Jingen Xi

Brown rot disease caused by Pyrrhoderma noxium is a widespread disease that severely affects the roots of rubber trees (Hevea brasiliensis Muell. Arg.). The economic losses, along with environmental and health problems arising from the use of disease control chemicals, have raised the interest of scholars to explore the use of biological control agents for the effective control of fungal pathogen P. noxium. Here, the inhibition effect of the culture filtrate of B. subtilis Czk1 on P. noxium was demonstrated. The findings indicate that the antifungal activity of this strain is mediated wholly or partly by compounds produced in the culture filtrate. The combined use of liquid chromatography–tandem mass spectrometry and antifungal activity assays rapidly identified compounds produced by B. subtilis Czk1. Metabolic profiles were assessed and used to identify major metabolites based on the scores of variable importance in the projection and the plot scores of principal component analysis. A total of 296 differential metabolites were screened, including 208 in positive ion mode and 88 in negative ion mode. Two key metabolites, diacetyl and trans-2-octenoic acid, were screened from 29 metabolites by antifungal activity assays. The median effective concentration (EC₅₀) of trans-2-octenoic acid and diacetyl were 0.9075 mg/mL and 4.8213 mg/mL, respectively. The antifungal metabolites can disrupt the internal structure of the pathogenic fungal mycelium, thereby impeding its growth. This study is expected to contribute to the existing knowledge of Czk1-produced metabolites and their future antifungal applications. This study is also expected to provide a new biopreservative perspective on unexplored antifungal metabolites produced by Czk1 as a biocontrol agent.

Agave species are widely planted for fiber production. However, the molecular basis of agave fiber development has not been well understood. In this study, we performed a transcriptomic analysis in A. amaniensi, a well-known variety with high-quality fiber production. Approximately 43.87 million clean reads were obtained using Illumina sequencing. The de novo assembly produced 66,746 unigrams, 54% of which were annotated in a public database. In the Nr database, 21,490 unigenes of A. amaniensis were shown to be most closely related to Asparagus officinalis. Nine expansin A orthologs with full coding regions were obtained, which were named EXP1a, EXP1b, EXP2, EXP3, EXP4a, EXP4b, EXP11, EXP12, and EXP13. The maximum likelihood phylogenetic tree revealed the species-specific expansion of expansin genes in Arabidopsis, rice and agave. The expression analysis suggested the negative correlation between the expression of expansin genes and the leaf growth rate, except AhEXP11. Moreover, expansin genes were differentially affected by abiotic and biotic stresses. Notably, AhEXP2 expression level was highly upgraded after the infection of Phytophthora nicotiana. Nutrient deficiency also influent expansin genes expression. Together, our research will benefit future studies related to fiber development, disease resistance and nutrient usage in agave.

Agave angustifolia is an important crassulacean acid metabolism plant species, with wide applications in beverage and sisal fiber production. In this study, we carried out a transcriptome analysis of A. angustifolia leaves, generating a total of 58,482,436 clean reads through Illumina paired-end sequencing. De novo transcriptome assembly generated 67,314 unigenes, with about half of them having homologs in four public databases. In the Nr database, Asparagus officinalis was shown to be most closely related to agave, and the early angiosperm Amborella trichopoda was selected as an outgroup species. We further identified five, two, seven, seven, seven, six and six CAD genes in asparagus, amborella, A. deserti, A. tequilana, A. americana, A. hybrid H11648 and A. angustifolia, respectively. The maximum likelihood phylogenetic tree revealed the species-specific expansion of CAD genes in arabidopsis, rice and agave. The expression analysis indicated the conservatively expressed CAD1/2/4/6, providing candidate targets for manipulation to improve lignin traits. The species-specific expression of CAD3/5/7 indicates the existence of different regulatory mechanisms controlling the expression of these genes in agave species. This study presents the first transcriptome dataset of A. angustifolia, facilitating future studies on lignin biosynthesis in agave.

