Rice is a major crop worldwide. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has become one of the most devastating diseases for rice. It has been clear that phosphorylation plays essential roles in plant disease resistance. However, the role of phosphorylation is poorly understood in rice-Xoo system. Here, we report the first study on large scale enrichment of phosphopeptides and identification of phosphosites in rice before and 24 h after Xoo infection. We have successfully identified 2367 and 2223 phosphosites on 1334 and 1297 representative proteins in 0 h and 24 h after Xoo infection, respectively. A total of 762 differentially phosphorylated proteins, including transcription factors, kinases, epi-genetic controlling factors and many well-known disease resistant proteins, are identified after Xoo infection suggesting that they may be functionally relevant to Xoo resistance. In particular, we found that phosphorylation/dephosphorylation might be a key switch turning on/off many epi-genetic controlling factors, including HDT701, in response to Xoo infection, suggesting that phosphorylation switch overriding the epi-genetic regulation may be a very universal model in the plant disease resistance pathway. The phosphosites identified in this study would be a big complementation to our current knowledge in the phosphorylation status and sites of rice proteins. This research represents a substantial advance in understanding the rice phosphoproteome as well as the mechanism of rice bacterial blight resistance.

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.

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.

Phytophthora-induced crop diseases, commonly known as “plant plagues”, pose a significant threat to global food security. In this study, strain ASG80 was isolated from sisal roots and demonstrated a broad-spectrum antagonistic activity against several Phytophthora species and fungal pathogens. Strain ASG80 was identified as Streptomyces luteireticuli via phylogenetic analysis, digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI). Whole-genome sequencing identified 40 biosynthetic gene clusters (BGCs) related to secondary metabolite production, including antimicrobial compounds. Strain ASG80 extract exhibited broad-spectrum inhibitory activity against Phytophthora nicotianae, P. vignae, P. cinnamomi, and P. sojae. Pot experiments showed that strain ASG80 extract significantly reduced sisal zebra disease incidence, with an efficacy comparable to the fungicide metalaxyl. These findings suggest that strain ASG80 is a promising biocontrol agent with substantial potential for managing Phytophthora-related diseases in agriculture.

Coffee is one of the most popular beverages around the world, which is mainly produced from the allopolyploid Coffea arabica. The genomes of C. arabica and its two ancestors C. canephora and C. eugenioides have been released due to the development of next generation sequencing. However, few studies on C. arabica are related to the PIN-FORMED (PIN) auxin efflux transporter despite its importance in auxin-mediated plant growth and development. In the present study, we conducted a genome-wide analysis of the PIN gene family in the three coffee species. Totals of 17, 9 and 10 of the PIN members were characterized in C. Arabica, C. canephora and C. eugenioides, respectively. Phylogenetic analysis revealed gene loss of PIN1 and PIN2 homologs in C. arabica, as well as gene duplication of PIN5 homologs during the fractionation process after tetraploidy. Furthermore, we conducted expression analysis of PIN genes in C. arabica by in silico and qRT-PCR. The results revealed the existence of gene expression dominance in allopolyploid coffee and illustrated several PIN candidates in regulating auxin transport and homeostasis under leaf rust fungus inoculation and the tissue-specific expression pattern of C. arabica. Together, this study provides the basis and guideline for future functional characterization of the PIN gene family.

Coffee leaf rust (CLR), caused by the obligate biotrophic fungus Hemileia vastatrix (Hv), is a devastating disease worldwide leading to severe reductions in yield and economic losses in coffee plantations, especially of Coffea arabica L. (Talhinhas et al. 2017). The frequent emergence of new Hv races is a major constraint on coffee production due to continuous exertion of selective pressure on the pathogen from pathogen-resistant cultivars under the coevolutionary 'arms race' (Silva et al. 2018). More than 50 physiological races of Hv have been described globally (Várzea & Marques 2005), while at least 16 Hv races have been detected in China (Bai et al. 2018; Zhang et al. 2014; Chen et al. 1998). Coffee is an important cash crop in China (Yan et al. 2019). Most of the coffee germplasm collections in China are in the main coffee-cropping regions, although documentation on the prevalent Hv races is lacking. A total of 57 CLR samples (each sample contained multi leaves with 20-30 pustules of coffee rust) were collected from 4 germplasm fields situated in the main coffee-cropping regions during the high seasonal incidence of CLR in 2018-2019: Field 1, Coffee Germplasm Collection of Malipo County, Wenshan (23°11' N, 104°55' E, 550 m); Field 2, Coffee Germplasm Collection I in Puer (22°47'45″ N, 100°58'59″ E, 1320 m); Field 3, Coffee Germplasm Collection II in Puer (22°37'36″ N, 100°59'50″ E, 1010 m); and Field 4, Coffee Germplasm Collection in Ruili (24°01' N, 97°51' E, 1260 m). Urediniospores were recovered on susceptible genotypes 849/1 Matari and 19/1 Cantura and tested on a set of coffee differentials at the CIFC (Oeiras, Portugal) following standard race-typing procedure described by D' Oliveirar & Rodiagues (1961). The coffee trees where the rusts isolated were used to verify virulence and avirulence. The infection type criteria determining virulence and avirulence based on the classification standards for disease resistance (D' Oliveirar, 1954-57). Twenty-seven pure-cultured Hv isolates were derived from single rust pustules taken from distinct sample groups. The predominant race XXXVII (v2,5,6,7,9) was present in Field 1, 2, and 3 at high frequency (74.04%) separately derived from the genotypes CATUAÍ, Arabica-Catimor Derivates, T2, CCC 24, Typica, T8667 Catimor HW 26/5 (F2) and Sarchimor. Race XXXIV (v2,5,7,9) was detected in Field 4 (3.70%). Races XXXVII and XXXIV had emerged in China during 2011-2015 (Bai et al. 2017 & 2018). A new race (v2,5,6,7) (7.41%) was isolated from the host DTART 316 and was able to infect the differentiators of physiologic Groups D, E, R, 4, 6, and a. Based on its pathological and genetic characteristics, Hv with high evolutionary potential has inevitably overcome the resistance of released coffee cultivars with increase virulence, thereby adapting to new hosts (Silva et al. 2018; Talhinhas et al. 2017; Zambolim 2016; McCook & Vandermeer 2015). The results obtained in this work corroborate the evidence that the emergence of new Hv races occurs preferentially at germplasm fields since the multi-selection pressures from various hosts. Our findings are of considerable importance given the potential of the coffee germplasm collections in coffee regions to promote evolution of new races. The continued emergence of new Hv races places the current commercial cultivars at risk from a loss of resistance. Monitoring the occurrence, dissemination, distribution, and pathogenicity of new races is essential for targeted resistance breeding and CLR control.