Ramie (Boehmeria nivea), native to China, is an economically important natural fiber-producing crop (Angelini and Tavarini 2013). In May 2025, leaf blight was observed on 20% cultivated ramie seedlings in a 5-ha field, Dazhou city (30°51′36″N, 107°19′48″E), Sichuan province, China. Leaf tissues adjacent to and including lesions were superficially disinfected with 70% ethanol for 20 s and 1% Sodium hypochlorite for 40 s, washed, dried, placed on PDA amended with streptomycin sulfate (50 mg/L) in dark at 25 ℃. Finally, three purified isolates, named B3, B6, and B26, showing similar morphology were obtained by transferring hyphal tips to fresh PDA plates. Cultured on PDA for 14 days, fungal colonies displayed gray aerial mycelia, with underside becoming slightly grayish-white. 28 days later, the circular colonies transitioned to grayish-white and soft texture with brownish-white underside. Colonies produced abundant solitary or catenate conidia. Conidia were pyriform, ovate or elliptical, with one to four transverse and zero to two longitudinal septa, and measured 20.6 to 48.7 × 19.0 to 8.5 µm (n = 50). The morphological characteristics of our isolates match those of Alternaria species (Li et al. 2023; Woudenberg et al. 2013). Our isolates were further identified by sequencing rDNA internal transcribed spacer regions (ITS) , anonymous region OPA10-2 genomic sequence (OPA10-2), and gene fragments of translation elongation factor 1-alpha (TEF1), endopolygalacturonase (endoPG), major allergen Alt a1 (Alt a1), RNA polymerase II second largest subunit (RPB2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and large subunit (LSU) and small subunit (SSU) ribosomal RNA, using primer pairs ITS1/ITS4, OPA 10-2R/OPA 10-2L, TEF1-728F/TEF1-986R, PG3/PG2b, Alt-F/Alt-R (Romain et al. 2021), RPB2-5F/RPB2-7cR, gpd1/gpd2 (Luo et al. 2022), LSU-F/LSU-R and SSU-F/SSU-R respectively. BLASTN searches indicated our ITS (PX069539 - PX069541), OPA10-2 (PX092332 - PX092334), TEF1 (PX092323 - PX092325), endoPG (PX092326 - PX092328), Alt a1 (PX092320 - PX092322), RPB2 (PX092335 - PX092337), GAPDH (PX092329 - PX092331), LSU (PX070146 - PX070148), and SSU (PX070153 - PX070155) sequences showed 99.34 ~ 100% and 99.68 ~ 100% identity to the corresponding sequences of A. alternata CBS 121456 (KP124369, KP124682, KP125147, KP124073, KP123917, KP124839, KP124221, KP124523, KP124993) and CBS 795.72 (KP124309, KP124616, KP125085, KP124009, KP123862, KP124778, KP124166, KP124461, KP124931), respectively. Based on combination of the nine DNA sequences, our phylogenetic tree of Alternaria species confirmed that three isolates were A. alternata. To test pathogenicity, 2 ~ 3 leaves of ramie seedlings were sprayed with conidial suspension (1 × 105 conidia/mL) of isolate B6, with controls treated using sterile dH2O. Each treatment, including 3 seedlings, was incubated in a greenhouse (at 25°C and 90% relative humidity, 12/12 h light/dark cycle). Leaf blight appeared on infected leaves after 15 days’ inoculation, while controls remained disease-free. The experiment was repeated five times, showing consistent disease symptoms. Koch's postulates were fulfilled by re-isolation of A. alternata from diseased leaves, based on morphology and molecular methods described above. To our knowledge, this is the first report of A. alternata causing leaf blight of ramie worldwide. Our study will provide a basis for developing targeted disease management strategies in ramie.

