Chromosome-scale genome assembly and annotation of Cotoneaster glaucophyllus.

Cotoneaster glaucophyllus is a semi-evergreen plant that blossoms in late summer, producing dense, attractive, fragrant white flowers with significant ornamental and ecological value. Here, a chromosome-scale genome assembly was obtained by integrating PacBio and Illumina sequencing data with the aid of Hi-C technology. The genome assembly was 563.3 Mb in length, with contig N50 and scaffold N50 values of ~6 Mb and ~31 Mb, respectively. Most (95.59%) of the sequences were anchored onto 17 pseudochromosomes (538.4 Mb). We predicted 35,856 protein-coding genes, 1,401 miRNAs, 655 tRNAs, 425 rRNAs, and 795 snRNAs. The functions of 34,967 genes (97.52%) were predicted. The availability of this chromosome-level genome will provide valuable resources for molecular studies of this species, facilitating future research on speciation, functional genomics, and comparative genomics within the Rosaceae family.

Transcriptomic and metabolomic differences between banana varieties which are resistant or susceptible to Fusarium wilt.

Background: Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense race 4 (Foc4), is the most lethal disease of bananas in Asia. Methods: To better understand the defense response of banana to Fusarium wilt, the transcriptome and metabolome profiles of the roots from resistant and susceptible bananas inoculated with Foc4 were compared. Results: After Foc4 inoculation, there were 172 and 1,856 differentially expressed genes (DEGs) in the Foc4-susceptible variety (G1) and Foc4-resistant variety (G9), respectively. In addition, a total of 800 DEGs were identified between G1 and G9, which were mainly involved in the oxidation-reduction process, cell wall organization, phenylpropanoid biosynthesis, and lipid and nitrogen metabolism, especially the DEGs of Macma4_08_g22610, Macma4_11_g19760, and Macma4_03_g06480, encoding non-classical arabinogalactan protein; GDSL-like lipase; and peroxidase. In our study, G9 showed a stronger and earlier response to Foc4 than G1. As the results of metabolomics, lipids, phenylpropanoids and polyketides, organic acids, and derivatives played an important function in response to Fusarium wilt. More importantly, Macma4_11_g19760 might be one of the key genes that gave G9 more resistance to Foc4 by a lowered expression and negative regulation of lipid metabolism. This study illustrated the difference between the transcriptomic and metabolomic profiles of resistant and susceptible bananas. These results improved the current understanding of host-pathogen interactions and will contribute to the breeding of resistant banana plants.

Integrated transcriptomic and proteomic analyses of two sugarcane (Saccharum officinarum Linn.) varieties differing in their lodging tolerance.

BACKGROUND: Lodging seriously affects sugarcane stem growth and sugar accumulation, reduces sugarcane yield and sucrose content, and impedes mechanization. However, the molecular mechanisms underlying sugarcane lodging tolerance remain unclear. In this study, comprehensive transcriptomic and proteomic analyses were performed to explore the differential genetic regulatory mechanisms between upright (GT42) and lodged (GF98-296) sugarcane varieties. RESULTS: The stain test showed that GT42 had more lignin and vascular bundles in the stem than GF98-296. The gene expression analysis revealed that the genes that were differentially expressed between the two varieties were mainly involved in the phenylpropanoid pathway at the growth stage. The protein expression analysis indicated that the proteins that were differentially expressed between the two varieties were related to the synthesis of secondary metabolites, the process of endocytosis, and the formation of aminoacyl-tRNA. Time-series analysis revealed variations in differential gene expression patterns between the two varieties, whereas significant protein expression trends in the two varieties were largely consistent, except for one profile. The expression of CYP84A, 4CL, and CAD from the key phenylpropanoid biosynthetic pathway was enhanced in GT42 at stage 2 but suppressed in GF98-296 at the growth stage. Furthermore, the expression of SDT1 in the nicotinate and nicotinamide metabolism was enhanced in GT42 cells but suppressed in GF98-296 cells at the growth stage. CONCLUSION: Our findings provide reference data for mining lodging tolerance-related genes that are expected to facilitate the selective breeding of sugarcane varieties with excellent lodging tolerance.

