainly in Groups II and IV, where motif composition and exon–intron structure were conserved. Codon usage bias was weak (effective number of codons: 52–54; codon adaptation index: 0.77–0.80). For 27 within-species paralogous TGA pairs, Ka/Ks distributions remained below 1 (range of 0.046–0.429), and no pair exceeded the Ks > 2 saturation criterion, indicating purifying selection. In the current duplication classification, 6–11 of the 10–13 TGA genes per species were assigned to WGD- or segmental-duplication classes, but family sizes remained similar to A. thaliana (10 genes); the data therefore do not indicate substantial net family expansion. Promoters were enriched in cis-elements responsive to light, JA, SA and abscisic acid (ABA). Expression varied between tissues, and several genes were enriched in fruit and leaves. Salt, drought and cold each induced a subset of TGA genes. The 12 ColeTGA genes resolved into four cultivar-dependent expression patterns; ColeTGA3 and ColeTGA2 showed stronger increases in the resistant ‘MY53’ genotype, whereas ColeTGA7 increased in both genotypes. Together, these comparisons clarify how TGA genes have been conserved and how they diverged among the six sampled Theaceae species.

For Fragaria (strawberry) species, individual chromosome identification is challenging due to the small size of chromosomes; consequently, the chromosome numbers of most cultivars remain unreported. In this study, we investigated the ploidy of 26 strawberry cultivars by counting root-tip chromosomes. Surprisingly, 25 cultivars were octoploid (2n = 8x = 56), whereas only ‘Tokun’ was aneuploid (2n = 10x − 3 = 67). To explore the breeding potential of this aneuploid, we performed reciprocal crosses between ‘Tokun’ and ‘Benihoppe’, a widely cultivated octoploid cultivar. Only the combination with ‘Benihoppe’ as female and ‘Tokun’ as male produced fertile progenies. The progenies had variable chromosome numbers of 61, 62 or 63, meaning that ‘Tokun’ produced aneuploid gametes with varying chromosome numbers ranging from 33 to 35. Some hybrids exhibited superior aroma, firmness, or soluble solids compared with their parents. Specifically, J2138 (2n = 9x − 2 = 61) was selected for its larger single-fruit weight, J2139 (2n = 9x − 2 = 61) and J2153 (2n = 9x − 2 = 61) for their white flesh, and J2151 (2n = 9x − 1 = 62) and J2156 (2n = 9x = 63) for their soluble solids content exceeding that of the higher parent, showing potential value for commercial production and breeding. Strawberry is usually propagated via stolons or through tissue culture; therefore, aneuploids obtained from 8x × aneuploid ‘Tokun’ crosses would be good sources for cultivar breeding.

Salt stress restricts tea production by causing Na⁺ accumulation in leaves, disrupting K⁺ homeostasis, and elevating ROS levels. In Camellia, the CHX genes that may counteract these effects remain poorly defined. Using a 14-genome panel, we identified 436 CHX genes and grouped them into 26 orthologous gene groups (OGGs), including 18 core, 2 soft-core, and 6 shell. A tea-only reference captured only part of this structure; three OGGs present in 7-12 genomes were absent from tea. At the family level, dispersed and tandem duplications were the most frequent duplication classes, whereas soft-core and shell genes showed distinct duplication profiles. Among 377 high-confidence gene pairs, 98.4% had Ka/Ks values below 1, indicating that purifying selection predominates across the family. Unexpectedly, core pairs had higher Ka/Ks values than dispensable pairs. Expression analysis showed that most CHX genes were expressed at low levels across tissues. Salt treatment induced six low-abundance genes, and qRT-PCR highlighted CsCHX.CR008, CsCHX.CR012, CsCHX.SH006, and CsCHX.CR017 as priority candidates for salt-tolerance studies. Collectively, this pan-genome-scale study establishes an evolutionary framework for the CHX family in the genus Camellia, showing that duplication, presence–absence variation, copy-number variation, and conservation class are associated with distinct salt-responsive expression patterns. These findings provide genomic resources and valuable insights for dissecting CHX function and supporting future breeding efforts toward improved salt tolerance in Camellia.

