Strawberry (Fragaria × ananassa Duch.) is an important fruit crop in China. Typical crown infection pockets symptoms were observed on the infected strawberry in Liaoning province, China (121°60'E, 38°90'N) in the autumn of 2017. The disease incidence was estimated to be around 5 to 10 %, but could reach 30 to 40 % in some heavily affected plastic tunnels. The infected plants early displayed water-soaked symptoms on the abaxial leaf surface and subsequently developed reddish-brown shaped stripes and coalesced lesions on the adaxial leaf surface around the main veins (Fig. 1-A, 1-B). Several variable-size (0.3-0.8 mm in diameter) pockets were observed inside the crown tissues after dissection (Fig. 1-C). The diseased plants rarely reached fruiting and were easily broken between the crown tissue and the stem, and would eventually die. To identify the causal agent of this disease, the several surface-disinfested infected main veins and crown tissues were individually ground in sterile water and plated on sucrose peptone agar(SPA) medium (Hayward 1960) with 10-fold serial dilutions and incubated at 25℃. A number of yellow colonies grew on the medium at the 10-4 dilution 7 days after plating (Fig. 1-D) in all specimens. The colonies were aerobic, yellow, viscous, smooth, and gram-negative, which is a typical characteristic of Xanthomonas. To confirm identity of the causal bacteria, 18 colonies selected randomly were subjected to polymerase chain reactions (PCR) for the amplification of the cpn60 (Sahin et al. 2010), gyrB, rpoD, and fyuA (C Manceau et al. 2011), respectively. The results showed that the 18 colonies are identical. The cpn60, gyrB, rpoD, and fyuA sequences of this isolate were deposited in GenBank with accession numbers MT513132.1, MW233896, MW233897, and MW233895, respectively. BLAST searches with sequences of this isolate cpn60, gyrB, rpoD, and fyuA revealed 97.7%, 96.4%, 97.8%, and 97.3% similarity with the corresponding sequences of X. fragariae strain NBC2815 (LT853880.1), respectively. The resulting concatenated data set of cpn60-gyrB-rpoD-fyuA was used to build a Multilocus Sequence Analysis (MLSA) by maximum likelihood criteria (Fig. 2). The cpn60-gyrB-rpoD-fyuA sequences of the isolate from Liaoning clustered in the clade containing the type strain of X. fragariae NBC2815, indicating that it belongs to X. fragariae. Thus, the bacterial strain from Liaoning was designated as X. fragariae strain YL19. To fulfill Koch's postulates, the base of leaf petioles of disease-free strawberry plants were syringe-infiltrated inoculated with bacterial suspension (2×108 CFU) prepared from colonies of X. fragariae YL19 washed from SPA plates. The inoculated and control (treated with sterile water) were placed in a chamber (25/20℃day/night,≥90% relative humidity(RH), 12/12 h photoperiod) for three months. After one month, water-soaked symptoms were observed in the crown tissues of all X. fragariae YL19-inoculated plants. Two months after inoculation, a significant crown pocket similarly to initial symptoms observed in the field was developed on all inoculated plants. No symptoms were observed in the control plants. The bacteria were re-isolated from the symptomatic leaves, petioles and crowns, and confirmed as X. fragariae YL19 by the above mentioned morphological and molecular analyses. Pathogenicity tests were conducted three times and the same results were obtained. It was reported that X. fragariae usually causes angular leaf spot, a serious bacterial disease in many strawberry production regions worldwide. The typical symptoms of angular leaf spot caused by X. fragariae include reddish-brown, irregular spots on the upper leaf surface, water-soaked lesions developed along leaf veins. Although angular leaf spot caused by X. fragariae has been reported in Tianjin and Taiwan province, China (Wang et al. 2017; Wu et al. 2020), there is no report about the symptoms that infection pockets on crowns caused by X. fragariae strain YL19 as described above. This result indicated that YL19 is different from the other two X. fragariae strains reported in China or the disease caused by YL19 could be a severe case of angular leaf spot and vascular decline or collapse in strawberry (Bradbury, 1977). . To the best of our knowledge, these results showed a previously unreported new strain YL19 of X. fragariae is the causal agent of crown infecton pocket in strawberry in China, it may lead to serious losses to the local strawberry industry. This report will assist in developing management measures for this disease promptly.

Xanthomonas fragariae (X. fragariae) is the causal agent of angular leaf spots (ALS) in strawberry plants. Recently, a study in China isolated X. fragariae strain YL19, which was observed to cause both typical ALS symptoms and dry cavity rot in strawberry crown tissue; this was the first X. fragariae strain to have both these effects in strawberry. In this study, from 2020 to 2022, we isolated 39 X. fragariae strains from diseased strawberries in different production areas in China. Multilocus sequence typing (MLST) and phylogenetic analysis showed that X. fragariae strain YLX21 was genetically different from YL19 and other strains. Tests indicated that YLX21 and YL19 had different pathogenicities toward strawberry leaves and stem crowns. YLX21 did not cause ALS symptoms, rarely caused dry cavity rot in strawberry crown after wound inoculation, and never caused dry cavity rot after spray inoculation, but it did cause severe ALS symptoms after spray inoculation. However, YL19 caused more severe symptoms in strawberry crowns under both conditions. Moreover, YL19 had a single polar flagellum, while YLX21 had no flagellum. Motility and chemotaxis assays showed that YLX21 had weaker motility than YL19, which may explain why YLX21 tended to multiply in situ within the strawberry leaf rather than migrate to other tissues, causing more severe ALS symptoms and mild crown rot symptoms. Taken together, the new strain YLX21 helped us reveal critical factors underlying the pathogenicity of X. fragariae and the mechanism by which dry cavity rot in strawberry crowns forms.

