Unveiling the predominance of Saccharum spontaneum alleles for resistance to orange rust in sugarcane using genome-wide association.

KEY MESSAGE: Six QTLs of resistance to sugarcane orange rust were identified in modern interspecific hybrids by GWAS. For five of them, the resistance alleles originated from S. spontaneum. Altogether, they efficiently predict disease resistance. Sugarcane orange rust (SOR) is a threatening emerging disease in many sugarcane industries worldwide. Improving the genetic resistance of commercial cultivars remains the most promising solution to control this disease. In this study, an association panel of 568 modern interspecific sugarcane hybrids (Saccharum officinarum x S. spontaneum) from Réunion's breeding program was evaluated for its resistance to SOR under natural conditions of infection. Two genome-wide association studies (GWAS) were conducted between disease reactions and 183,842 single nucleotide polymorphism (SNP) markers obtained by targeted genotyping-by-sequencing. Five resistance quantitative trait loci (QTLs), named Oru1, Oru2, Oru3, Oru4 and Oru5, were identified using a single-locus GWAS (SL-GWAS). These five QTLs all originated from the species S. spontaneum. A multi-locus GWAS (ML-GWAS) uncovered an additional but less significant resistance QTL named Oru6, which originated from S. officinarum. All six QTLs had a moderate to major phenotypic effect on disease resistance. Prediction accuracy estimated with linear regression models based on each of the five QTLs identified by SL-GWAS was between 0.16-0.41. Altogether, these five QTLs provided a relatively high prediction accuracy of 0.60. In comparison, accuracies obtained with six genome-wide prediction models (i.e., GBLUP, Bayes-A, Bayes-B, Bayes-C, Bayesian Lasso and RKHS) reached only 0.65. The good prediction accuracy of disease resistance provided by the QTLs and the predominant S. spontaneum origin of their resistance alleles pave the way for effective marker-assisted breeding strategies.

Complete sequence and genome characterization of miscanthus virus M, a new betaflexivirus from Miscanthus sp.

A novel betaflexivirus, tentatively named "miscanthus virus M" (MiVM), was isolated from Miscanthus sp. The complete genome of MiVM is 7,388 nt in length (excluding the poly(A) tail). It contains five open reading frames and has a genome organization similar to those of members of the families Alphaflexiviridae and Betaflexiviridae (subfamily Quinvirinae). The amino acid sequences of both the replicase and coat protein shared less than 45% identity with the corresponding sequences of members of either family. Phylogenetic analysis confirmed that MiVM belongs to the family Betaflexiviridae and subfamily Quinvirinae but it was too distantly related to be included in any currently recognized genus in this family. We therefore propose that miscanthus virus M represents a new species and a new genus in the family Betaflexiviridae.

Historical Review on Sugarcane Streak Mosaic Virus That Has Recently Emerged in Africa.

Sugarcane streak mosaic virus (SCSMV), now assigned to the genus Poacevirus of the family Potyviridae, was reported for the first time in 1932 in Louisiana and was believed to be strain F of sugarcane mosaic virus (SCMV) for more than six decades. SCMV-F was renamed SCSMV in 1998 after partial sequencing of its genome and phylogenetic investigations. Following the development of specific molecular diagnostic methods in the 2000s, SCSMV was recurrently found in sugarcane exhibiting streak mosaic symptoms in numerous Asian countries, but not in the Western hemisphere or in Africa. In this review, we give an overview of the current knowledge on this disease and the progression in research on SCSMV. This includes symptoms, geographical distribution and incidence, diagnosis and genetic diversity of the virus, epidemiology, as well as control. Finally, we highlight future challenges as sugarcane streak mosaic has recently been found in Africa where this disease represents a new threat to sugarcane production.

Genetic Diversity, Evolution, and Diagnosis of Sugarcane Yellow Leaf Virus from 19 Sugarcane-Producing Locations Worldwide.

Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf, has been reported in an increasing number of sugarcane-growing locations since its first report in the 1990s in Brazil, Florida, and Hawaii. In this study, the genetic diversity of SCYLV was investigated using the genome coding sequence (5,561 to 5,612 nt) of 109 virus isolates from 19 geographical locations, including 65 new isolates from 16 geographical regions worldwide. These isolates were distributed in three major phylogenetic lineages (BRA, CUB, and REU), except for one isolate from Guatemala. Twenty-two recombination events were identified among the 109 isolates of SCYLV, thus confirming that recombination was a significant driving force in the genetic diversity and evolution of this virus. No temporal signal was found in the genomic sequence dataset, most likely because of the short temporal window of the 109 SCYLV isolates (1998 to 2020). Among 27 primers reported in the literature for the detection of the virus by RT-PCR, none matched 100% with all 109 SCYLV sequences, suggesting that the use of some primer pairs may not result in the detection of all virus isolates. Primers YLS111/YLS462, which were the first primer pair used by numerous research organizations to detect the virus by RT-PCR, failed to detect isolates belonging to the CUB lineage. In contrast, primer pair ScYLVf1/ScYLVr1 efficiently detected isolates of all three lineages. Continuous pursuit of knowledge of SCYLV genetic variability is therefore critical for effective diagnosis of yellow leaf, especially in virus-infected and mainly asymptomatic sugarcane plants.

Genome characterization and complete sequence of a new badnavirus from Pandanus amaryllifolius.