TGA (TGACG motif-binding factor) proteins are plant-specific group D basic leucine zipper (bZIP) transcription factors that bind as-1/TGACG elements. They integrate jasmonic acid (JA) and salicylic acid (SA) signaling with growth, development and stress responses. Tea (Camellia sinensis) and oil tea (Camellia oleifera) are Theaceae crops grown for beverages and edible oil, and anthracnose, drought and chilling reduce their yield and quality. TGA genes had not been characterized in either crop. We therefore identified TGA genes ge-nome-wide in six representative Theaceae species: Camellia chekiangoleosa, C. oleifera, C. sinensis, Camellia crapnelliana, Camellia japonica and Stewartia sinensis. We then examined their phylogeny, gene structure and conserved motifs, codon usage, duplication and col-linearity, and promoter cis-elements. Transcriptome data and qRT-PCR provided expres-sion evidence for C. oleifera TGA (ColeTGA) genes after inoculation with Colletotrichum fruc-ticola. The survey yielded 68 non-redundant TGA genes, 10 to 13 per species, each with in-tact bZIP and DOG1 domains and a predicted nuclear localization. Phylogenetic analysis resolved five groups, and Theaceae members clustered mainly in Groups II and IV, where motif composition and exon–intron structure were conserved. Codon usage bias was weak (effective number of codons 52–54; codon adaptation index 0.77–0.80). The mean Ka/Ks was 0.25, indicating purifying selection. Whole-genome and segmental duplication drove most family expansion (60–91.67%), while tandem duplication was rare. Promoters were enriched in cis-elements responsive to light, JA, SA and abscisic acid (ABA). Expres-sion varied among tissues, and several genes were enriched in fruit and leaves. Salt, drought and cold each induced subsets of TGA genes. After inoculation with C. fructicola, the 12 ColeTGA genes showed four expression patterns. ColeTGA2, ColeTGA3, ColeTGA4, ColeTGA6, ColeTGA10 and ColeTGA12 were strongly activated. Together, these compari-sons clarify how TGA genes have been conserved and how they diverged among Theaceae lineages. They also identify candidates for functional tests of anthracnose resistance and for stress-tolerance breeding in tea and oil tea.

To comprehensively evaluate 212 tomato accessions and gain an in-depth understanding of their genetic background, 17 major agronomic traits were assessed, and whole-genome resequencing was performed on all materials. The results indicated that the genetic diversity of quantitative traits was abundant, with the genetic diversity index (H′) ranging from 0.79 to 2.03. In contrast, the genetic diversity of qualitative traits was relatively low, with the H′ falling between 0.363 and 0.936. The relationships between phenotypes were intricate and characterized by information redundancy. The top five principal components captured 69.014% of the phenotypic information. The F and D score-based comprehensive evaluation methods demonstrated strong consistency (r = 0.955 **). Among the 17 accessions ranked in the top 20 by both scores, 12 belonged to the large-fruit yellowish late-ripening type with distinct genetic backgrounds. These preliminary efforts not only provide an idea, a framework and a dataset for the integrated analysis of phenotypic evaluation, phenotypic clustering and population structure, but also lay a foundation for future inter-data network research, as well as potential material support for subsequent breeding efforts.

Accurate recognition of the canopy is a prerequisite for precision orchard yield estimation. This paper proposed an enhanced LA-dpv3+ approach for the recognition of cherry canopies based on UAV image data, with a focus on enhancing feature representation through the implementation of an attention mechanism. The attention mechanism module was introduced to the encoder stage of the DeepLabV3+ architecture, which improved the network’s detection accuracy and robustness. Specifically, we developed a diagonal discrete cosine transform feature strategy within the attention convolution module to extract finer details of canopy information from multiple frequency components. The proposed model was constructed based on a lightweight DeepLabv3+ network architecture that incorporates a MobileNetv2 backbone, effectively reducing computational costs. The results demonstrate that our proposed method achieved a balance between computational cost and the quality of results when compared to competing approaches. Our model’s accuracy exceeded 89% while maintaining a modest model size of only 46.8 MB. The overall performance indicated that with the help of a neural network, segmentation failures were notably reduced, particularly in high-density weed conditions, resulting in significant increases in accuracy (ACC), F1-score, and intersection over union (IOU), which were increased by 5.44, 3.39, and 8.62%, respectively. The method proposed in this paper may be applied to future image-based applications and contribute to automated orchard management.

Jacobaea maritima is an important horticulture plant in the genus Jacobaea. Here, we assembled the complete chloroplast genome of J. maritima. The chloroplast genome was 153,857 bp in length, with a pair of inverted repeat regions (IRs) (27,936 bp) separated by a large single-copy region (LSC) (82,771 bp) and a small single-copy region (SSC) (15,214 bp). The complete chloroplast genome contained 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis showed Jacobaea was more closely related to Senecio, Crassocephalum and Gynura. The chloroplast genome of J. maritima can provide data to support future phylogenetic studies of Jacobaea.

Gardenia jasminoides , belonging to the Rubiaceae family, is widely distributed and planted in China. It has traditionally been used as an ornamental and medicinal plant in several Asian countries. The rapid development of high-throughput sequencing technology makes it feasible to obtain complete chloroplast (cp) genome sequences and will deepen our understanding of evolution of G. jasminoides . In this study, we sequenced the complete cp genomes of two botanical varieties of G. jasminoides . The complete cp genomes of both botanical varieties of G. jasminoides showed highly conserved structures and the length was 154,954 base pairs (bp) for G. jasminoides var. radicans (GJR) and 155,098 bp for G. jasminoides var. grandiflora (GJG). A total of 132 and 133 genes were identified in GJR and GJG, respectively. The cp genomes of two newly sequenced G. jasminoides were further compared with two published G. jasminoides cp genomes. Multiple repeats and simple sequence repeats (SSRs) were detected among different genotypes of G. jasminoides . The intron sequences of rps16 and rpl16 genes were slightly divergent among four genotypes of G. jasminoides . Phylogenetic analyses based on the complete cp genome sequences showed that G. jasminoides was closely associated with Fosbergia shweliensis , with Coffea as their close relative. Taken together, the complete cp genomes of GJG and GJR provided significant insights and important information that can be used to identify related species and reconstruct their phylogeny.