Ramie (Boehmeria nivea), native to China, is a natural fiber-yielding crop. The ramie fibers are long, pure white in color, silky in texture, and highly durable and hygroscopic (Angelini and Tavarini 2013). In May 2025, anthracnose symptoms were observed on 10% of cultivated ramie plants in a 10-ha field, Dazhou City (30.86°N, 107.33°E), Sichuan Province, China. Leaf tissues adjacent to and including lesions were excised, superficially disinfected with 70% ethanol for 20 s and 1% NaClO for 40 s, and washed with sterile distilled water at least five times. The disinfected tissues were incubated on PDA amended with streptomycin sulfate (50 mg/L) in the dark at 25 ℃. Two or three days later, hyphal tips from the edges of growing colonies were transferred to fresh PDA plates. Three representative isolates, G21, G22, and G23, showed identical morphological characteristics. The colonies exhibited cottony aerial mycelia on SNA plates. The upper and lower surfaces of mycelia were initially grayish-white and gradually became brownish-white. Setae were observed on the hyphae. Asci were 60.5 ± 5.4 × 13.7 ± 1.5 µm in size (n = 20), eight-spored, fasciculate, and clavate. Ascospores were 24.2 ± 3.6 × 5.1 ± 0.7 µm in size (n = 30) and slightly curved with obtuse to slightly rounded ends. Meanwhile, colonies produced abundant conidia, which were unicellular, hyaline, aseptate, smooth-walled, straight, cylindrical and rounded at both ends, measuring 18.1 ± 1.5 × 5.5 ± 1.2 µm (n = 30). These morphological characteristics match those of Colletotrichum species (Liu et al. 2022; Xue et al. 2020). Three isolates were properly preserved in our lab. All the isolates were further identified by sequencing rDNA internal transcribed spacer (ITS) regions, actin (ACT), beta-tubulin (TUB2), histone3 (HIS), chitin synthase (CHS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes, using primer pairs ITS1/ITS4, ACT-512F/ACT-783R, T1/Bt2b, CYLH3F/CYLH3R, CHS-79F/CHS-345R and GDF1/GDR1 (Liu et al. 2022), respectively. BLASTn searches indicated our ITS (PX090878-PX090880), ACT (PX092338-PX092340), TUB2 (PX092341-PX092343), HIS (PX092350-PX092352), CHS (PX092344-PX092346) and GAPDH (PX092347-PX092349) sequences showed 99.48-100% identity to the corresponding sequences of C. reniforme LC8230 (MZ595847.1, MZ664145.1, MZ673968.1, MZ673867.1, MZ799290.1, and MZ664110.1). Based on concatenated ITS, ACT, TUB2, HIS, CHS, and GAPDH sequences, the constructed phylogenetic tree of Colletotrichum species confirmed that our isolates were C. reniforme. In the pathogenicity test, healthy leaves of ramie seedlings were sprayed with conidial suspension (1 × 105 conidia/mL) of G21, with controls treated with sterile dH2O. Each treatment was incubated in a greenhouse (at 25°C under 90% relative humidity and a 12/12 h light/dark cycle). The experiment was repeated three times. Ten days after inoculation, anthracnose symptoms appeared on inoculated leaves, while controls remained healthy. Koch's postulates were fulfilled by re-isolation of C. reniforme from diseased leaves, based on morphology and molecular methods described above. C. gloeosporioides (Wang et al. 2010) and C. higginsianum (Wang et al. 2011) were previously reported as causal agents of anthracnose on ramie. To our knowledge, this is the first report of C. reniforme causing anthracnose of ramie worldwide. Our study will assist in monitoring the diversity of infectious agents causing ramie anthracnose in China.