Agave species are widely cultivated crassulacean acid metabolism (CAM) plants for alcoholic beverages, food and fiber production. Among these, the Agave hybrid H11648 ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for sisal fiber in the tropical areas of Brazil, China, and African countries. The plants of Agave hybrid H11648 have a long life cycle and large leaves, which require a huge amount of nitrogen nutrient. However, the molecular basis of nitrogen transport and allocation has not been well understood in agave. In this study, we identified 19 NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY(NPF) genes (called AhNPFs) with full-length coding sequences in Agave hybrid H11648. Our analysis of gene expression in various types of tissues revealed the tissue-specific expression pattern of AhNPFs. We further examined their expression patterns at different leaf developmental stages, under abiotic/biotic stresses and nutrient deficiency. The results reveal several candidate regulators in the agave NPF family, including AhNPF4.3/5.2/7.1. We first characterized the NPF genes in agave based on published leaf transcriptome datasets and emphasized their potential functions. The study will benefit future studies related to nitrogen nutrient in agave.

Agave sisalana is one of the Agave cultivars for sisal fiber production around the tropical areas of the world. In the present study, we successfully sequenced and assembled its chloroplast genome. The full size of the genome is 157,268 bp with a GC content at 37.85%. The genome is constructed with a large single copy region (LSC, 85,894 bp), a pair of inverted repeat regions (IR, 26,573 bp) and a small single copy region (SSC, 18,228 bp). Besides, 86 protein-coding genes, 38 tRNAs and 8 rRNAs are annotated on the chloroplast genome. Phylogenetic result reveals that A. sisalana is closely related with A. americana and A. H11648.

Coffee (Coffea arabica L.) is a very important crop in China and in the global economy. During March 2019, symptoms of leaf blight were observed on coffee planted at Hainan and Yunnan Provinces in ...

Sisal is widely cultivated in tropical areas for fiber production. The main sisal cultivar, Agave H11648 ((A. amaniensis × A. angustifolia) × A. amaniensis) has a relatively scarce molecular basis and no genomic information. Next-generation sequencing technology has offered a great opportunity for functional gene mining in Agave species. Several published Agave transcriptomes have already been reused for gene cloning and selection pressure analysis. There are also other potential uses of the published transcriptomes, such as meta-analysis, molecular marker detection, alternative splicing analysis, multi-omics analysis, genome assembly, weighted gene co-expression network analysis, expression quantitative trait loci analysis, miRNA target site prediction, etc. In order to make the best of our published transcriptome of A. H11648 leaf, we here represent a data descriptor, with the aim to expand Agave bio information and benefit Agave genetic researches.

Agave plants are important crassulacean acid metabolism (CAM) plants with multiple agricultural uses, such as being used in tequila and fiber production. Agave hybrid H11648 ((A. amaniensis Trel. and Nowell × A. angustifolia Haw.) × A. amaniensis) is the main cultivated Agave species for fiber production in large tropical areas around the world. In this study, we conducted a transcriptome analysis of A. H11648. About 49.25 million clean reads were obtained by Illumina paired-end sequencing. De novo assembly produced 148,046 unigenes with more than 40% annotated in public databases, or matched homologs in model plants. More homologous gene pairs were found in Asparagus genome than in Arabidopsis or rice, which indicated a close evolutionary relationship between Asparagus and A. H11648. CAM-related gene families were also characterized as previously reported in A. americana. We further identified 12 cellulose synthase genes (CesA) in Asparagus genome and 38 CesA sequences from A. H11648, A. americana, A. deserti and A. tequilana. The full-length CesA genes were used as references for the cloning and assembly of their homologs in other Agave species. As a result, we obtained CesA1/3/4/5/7 genes with full-length coding region in the four Agave species. Phylogenetic and expression analysis revealed a conserved evolutionary pattern, which could not explain the distinct fiber traits in different Agave species. We inferred that transcriptional regulation might be responsible for Agave fiber development. This study represents the transcriptome of A. H11648, which would expand the number of Agave genes and benefit relevant studies of Agave fiber development.