Validation and Application of a Molecular Detection System for Fusarium Wilt of Banana in China.

Fusarium wilt of banana is a devastating disease caused by Fusarium oxysporum f. sp. cubense (Foc). It has restricted the development of the banana industry worldwide and is particularly serious in China because of the large planting areas and special planting patterns. However, there is no rapid and accurate approach to detect the Foc strains that specifically occur in China because of the rich genetic diversity observed in this pathosystem. In this study, we evaluated the performance of 10 previously published PCR primer pairs on 103 representative Foc strains in China and neighboring countries and screened out a set of primers (Foc-specific primer pair SIX9-Foc-F/R, Foc R1-specific primer pair SIX6b-210-F/R, Foc R4-specific primer pair Foc-1/2, and Foc TR4-specific primer pair W2987F/R) suitable for the detection of Foc strains in China and the surrounding Southeast Asian countries. Moreover, we developed a molecular detection system to accurately identify the different physiological races of Foc. The findings of this study provide technical support for preventing and controlling the spread of Fusarium wilt of banana in the field in China.

Soil bacterial communities associated with marbled fruit in Citrus reticulata Blanco 'Orah'.

Citrus reticulata Blanco 'Orah' is grown throughout southern China and provides enormous economic value. However, the agricultural industry has suffered substantial losses during recent years due to marbled fruit disease. The present study focuses on the soil bacterial communities associated with marbled fruit in 'Orah'. The agronomic traits and microbiomes of plants with normal and marbled fruit from three different orchards were compared. No significant differences were found in agronomic traits between the groups, except for higher fruit yields and higher quality of fruits in normal fruit group. Additionally, a total of 2,106,050 16S rRNA gene sequences were generated via the NovoSeq 6000. The alpha diversity index (including the Shannon and Simpson indices), Bray-Curtis similarity, and principal component analyses indicated no significant differences in microbiome diversity between normal and marbled fruit groups. For the healthy 'Orah', the most abundant associated phyla were Bacteroidetes, Firmicutes, and Proteobacteria. In comparison, Burkholderiaceae and Acidobacteria were the most abundant taxa with the marbled fruit group. In addition, the family Xanthomonadaceae and the genus Candidatus Nitrosotalea were prevalent with this group. Analysis using the Kyoto Encyclopedia of Genes and Genomes pathways showed that several pathways related to metabolism significantly differed between the groups. Thus, the present study provides valuable information regarding soil bacterial communities associated with marbled fruit in 'Orah'.

Integrated metabolomic and transcriptomic analyses of regulatory mechanisms associated with uniconazole-induced dwarfism in banana.

BACKGROUND: Uniconazole is an effective plant growth regulator that can be used in banana cultivation to promote dwarfing and enhance lodging resistance. However, the mechanisms underlying banana dwarfing induced by uniconazole are unknown. In uniconazole-treated bananas, gibberellin (GA) was downregulated compared to the control groups. An integrative analysis of transcriptomes and metabolomes was performed on dwarf bananas induced by uniconazole and control groups. The key pathways involved in uniconazole-induced dwarfism in banana were determined according to the overlap of KEGG annotation of differentially expressed genes and (DEGs) differential abundant metabolites (DAMs). RESULTS: Compared with the control groups, the levels of some flavonoids, tannins, and alkaloids increased, and those of most lipids, amino acids and derivatives, organic acids, nucleotides and derivatives, and terpenoids decreased in uniconazole-treated bananas. Metabolome analysis revealed the significant changes of flavonoids in uniconazole-treated bananas compared to control samples at both 15 days and 25 days post treatment. Transcriptome analysis shows that the DEGs between the treatment and control groups were related to a series of metabolic pathways, including lignin biosynthesis, phenylpropanoid metabolism, and peroxidase activity. Comprehensive analysis of the key pathways of co-enrichment of DEGs and DAMs from 15 d to 25 d after uniconazole treatment shows that flavonoid biosynthesis was upregulated. CONCLUSIONS: In addition to the decrease in GA, the increase in tannin procyanidin B1 may contribute to dwarfing of banana plants by inhibiting the activity of GA. The increased of flavonoid biosynthesis and the change of lignin biosynthesis may lead to dwarfing phenotype of banana plants. This study expands our understanding of the mechanisms underlying uniconazole-induced banana dwarfing.