Daylily (Hemerocallis citrina) is widely cultivated in China as vegetable and medicine. Its flower buds are nutritious vegetables rich in ascorbic acid, mineral elements and et al (Wang et al. 2024). Whereas, little is known about the pathogen identification in daylily. In April 2023, leaf spot symptoms were observed on 20% daylily seedlings in Dazhou city (30.91° N, 106.87° E), Sichuan province, China. The symptomatic leaves were superficially disinfected with 70% ethanol for 20 s, rinsed twice in sterile dH2O and subsequently disinfected with 1% NaClO for 40 s, and rinsed twice in sterile dH2O again. The disinfected leaves were cut into pieces (5 × 5 mm), placed on PDA amended with streptomycin sulfate (50 mg/L), and incubated in dark at 25 ℃ for two days. The fungal isolates, displaying morphological features of Fusarium species (Leslie and Summerell 2006), were purified through transferring single spores. Consequently, two distinct type fungal isolates were obtained. Cultured on PDA, Type Ⅰ (Q22, Q26, Q27) and Type Ⅱ (Q29, Q29-1) isolates showed similar growth phenotypes. Type Ⅰ and Ⅱ isolates’ cultures were initially white but gradually became yellow, and scarlet diffusible pigments were produced with time (Fig. S1). On SNA medium, Type Ⅰ isolates produced macroconidia with 3 to 6 septa, which measured 5.56±0.54 × 48.65±6.12 µm (n = 50). While, Type Ⅱ isolates’ macroconidia contained 3 to 11 septa that measured 4.08±0.93 × 51.40±12.83 µm (n = 50) (Fig. S1). All the isolates were properly preserved in our lab. To further identify these isolates, DNA fragments of Beta-tubulin (TUB2) (Glass and Donaldson 1995), translation elongation factor-1 alpha (TEF1) (Rehner and Buckley 2005), and DNA-directed RNA polymerase II largest (RPB1) (Hofstetter et al. 2007) and second largest subunit (RPB2) (O'Donnell et al. 2012) were amplified and sequenced. BLASTN analyses of TUB2 (PP266396 ~ PP266398), TEF1 (PP404039 ~ PP404041), RPB1 (PP404042 ~ PP404044) and RPB2 (PP408000 ~ PP408002) of Type Ⅰ isolates showed 99.35 ~ 100% identity to those of F. asiaticum NRRL 13818 (AF212745.1, MW233069.1, MW233240.1, JX171573.1). Type Ⅱ isolates’ sequences (PP408003 ~ PP408010) showed their homology with those of F. meridionale NRRL 28436 (AF212730.1, MW233092.1, MW233263.1, MW233435.1) at 100% identity. The phylogenetic tree based on combined datasets of TUB2, TEF1, RPB1 and RPB2 of Fusarium species confirmed that Type Ⅰ and Ⅱ isolates were F. asiaticum and F. meridionale, respectively (Fig. S2). Seedlings of cultivar “chuanhuanghua No.1” (n = 5) in a greenhouse (25°C, relative humidity 90%) were inoculated with conidial suspension (3 × 105 conidia / mL). Controls were treated with sterile dH2O. Fifteen days post-inoculation, natural symptoms appeared on inoculated leaves (Fig. S3). Whereas, non-inoculated controls were disease-free. The pathogenicity assay was repeated three times. F. asiaticum and F. meridionale were successfully re-isolated from diseased leaves and verified using morphological and molecular methods described above, fulfilling Koch’s postulates. F. ussurianum, a Fusarium graminearum species complex (FGSC) member, and F. proliferatum were identified as causal agents of leaf spot on daylily in China (Chen et al. 2024; Li et al. 2018). To our knowledge, this is the first report of F. asiaticum and F. meridionale causing leaf spot on daylily worldwide. Our studies demonstrate that FGSC members are the common pathogens causing leaf spot on daylily in Sichuan, China.

