Xiaoli Hu

Agave triangularis Jacobi is an ornamental agave species that represents a valuable genetic resource for enhancing resistance and tolerance in cultivated agaves such as A. tequilana and A. H11648. In this study, we performed the first de novo transcriptome assembly of A. triangularis using Illumina sequencing. A total of 131,321 transcripts were assembled, comprising 119,764,849 bp. Functional annotation revealed a close evolutionary relationship between A. triangularis and Asparagus officinalis, supporting its phylogenetic placement within the Asparagaceae family. We further identified five SRO genes in both A. triangularis and A. H11648. Their expression profiles in A. H11648, analyzed by qRT-PCR, suggested involvement in leaf development. Notably, AhSRO2 and AhSRO3 were significantly up-regulated following oomycete infection, while AhSRO3 was markedly induced under low-temperature stress. These findings highlight AhSRO2 and AhSRO3 as promising candidate genes for further functional investigation. This study provides the first reference transcriptome for A. triangularis, offering a valuable resource for gene discovery and comparative evolutionary studies in agave. The expression patterns of SRO genes establish a framework for understanding their potential roles in leaf development and stress responses, supporting future efforts toward genetic improvement in agave species.

Agave hybrid cultivar 11,648 has been planted for sisal fiber production in China since the 1960s. However, little is known about the population structure and genetic diversity of agave germplasms in China. Therefore, we developed a group of core SNP markers to evaluate the population structure and genetic diversity of 125 agave germplasms in China, including 20 cultivars, 14 breeding lines, and 89 transplanted resources from different areas. Cost-effective amplicon sequencing technology was used to identify genetic variants. The results grouped most cultivars and breeding lines together, which indicated that local agave breeding programs aimed to improve fiber and disease-resistance traits. These breeding programs have reduced genetic diversity, even with the gene flows from other Agave species. The neighbor-joining phylogenetic tree revealed the relationships between A. H11648 and its parents. The phylogenetic relationship between A. sisalana and A. amanuensis is doubtful, even if they are considered heterotypic synonyms. The 11 agave germplasms introduced from Mexico suggest the abundant diversity of agave germplasms in Mexico, which is also the source of agave germplasms in China. This study provides a sketch map for agave germplasms in China, which will benefit future studies related to population genetics and breeding works of agave.

Coffee is a significant traded commodity for developing countries. Among the various diseases affecting coffee, anthracnose caused by Colletotrichum spp. has re-emerged as a major constraint on global coffee production. To better understand the Colletotrichum species complex associated with coffee anthracnose, we characterized Colletotrichum spp. using a combination of phenotypic traits, MAT1-2 (ApMat) gene analysis, multi-locus phylogenetic (ITS, ACT, CHS-1, and GAPDH), and pathogenicity assays. A total of 74 Colletotrichum isolates were collected from coffee plants exhibiting anthracnose symptoms across nine coffee plantations in China. Among these, 55 isolates were identified as the C. gloeosporioides species complex using the ApMat locus, while the remaining 19 isolates were identified through multi-locus phylogenetic analyses. The isolates represented seven Colletotrichum species from five species complexes: C. gloeosporioides (including C. siamense, C. nupharicola, and C. theobromicola), C. boninens (C. karstii), C. gigasporum (C. gigasporum), C. orchidearum (C. cliviicola), and C. magnum (C. brevisporum). This is the first report of C. nupharicola and C. cliviicola causing coffee anthracnose worldwide, and the first report of C. nupharicola in China. Pathogenicity tests confirmed that all seven species were capable of infecting coffee leaves. This research enhances our understanding of the Colletotrichum species responsible for coffee anthracnose, and provides valuable insights for developing effective disease management strategies.

Agave, with its unique appearance and ability to produce hard fibers, holds high economic value. However, low temperatures during winter can restrict its growth and even damage the leaves, causing a loss of ornamental appeal or affecting the fiber quality. Conversely, the plant cyclic nucleotide-gated channel (CNGC) family plays an important role in the growth and development of plants and the response to stress. Studying the CNGC family genes is of great importance for analyzing the mechanism by which agave responds to cold stress. This research conducted a transcriptomic analysis of the ornamental plant Agave macroacantha. Through assembly via Illumina sequencing, 119,911 transcripts were obtained, including 78,083 unigenes. In total, 6, 10, 11, and 13 CNGC genes were successfully identified from A. macroacantha, Agave. H11648, Agave. deserti, and Agave. tequilana, respectively. These CNGC genes could be divided into four groups (I, II, III, and IV), and group IV could be divided into two subgroups (IV-A and IV-B). The relative expression levels were quantified by qRT-PCR assays, which revealed that AhCNGC4.1 was significantly upregulated after cold treatment and Ca(NO₃)₂ treatment, suggesting its importance in cold stress and calcium signaling. Additionally, the Y2H assay has preliminarily identified interacting proteins of AhCNGC4.1, including AhCML19 and AhCBSX3. This study has established a completely new transcriptome dataset of A. macroacantha for the first time, enriching the bioinformatics of agave’s transcriptome. The identified CNGC genes are of great significance for understanding the evolution of agave species. The cloned CNGC genes, expression pattern analysis, and protein interaction results laid a foundation for future research related to the molecular functions of agave CNGC genes in cold tolerance.

Agave is a significant fiber crop in tropical regions, known for its high fiber strength. Lignin is closely associated with fiber strength, and phenylalanine ammonia-lyase (PAL) serves as the initial enzyme in biosynthesis of lignin. Hence, it is of considerable significance to study the genes of PAL family to analyze the characteristics and mechanism of sisal fiber development. In this research, we conducted a transcriptomic analysis of Agave schidigera, a widely recognized ornamental plant in agave. Approximately 29.85 million clean reads were acquired through Illumina sequencing. In total, 116,602 transcripts including 72,160 unigenes were assembled, and 22.06~63.56% of those unigenes were annotated in public databases. Two, six, six and six PAL genes were successfully identified and cloned from A. schidigera, A. deserti, A. tequilana and A. H11648, respectively. After phylogenetic analysis, these genes were clustered into two branches. Genes AhPLA2a and AhPLA2c exhibited higher expression levels compared to other genes but had different expression patterns. Moreover, AhPLA2a and AhPLA2c were expressed at high levels under full-nutrient, nitrogen-free and phosphorus-free stresses. Most PAL genes were induced by Phytophthora nicotianae Breda, especially AhPAL1a, AhPAL1b, AhPAL2b and AhPAL2c. This research is the first work to present a de novo transcriptome dataset for A. schidigera, enriching its bioinformation of transcripts. The cloned PAL genes and the expression analyses will form the basis of future research on lignin biosynthesis, the relationship between lignin and fiber strength, and stress resistance in Agave species.