First Report of Leaf Spot Caused by Colletotrichum citricola on Cavendish bananas in China.

Cavendish banana (Musa spp. AAA group) is an important tropical and subtropical fruit with significant economic value. It is widely planted in Guangxi, Yunnan, Hainan, Fujian and Guangdong provinces in China. In November 2020, leaf spots were observed on nearly 80% of the plants growing in three Cavendish banana plantations in Chongzuo, Guangxi, China. The symptoms on Cavendish banana leaves initially appeared as small black necrosis spots, which gradually expanded and connected, eventually covered the entire leaf. Three diseased leaves from three plantations were collected, sectioned into small pieces (5 ×5 mm), surface sterilized (10 s in 75% ethanol, followed by 1 min in 1% sodium hypochlorite and rinsed three times in sterile water) and placed on potato dextrose agar (PDA) at 28℃ for 5 days for pathogen isolation. The fungal colonies were white, cottony, while the reverse sides were white, concentric circles with yellowish-brown discoloration in 7-day cultures. The conidia were hyaline, aseptate, cylindrical, oval, measuring 10.3 to 17.71 µm (mean 14.06 ± 1.45 µm; n = 200) in length and 4.48 to 9.57 µm (mean 7.46 ± 0.69 µm; n = 200) in width. Three representative isolates (DX1-5, LZ4-5, and FS1-3) were obtained by monosporic isolation. The partial internal transcribed spacer (ITS) regions, actin (ACT), chitin synthase (CHS-1), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), calmodulin (CAL), and ß-tubulin (TUB2) were amplified from genomic DNA for the three isolates (Weir et al. 2012). The sequences of the amplified fragments were deposited in GenBank (accessions OL361844 to OL361858, for GAPDH, CAL, ACT, CHS-1, and TUB2 of isolate DX1-5, LZ4-5 and FS1-3; OL305066 to OL305068 for ITS) and showed over 99% identities with the corresponding sequences of C. citricola. A neighbor-joining phylogenetic tree based on the above six genes of type or ex-type specimens of Colletotrichum (Fu et al. 2019) was constructed with MEGA 5.2 using the concatenation of multiple sequences (Kumar et al. 2016). All three isolates clustered together with the type culture of C. citricola (CBS 134228, CBS 134229, CBS 134230) with 82% bootstrap support in the phylogenetic tree. According to the molecular and morphological characteristics, all three isolates were identified as C. citricola. Pathogenicity tests were conducted on one-month-old primary hardened tissue culture plantlets. Tender, healthy leaves were gently scratched with a sterile needle, and each wound site was inoculated with sterile cotton impregnated with conidial suspension (106 spores/ml) for each isolate. Wounded leaves were treated with sterile cotton impregnated with conidial suspension of C. fructicola as positive controls and sterile water as negative controls. Each isolate was inoculated with three tissue culture plantlets, six inoculated sites on each plantlet, the same as controls. All inoculated tissue culture plantlets were covered with plastic bags to maintain high humidity and placed in a 28℃ growth chamber with constant light. Black necrotic lesions were clearly observed on the inoculated leaves and the positive controls after 7 days, whereas no symptoms appeared on the negative control leaves. The fungus was re-isolated from inoculated leaves, and these isolates matched the morphological and molecular characteristics of the original isolates confirming Koch's postulates. To our knowledge, this is the first report of leaf spot caused by C. citricola on Cavendish banana worldwide.

Antifungal mechanism of Bacillus amyloliquefaciens strain GKT04 against Fusarium wilt revealed using genomic and transcriptomic analyses.