Hemerocallis citrina is a popular vegetable crop. Its eatable flower buds contain abundant nutrients, especially lecithin (Guo et al., 2022). In March 2021, leaf spot disease was observed on 90% cultivated H. citrina seedlings in Dazhou city (31°17'56″ N, 107°31'59″ E), Sichuan, China. Totally, 15 diseased seedlings were sampled (three samples per 666 m2). The symptomatic leaves were cut into pieces (5 × 3 mm), superficially disinfected with 70% ethanol for 20 s and 1% Sodium hypochlorite (NaClO) for 40 s, and washed with sterile distilled water six times. The disinfected tissues were incubated on PDA amended with streptomycin sulfate (50 mg/L) in dark at 25 ℃. Two days later, hyphal tips from the edges of growing colonies were transferred to fresh PDA plates. Finally, 40 purified isolates were obtained. Using primer pairs ITS1/ITS4 (Glass & Donaldson, 1995), amplified rDNA internal transcribed spacer (ITS) regions indicated that these isolates belonged to different genera, mainly including Epicoccum, Fusarium and Colletotrichum. Six isolates of Epicoccum genus similar in morphology, named HHC46, HHC47, HHC491, HHC492, HHC51 and HHC58, were selected for identification. Cultured on oatmeal agar for 7 days, colonies were initially white and villose. Fourteen days later, mycelia started to secrete scarlet pigment. The NaOH spot test showed color changed from green to red, identical to that in Epicoccum species (Boerema et al., 2004). Meanwhile, colonies produced abundant conidia. Conidia were ellipsoidal, aseptate, and 4.1 to 6.5 × 1.3 to 2.9 µm (n = 30). Chlamydospores were also observed, globose to subglobose. The morphological features were similar to those of Epicoccum latusicollum (Xu et al., 2022). The DNA sequences of Beta-tubulin (TUB2) and DNA-directed RNA polymerase II second largest subunit (RPB2) of six isolates were amplified and sequenced, using primer pairs Bt2a/Bt2b (Glass & Donaldson, 1995), and RPB2-5f2/RPB2-7cr (O'Donnell et al., 2012), respectively. BLASTN searches indicated our ITS (OP107240 - OP107245), TUB2 (OP131865 - OP131870) and RPB2 (OP131871 - OP131876) sequences except one TUB2 (OP131867), showed 100% identity to the corresponding sequences of E. latusicollum CGMCC:3.18346 (KY742101, KY742343 and KY742174, respectively). There was a nucleotide divergence between OP131867 and reference sequence. Based on concatenated ITS, TUB2 and RPB2 sequences, the constructed phylogenetic tree of Epicoccum species, confirmed that our isolates were E. latusicollum. To test pathogenicity, 2-year-old healthy seedlings of cultivar "chuanhuanghua No.1" were sprayed with conidial suspension of HHC51 (105 conidia/mL), with controls treated with sterile distilled water. Each treatment (biological replicates = 3) was incubated in a greenhouse (at 25°C under 90% relative humidity, 16/8 h light/dark cycle). The experiment was repeated twice. After 18 days, leaf spot symptom in inoculated seedlings appeared. Whereas, non-inoculated controls showed no symptom. The pathogens were re-isolated from diseased leaves and identified as E. latusicollum, based on morphology and molecular methods described above. E. sorghinum was previously reported as causal agent of leaf spot in H. citrina (Ma et al., 2021). To our knowledge, this is the first report of E. latusicollum causing leaf spot in H. citrina worldwide. Our study will assist with monitoring disease distribution in H. citrina and host diversity of E. latusicollum (Chen et al., 2017).

Ascorbate peroxidase (APX) plays a key role in scavenging reactive oxygen species (ROS) in higher plants. However, there is very little information available on the APXs in kiwifruit (Actinidia), which is an economically and nutritionally important horticultural crop with exceptionally high ascorbic acid (AsA) accumulation. This study aims to identify and characterize two cytosolic APX genes (AcAPX1 and AcAPX2) derived from A. chinensis 'Hongyang'. The constitutive expression pattern was determined for both AcAPX1 and AcAPX2, and showed relatively higher expression abundances of AcAPX1 in leaf and AcAPX2 in root. Transcript levels of AcAPX1 and AcAPX2 were increased in kiwifruit roots treated with NaCl. Subcellular localization assays using GFP-fusion proteins in Arabidopsis protoplasts showed that both AcAPX1 and AcAPX2 are targeted to the cytosol. Recombinant AcAPX1 or AcAPX2 proteins were successfully expressed in the prokaryotic expression system and their individual ascorbate peroxidase activities were determined. Finally, constitutive over-expression of AcAPX1 or AcAPX2 could dramatically increase total AsA, glutathione level and salinity tolerance under NaCl stress in Arabidopsis thaliana. Our findings revealed that cytosolic AcAPX1/2 may play an important protective role in the responses to unfavorable environmental stimuli in kiwifruit.

The genus Actinidia, also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual Actinidia species' relationships, which need further revision through more accurate approaches. Compared to the nuclear genome, the chloroplast genome has simple heredity characteristics, conserved genome structure and small size, suitable for deciphering complicated species' phylogenetic relationships. Here, the genome-wide comprehensive comparative analyses were performed over 29 independent chloroplast genomes' sequences derived from 25 Actinidia taxa. The average genome size is 156,673.38 bp, with an average 37.20% GC content. The long repeat sequences rather than SSRs (simple sequence repeats) in Actinidia were revealed to be the causal agent leading to the chloroplast genome size expansion. The clpP gene sequences with exon merge and intron deletion were annotated in all the 29 chloroplast genomes tested, which has been previously reported to be lost in Actinidia species. Comprehensive sequence analyses indicated the distinct variation at the clpP gene locus was Actinidiaceae-specific, emerging after the Actinidiaceae-other Ericales species divergence. Four highly divergent sequences (i.e., rps16 ~ trnQ-UUG, rps4 ~ trnT-UGU, petA ~ psbJ, and rps12 ~ psbB) evolved in the LSC (large single-copy) and SSC (small single-copy) regions embodying rps12 ~ psbB (including clpP gene and its up/downstream noncoding sequence) were identified as variation hot spots in Actinidia species. Based on either LSC region alone, combined sequences of LSC and SSC or the whole chloroplast genome sequences, three identical phylogenetic trees of the 25 Actinidia taxa with relatively improved resolution were reconstructed, consistently supporting the reticulate evolutionary lineage in Actinidia. Our findings could help to better understand the evolution characteristics of chloroplast genomes and phylogenetic relationships among Actinidia species.