Xanthomonas fragariae usually causes angular leaf spot (ALS) of strawberry, a serious bacterial disease in many strawberry-producing regions worldwide. Recently, a new strain of X. fragariae (YL19) was isolated from strawberry in China and has been shown to cause dry cavity rot in strawberry crown. In this study, we constructed a green fluorescent protein (GFP)-labeled Xf YL19 (YL19-GFP) to visualize the infection process and pathogen colonization in strawberries. Foliar inoculation of YL19-GFP resulted in the pathogen migrating from the leaves to the crown, whereas dip inoculation of wounded crowns or roots resulted in the migration of bacteria from the crowns or roots to the leaves. These two invasion types both resulted in the systematic spread of YL19-GFP, but inoculation of a wounded crown was more harmful to the strawberry plant than foliar inoculation. Results increased our understanding of the systemic invasion of X. fragariae, and the resultant crown cavity caused by Xf YL19.

Embryo abortion severely limits fruit set and yield stability in longan ( Dimocarpus longan ), yet the upstream physiological triggers and coordinated molecular program remain incompletely defined. Here, we characterized normal seed-forming (NF) and aborted seed-forming (AF) fruits at the critical abortion window by integrating phenotyping, mineral nutrient profiling, embryo-targeted RNA sequencing, and quantitative proteomics, followed by cross-omics association analyses. Orchards with high abortion incidence exhibited markedly low available boron, and aborted embryos displayed a distinctive nutrient-partitioning pattern characterized by severe embryonic boron depletion despite broad changes in other elements. Transcriptome analysis identified 3,865 differentially expressed genes (1,993 upregulated and 1,872 downregulated in AF), with enrichment in pathways related to phenylpropanoid biosynthesis, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, plant hormone signal transduction, and MAPK signaling. Quantitative proteomics revealed 1,518 differentially accumulated proteins (342 increased and 1,176 decreased in AF), highlighting a global trend toward reduced protein abundance in aborted embryos. Integrated transcriptome–proteome analysis detected 374 shared features with strong concordance between mRNA and protein fold changes (93.6% concordant; r = 0.82), reinforcing a coordinated regulatory program at the abortion stage. Across datasets, embryo abortion was associated with disrupted boron-related cell wall processes, altered carbohydrate transport and mobilization, extensive hormone/MAPK rewiring, and pronounced repression of chloroplast-associated programs including photosynthetic light reactions and pigment/tetrapyrrole metabolism, coupled with redox and energy imbalance. qRT-PCR of eight mechanism-anchored candidates supported RNA-seq trends. Together, these results support a model in which embryonic boron depletion and impaired cell wall integrity are associated with, and may contribute to, a cascade of metabolic and signaling reprogramming that culminates in embryo growth arrest and degeneration, providing actionable markers and targets to improve seed development and fruit set in longan.

Aims: Taro corm development depends on carbohydrate metabolism, but cultivar-level annotation differences complicate the integration of genome comparisons and expression data. We assembled a GY2 reference genome and analysed developmental and tissue transcriptomes to characterise corm-associated transcription in a sequence-aware comparative framework. Data resources generated: The 2.309-Gb GY2 assembly contains 14 pseudomolecules and 20,063 primary gene models. Comparisons with LXY and Bun Long were integrated with six-stage corm and four-tissue RNA-seq datasets. Gene annotations, genomic comparisons, processed expression matrices and analysis scripts are supplied in Data S1, with figure source data in Data S2. Key results: The 14 GY2 pseudomolecules represent 98.83% of the assembly; contig and scaffold N50 values are 11.55 and 182.12 Mb, and liliopsid BUSCO completeness is 97.7%. Genome sequence searches reduced candidate assembly-specific orthogroups from 1,820 to 168. A total of 11,884 genes varied significantly across corm stages. Among 593 strictly corm-enriched genes, 522 were also development-responsive, including nine of 20 selected carbohydrate-associated genes. Utility of the resource: Consistent GY2 v3 gene identifiers link genomic homology, collinearity and gene-level expression, supporting cross-cultivar comparisons and prioritisation of corm-associated candidate genes.

Longan ( Dimocarpus longan Lour.) is an economically important fruit tree in tropical and subtropical Asia, yet population-level genomic resources supporting germplasm conservation and breeding remain limited. We resequenced 185 longan accessions and generated a high-density genome-wide SNP dataset for population genomic analyses, including phylogenetic inference, principal component analysis, model-based ancestry estimation, linkage disequilibrium analysis, and genome-wide diversity/differentiation scans. The analyses consistently resolved the panel into four genetic groups, while several accessions showed mixed ancestry, suggesting historical germplasm exchange. Genome-wide diversity and differentiation analyses indicated heterogeneous within-group variation but overall low differentiation among groups, with comparatively greater divergence involving group 4. Linkage disequilibrium decay revealed differences in haplotype structure among groups. A genome-wide scan integrating diversity reduction and elevated differentiation identified a narrow candidate interval on chromosome 11 (17.79–17.98 Mb) showing a localized sweep-like signature. These results provide a population-genomic framework for longan germplasm classification, conservation, and breeding-oriented follow-up.