The application of endophytic bacteria, particularly members of the genus Bacillus, offers a promising strategy for the biocontrol of plant fungal diseases, owing to their sustainability and ecological safety. Although multiple secondary metabolites that demonstrate antifungal capacity have been identified in diverse endophytic bacteria, the regulatory mechanisms of their biosynthesis remain largely unknown. To elucidate this, we sequenced the entire genome of Bacillus amyloliquefaciens GKT04, a strain isolated from banana root, which showed high inhibitory activity against Fusarium oxysporum f. sp. cubense race 4 (FOC4). The GKT04 genome consists of a circular chromosome and a circular plasmid, which harbors 4,087 protein-coding genes and 113 RNA genes. Eight gene clusters that could potentially encode antifungal components were identified. We further applied RNA-Seq analysis to survey genome-wide changes in the gene expression of strain GKT04 during its inhibition of FOC4. In total, 575 upregulated and 242 downregulated genes enriched in several amino acid and carbohydrate metabolism pathways were identified. Specifically, gene clusters associated with difficidin, bacillibactin, and bacilysin were significantly upregulated, and their gene regulatory networks were constructed. Our work thereby provides insights into the genomic features and gene expression patterns of this B. amyloliquefaciens strain, which presents an excellent potential for the biocontrol of Fusarium wilt.

Comparative transcriptome analysis reveals resistance-related genes and pathways in Musa acuminata banana 'Guijiao 9' in response to Fusarium wilt.

Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most devastating diseases in bananas resulting in significant loss of Cavendish bananas production worldwide. Here we show the agronomic traits and the resistance of 'Guijiao 9' in the field trials from 2012 to 2017. And then we dissect and compare the transcriptome response from these two cultivars (cv. 'Guijiao 9' and cv. Williams) in an attempt to understand the molecular basis that contribute to the enhanced Foc tropical race 4 (Foc-TR4) resistance. 'Guijiao 9' is a Cavendish cultivar with strong resistance to Foc-TR4, which was reflected in a lower disease severity and incidence in glasshouse and field trails, when compared to the susceptible cultivar Williams. Gene expression profiles of 'Guijiao 9' and Williams were captured by performing RNA-Seq analysis on 16 biological samples collected over a six day period post inoculation with Foc-TR4. Transcriptional reprogramming in response to Foc-TR4 was detected in both genotypes but the response was more drastic in 'Guijiao 9' than in Williams. Specific genes involved in plant-pathogen interaction and defense signaling including MAPK, calcium, salicylic acid, jasmonic acid and ethylene pathways were analyzed and compared between 'Guijiao 9' and Williams. Genes associated with defense-related metabolites synthesis such as NB-LRR proteins, calmodulin-binding protein and phenylpropanoids biosynthesis genes were significantly up-regulated in 'Guijiao 9' resistant to Foc-TR4 infection. Taken together, this study highlights the important roles of plant hormone regulation and defense gene activation in mediating resistance in 'Guijiao 9'.

Transcriptome analysis of starch and sucrose metabolism across bulb development in Sagittaria sagittifolia.

Sagittaria sagittifolia L is an important bulb vegetable that has high nutritional and medical value. Bulb formation and development are crucial to Sagittaria sagittifolia; however, its sucrose metabolism is poorly understood and there are a lack of sufficient transcriptomic and genomic data available to fully understand the molecular mechanisms underlying bulb formation and development as well as the bulb transcriptome. Five cDNA libraries were constructed at different developmental stages and sequenced using high-throughput Illumina RNA sequencing. From approximately 63.53 Gb clean reads, a total of 60,884 unigenes, with an average length of 897.34 bp and N50 of 1.368 kb, were obtained. A total of 36,590 unigenes were successfully annotated using five public databases. Across different developmental stages, 4195, 827, 832, 851, and 1494 were differentially expressed in T02, T03, T04, T05, and T06 libraries, respectively. Gene ontology (GO) analysis revealed several differentially-expressed genes (DEGs) associated with catalytic activity, binding, and transporter activity. The Kyoto encyclopedia of genes and genomes (KEGG) revealed that these DEGs are involved in physiological and biochemical processes. RT-qPCR was used to profile the expression of these unigenes and revealed that the expression patterns of the DEGs were consistent with the transcriptome data. In this study, we conducted a comparative gene expression analysis at the transcriptional level using RNA-seq across the different developmental stages of Sagittaria sagittifolia. We identified a set of genes that might contribute to starch and sucrose metabolism, and the genetic mechanisms related to bulblet development were also explored. This study provides important data for future studies of the genetic and molecular mechanisms underlying bulb formation and development in Sagittaria sagittifolia.