WRKY转录因子参与调控植物生长发育和多种胁迫应答,是一类非常重要的植物转录因子.为解析藜麦WRKY基因的进化特征及挖掘响应胁迫的WRKY基因,本研究利用系统的生物信息学方法在全基因组水平对WRKY基因进行了鉴定,并对其染色体定位、分组、系统进化、共线性分析以及多胁迫条件下的表达模式进行了分析.藜麦基因组中鉴定得到90个WRKY基因;划分为3组:Ⅰ组(18个)、Ⅱ组(46个)和Ⅲ组(12个),其中Ⅱ组成员进一步被划分为5个亚组:Ⅱ-a(9个),Ⅱ-b(4个),Ⅱ-c(13个),Ⅱ-d(10个)和Ⅱ-e(10个).另外,14个WRKY成员因为WRKYGQK短肽的缺失,以及锌指结构变异较大而未划分到任何分组.本研究分组与藜麦WRKY基因进化树中家族成员的聚类结果完全一致,进一步支持了成员分组的可靠性.此外,不同分组的WRKY成员的蛋白序列呈现出小组特异的氨基酸保守域组成.藜麦和祖先二倍体苍白茎藜、瑞典藜的同源基因组模块分析表明,藜麦WRKY基因数目的增加主要来自全基因组倍增.在干旱、高温、盐、低磷胁迫和花生褪绿扇形斑病毒(GCFSV)侵染下,大量WRKY基因的表达水平被显著性诱导或抑制,说明这些WRKY基因很可能参与了调控藜麦的逆境应答反应.研究结果可为藜麦的抗逆研究提供优良的候选WRKY基因,为藜麦的抗逆研究提供参考依据.

In this study, we describe a multiplex PCR method for the detection of five food-relevant virulence pathogenicity genes of intestinal pathogens. Five pairs of primers were designed based on nuc gene for Staphylococcus aureus, hlyA gene of Listeria monocytogenes, ipaH gene of Shigella flexneri, lysP gene of Yersinia enterocolitica and tpi gene of Clostridium difficile. Conditions were optimized to amplify fragments of those genes simultaneously in one PCR amplification. After developing and optimizing the multiplex PCR reaction system, the specificity and sensitivity of the multiple PCR assays were evaluated. The optimized program is also applied to retail meat for testing. The result indicated that when the annealing temperature was 54 °C and the primer concentrations of S. aureus, L. monocytogenes, S. flexneri, Y. enterocolitica and C. difficile are 10, 10, 5, 3 and 2 μM, the five strains could expand 484, 345, 204, 156, 88 bp of clear fragments, respectively. So was the multiple PCR in artificially contaminated beef produce. All cultures were cultured and separated by traditional methods. The multiplex PCR method offers a rapid, simple, and accurate identification of pathogens and could be used in food safety investigations, clinical diagnosis as well as for the surveillance of the spreading determinants of pathogens in epidemiological studies.

Elytrigia repens (L.) Nevski, belonging to Triticeae of Poaceae, is a wild-growing perennial grass, widely distributed in Qinghai-Tibetan Plateau of China. In this study, the complete chloroplast genome of E. repens was sequenced and analyzed. The complete chloroplast genome size is 134,749 bp with 38.3% GC content. It includes 136 genes, including 89 protein-coding genes, 39 tRNAs genes, and 8 rRNAs genes. Based on chloroplast genome sequences, further phylogenetic analyses between E. repens and other Triticeae species revealed that E. repens, Connorochloa tenuis and three Elymus species formed a distinct clade, showing closer relationships.

万寿菊(Tagetes erecta L.)中含有类胡萝卜素,不仅可用于天然色素提取,还是研究类胡萝卜素合成代谢的植物材料.番茄红素β-环化酶(lycopene beta cyclase,LCYB)是类胡萝卜素合成代谢途径中的一个关键酶,文章通过对万寿菊中TeLCYB基因克隆、植物表达载体构建、并利用农杆菌介导法进行番茄遗传转化,获取TeLCYB基因转化番茄植株.分子鉴定和表型分析结果表明,万寿菊TeLCYB基因在番茄中表达,并改变转基因番茄果实颜色.高效液相色谱测定显示,TeLCYB基因的表达显著增加了番茄果实中β-胡萝卜素的量.该文研究结果表明TeLCYB基因具有功能活性,可用于改良植物果实的色素营养品质.

WRKY是植物中一类重要的转录因子,广泛调控了植物的生长发育和逆境胁迫应答.基于青稞白粉病侵染幼苗的转录组测序数据,本研究鉴定得到41个青稞WRKY转录因子,被划分为3个大组:Ⅰ组(6个)、Ⅱ组(21个)和Ⅲ组(12个).另外,HvWRKY40和HvWRKY41没有分组.青稞WRKY基因进化分析的聚类结果和分组结果一致,进一步支持了我们分组的正确性.包括HvWRKY2、HvWRKY8、HvWRKY13、HvWRKY34和HvWRKY41,以及HvWRKY4、HvWRKY7、HvWRKY20、HvWRKY26和HvWRKY30在内的两组WRKY基因,表现出明显的先升高(36 h和72 h),后降低(168 h)的基因表达趋势.这些WRKY基因很可能参与了调控青稞抗白粉病的分子应答机制.青稞WRKY家族的蛋白相互作用网络中,HvWRKY3、HvWR-KY8、HvWRKY9属于网络中的主要中心节点.此外,HvWRKY3、HvWRKY8、HvWRKY9、HvWRKY30、Hv-WRKY34、HvWRKY38、HvWRKY39彼此之间相互作用,是蛋白互作网络的核心网络.本研究挖掘了青稞的WRKY家族成员,系统分析了家族成员的分组、家族成员的WRKY保守域特点、家族成员之间的进化关系、白粉菌侵染下的基因表达水平和家族成员的蛋白互作网络.本研究可为今后青稞的抗逆研究提供优良的候选WRKY基因.

Hsf转录因子参与调控植物在生物和非生物胁迫下的防御应答机制.基于系统的生物信息学分析方法,对藜麦Hsf家族成员进行序列特征、进化和多种生物和非生物逆境胁迫下的基因表达水平分析.在藜麦基因组中共鉴定得到31个Hsf转录因子,主要分布在7号染色体.系统进化树将藜麦31个Hsf成员划分到A1-A9、B1-B5和C组中;但藜麦Hsf成员在A6、A8、B5亚组中出现了缺失.藜麦Hsf成员的HR-A/B区域蛋白序列比对结果进一步支持了进化树中藜麦Hsf成员的聚类结果.藜麦Hsf成员蛋白序列中保守区域的分布呈现出组别特异性.A组Hsf成员的蛋白序列包括HSF domain、HR-A/B,NLS、NES和CTAD在内的保守区域;B组和C组的Hsf成员则缺失了CTAD.在干旱、高温、盐、低磷胁迫和GCFSV病毒侵染下,31个藜麦Hsf基因的表达模式被阐明;其中大量Hsf基因的表达水平被显著地诱导表达,推测其参与了藜麦在生物和非生物胁迫下的防御应答反应.本研究结果可为藜麦抗逆品种的遗传育种提供大量优良候选Hsf基因.

Kiwifruit (Actinidia spp.) plants produce economically important fruits containing abundant, balanced phytonutrients with extraordinarily high vitamin C contents. Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species. To efficiently store, analyze, integrate, and disseminate these large-scale datasets to the research community, we constructed the Kiwifruit Genome Database (KGD; http://kiwifruitgenome.org/). The database currently contains all publicly available genome and gene sequences, gene annotations, biochemical pathways, transcriptome profiles derived from public RNA-Seq datasets, and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies. A set of user-friendly query interfaces, analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit, which include JBrowse, a popular genome browser, and the NCBI BLAST sequence search tool. Other notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology (GO) term and pathway enrichment analysis.

bZIP转录因子调控着植物的生长发育和逆境胁迫应答,是植物中一类重要的转录因子.基于系统的生物信息学方法,鉴定得到79个中华猕猴桃bZIP转录因子,进化分析结果揭示中华猕猴桃bZIP家族成员在J、K、L三个分组中出现了成员的缺失.中华猕猴桃bZIP家族成员的bZIP保守域主要由碱性结构域和亮氨酸拉链结构域组成,其亮氨酸拉链结构域的第4、5肽段的第7位的亮氨酸残基存在一定程度的变异.bZIP保守域之外,在中华猕猴桃的18个bZIP家族成员中,还发现包括bZIP_ C保守域在内的8种其他类型的保守域,集中分布在A、C、D和G组bZIP成员中.通过与葡萄和番茄bZIP同源基因的比较,阐明中华猕猴桃基因组的两次三倍倍增是其bZIP基因数目增加的主要原因.中华猕猴桃不同发育时期果实的转录组揭示了参与调控果实成熟的57个bZIP基因的表达水平.本研究阐明了中华猕猴桃bZIP家族成员的进化特征、保守域组成、家族成员数目扩增的主要原因,提供了涉及果实发育的优良候选基因.

Penicillium expansum is a destructive phytopathogen causing postharvest decay on many stored fruits. To develop effective and safe management strategies, it is important to investigate its pathogenicity-related mechanisms. In this study, a bioinformatic pipeline was constructed and 50 core effector genes were identified in P. expansum using multiple RNA-seq data sets and their putative functions were implicated by comparatively homologous analyses using pathogen–host interaction database. To functionally characterize P. expansum LysM domain proteins during infection, null mutants for the 15 uncharacterized putative LysM effectors were constructed and the fungal growth rate on either PDA or Cazpek medium or lesion expansion rate on the infected apple fruits was evaluated. The results showed the growth rate of knockout mutants from PeLysM5, PeLysM12 and PeLysM15 was retarded on PDA medium. No significant difference in growth rate was observed between wild type and all mutants on solid Cazpek medium. Nevertheless, the hypha of wild type displayed deeper yellow on the back of Cazpek medium than those of knockout mutants. On the infecting apples fruits, the knockout mutants from PeLysM5, PeLysM7, PeLysM8, PeLysM9, PeLysM10, PeLysM11, PeLysM14, PeLysM15, PeLysM16, PeLysM18 and PeLysM19 showed enhanced fungal virulence, with faster decaying on infected fruits than those from wild type. By contrast, the knockout mutation at PeLysM12 locus led to reduced lesion expansion rate on the infected apple fruits. In addition, P. expansum-apple interaction RNA-seq experiment was performed using apple fruit tissues infected by the wild type and knockout mutant ΔPeLysM15, respectively. Transcriptome analyses indicated that deletion of PeLysM15 could activate expression of several core effector genes, such as PEX2_055830, PEX2_036960 and PEX2_108150, and a chitin-binding protein, PEX2_064520. These results suggest PeLysM15 may play pivotal roles in fungal growth and development and involve pathogen–host interaction by modulating other effector genes’ expression. Our results could provide solid data reference and good candidates for further pathogen-related studies in P. expansum.

Genomic and transcriptomic sequences of Tagetes erecta are very limited in public databases, despite its nutritional and economical value. In this study, nine cDNA libraries were constructed from leaves, immature and mature flowers and sequenced using Illumina Hiseq 2000. Over 45.66 Gb nucleotides were generated and a total of 72,499 unigenes were assembled, 34,892 (48.13%) of which were annotated in NR, Swiss-prot, COG, GO, KOG, KEGG and Pfam. 11,721 differentially expressed genes were identified in leaves, immature flowers and mature flowers. The differentially expressed genes between immature flowers and mature flowers were mainly involved in photosynthesis and secondary metabolite biosynthesis. Additionally, the catalysis-related unigenes and their expression involved in carotenoids biosynthesis were determined. Using our newly identified reference genes as internal control, the expression profiles of carotenoids biosynthetic genes were verified by real-time qRT-PCR, and four of the unigenes were cloned for full length sequences confirmation. Furthermore, gene expansions occurred among the catalytic gene families in carotenoids biosynthesis pathway, which might explain the high pigment content in T. erecta.

Marigold(Tagetes erecta)is one of important plant resources for natural xanthophylls extraction.China has become the world’s leading producer of xanthophyll from marigold.In this paper,eight marigold cultivars which were renowned at home and abroad were cultivated on a small scale in Hefei,Anhui Province for preliminary screening to be suitable for local scale planting by agronomic traits and xanthophyll content.The results indicated that all tested marigold cultivars exhibited good growth adaptability.High performance liquid chromatography determination showed that xanthophyll content of orange flowers was higher than that of yellow flowers.Comprehensive analysis of agronomic traits and pigment content suggests that the domestic cultivar"JUWANG"is suitable for local scale planting and breeding.This study can provide the basis for further investigation of pigment synthesis regulation of marigold and its industrialization development in Anhui Province.

EIN3/EIL transcription factors play key roles in plants, widely regulating plant growth and development, especially fruit ripening. In this study, bioinformatics and comparative genomic studies were performed in the EIN3/EIL family members of Actinidia chinensis. Consequently, 8 EIN3/EIL genes were identified in the genome of A. chinensis. Their protein sequences included one highly acidic domain, one proline-rich domain, and 5–7 basic domains. In the phylogenetic tree of EIN3/EILgenes from 20 plant genomes, convergent and divergent evolution simultaneously existed in many plant species. EIN3/EILgene expansions in A. chinensis resulted from whole genome triplication events. RNA-seq data indicated that EIN3/EIL genes represented two diametrical expression patterns during fruit development in A. chinensis. Our study identified the EIN3/EIL family members in A. chinensis and revealed the conserved regions in protein sequences among family members, the evolution tendency in different plant species, the member expansions resulting from plant genome duplications, and the significant differences of gene expression levels during fruit development. Our results will provide EIN3/EIL gene candidates, and a data foundation for the functional studies of EIN3/EIL genes in A. chinensis.

The appropriate reference genes are important and essential for reliable results of transcript normalization in real-time qRT-PCR. In the current study, we identified 1203 stably expressed genes from 35,286 genes' expression profiles in developmental fruits of Actinidia chinensis. We manually selected six candidate genes and assessed their expression levels, using two sets of fruit samples of A. chinensis: flesh fruits at four developmental stages and post-harvested fruits. The expression stability of these six genes was assessed by three independent algorithms: geNorm, NormFinder, and BestKeeper. Statistical results indicated these six genes can serve as internal control in both developmental and post-harvested fruits. Among these genes, UBQ_CONJ_E2 (Ubiquitin-conjugating enzyme E2 36) and TUB_FCB (Tubulin folding cofactor B) were the two best reference genes identified in this study. The identification and validation of these reference genes can be helpful for elucidating the studies of fruit development and post-harvested fruits' storage in A. chinensis and other fruit crops of Actinidiaceae.

Protein-protein interactions (PPIs) are involved in almost all biological processes and form the basis of the entire interactomics systems of living organisms. Identification and characterization of these interactions are fundamental to elucidating the molecular mechanisms of signal transduction and metabolic pathways at both the cellular and systemic levels. Although a number of experimental and computational studies have been performed on model organisms, the studies exploring and investigating PPIs in tomatoes remain lacking. Here, we developed a Predicted Tomato Interactome Resource (PTIR), based on experimentally determined orthologous interactions in six model organisms. The reliability of individual PPIs was also evaluated by shared gene ontology (GO) terms, co-evolution, co-expression, co-localization and available domain-domain interactions (DDIs). Currently, the PTIR covers 357,946 non-redundant PPIs among 10,626 proteins, including 12,291 high-confidence, 226,553 medium-confidence, and 119,102 low-confidence interactions. These interactions are expected to cover 30.6% of the entire tomato proteome and possess a reasonable distribution. In addition, ten randomly selected PPIs were verified using yeast two-hybrid (Y2H) screening or a bimolecular fluorescence complementation (BiFC) assay. The PTIR was constructed and implemented as a dedicated database and is available at http://bdg.hfut.edu.cn/ptir/index.html without registration.