A new badnavirus was sequenced from fragrant pandan grass (Pandanus amaryllifolius) displaying mosaic and chlorosis on the leaves. The complete genome sequence was determined by high-throughput sequencing. The new badnavirus was tentatively named "pandanus mosaic associated virus" (PMaV). Similar to those of other members of the genus Badnavirus, the genome of PMaV consists of a circular DNA molecule of 7,481 bp with three open reading frames (ORF) potentially coding for three proteins. ORF3 encodes a polyprotein with conserved protein domains including zinc finger, trimeric dUTPase, aspartic protease, reverse transcriptase (RT), and RNase H domains. Pairwise comparisons of the highly conserved RT + RNase H region revealed the highest nucleotide (nt) sequence identity (70.71%) to taro bacilliform CH virus-Et17 (MG017324). In addition to PMaV, viral sequences corresponding to orchid fleck dichorhavirus (OFV) were detected in the same plant sample. The complete sequence of the OFV coding region shared >98% nt sequence identity with other isolates of OFV available in the GenBank database. Disease symptoms could not be attributed exclusively to PMaV or OFV, as both viruses were present in the pandan grass exhibiting mosaic and chlorosis.

Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses.

Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Predictive Modeling of Brown Rust of Sugarcane Based on Temperature and Relative Humidity in Florida.

Logistic regression models were developed from 5 years (2014 to 2018) of disease severity and weather data in an attempt to predict brown rust of sugarcane at the Everglades Research and Education Center in Belle Glade, Florida. Disease severity (percentage area of the top visible dewlap leaf covered by rust) was visually assessed in the field every 2 weeks for two varieties susceptible to brown rust. A total of 250 variables were derived from weather data for 10- to 40-day periods before each brown rust assessment day. A subset of these variables were then evaluated as potential predictors of severity of brown rust based on their individual correlation or their biological meaningfulness. Analyses of correlation and stepwise logistic regression allowed us to identify afternoon humid thermal ratio (AHTR), temperature-based duration variables, and their interaction terms as the most significant variables associated with brown rust epidemics of sugarcane in Florida. The nine best predictive models were identified based on model accuracy, sensitivity, specificity, and estimates of the prediction error. The prediction accuracy of these models ranged from 73 to 85%. Single-variable model BR2 (based on AHTR) classified 89% of the epidemic and 81% of the nonepidemic status of the disease. More than 83% of the epidemics and 81% of the nonepidemic status of sugarcane brown rust was correctly classified via multiple-variable models. These models can be used as components of a rust disease warning system to assist in the management of brown rust epidemics of sugarcane in south Florida.

Eight Species of Poaceae Are Hosting Different Genetic and Pathogenic Strains of Sugarcane Mosaic Virus in the Everglades Agricultural Area.

Sugarcane mosaic virus (SCMV) was detected by reverse transcription polymerase chain reaction in eight different species of the Poaceae family in the Everglades Agricultural Area (EAA) of south Florida: broadleaf signalgrass (Urochloa platyphylla), Columbus grass (Sorghum almum), goosegrass (Eleusine indica), maize (Zea mays), sorghum (Sorghum bicolor), St. Augustine grass (Stenotaphrum secundatum), southern crabgrass (Digitaria ciliaris), and sugarcane (Saccharum interspecific hybrids). Based on their coat protein (CP) gene sequence, 62 isolates of SCMV from Florida and 29 worldwide isolates representing the known genetic diversity of this virus were distributed into eight major phylogenetic groups. SCMV isolates infecting Columbus grass, maize, and sorghum in Florida formed a unique group, whereas virus isolates infecting sugarcane in the United States (Florida and Louisiana) clustered with isolates from other countries. Based on the entire genome coding region, SCMV isolates infecting sugarcane in Florida were closest to virus isolates infecting sorghum species or St. Augustine grass. Virus isolates from Columbus grass, St. Augustine grass, and sugarcane showed different virulence patterns after mechanical inoculation of Columbus grass, St. Augustine grass, and sugarcane plants, thus proving that these isolates were different pathogenic strains. Sugarcane was symptomless and tested negative for SCMV by tissue blot immunoassay after inoculation with crude sap from SCMV-infected Columbus grass, indicating that Columbus grass was not a reservoir for SCMV infecting sugarcane in the EAA. Close CP sequence identity between isolates of SCMV from Columbus grass, maize, and sorghum suggested that the same virus strain was naturally spreading between these three plants in south Florida.

Draft Genome Sequence Resource for the Orange Rust Pathogen of Sugarcane Puccinia kuehnii.

Puccinia kuehnii is an obligate biotrophic fungal pathogen that causes orange rust of sugarcane, which is prevalent in many countries around the globe. In the United States, orange rust was first detected in sugarcane in Florida in 2007 and poses a persistent and economically damaging threat to the sugarcane industry in this region. Here, we generated the first genome assemblies for two isolates of P. kuehnii (1040 and 2143) collected in Florida in 2017 from two sugarcane cultivars, CL85-1040 and CP89-2143, respectively. These two rust genome resources will be of immense value for future genomic studies, particularly further exploration of the predicted secretomes that may help define key pathogenicity determinants for this economically important pathogen.

Molecular Detection and Quantification of Xanthomonas albilineans in Juice from Symptomless Sugarcane Stalks Using a Real-Time Quantitative PCR Assay.

Leaf scald, a bacterial disease caused by Xanthomonas albilineans (Ashby) Dowson, is a major limiting factor for sugarcane production worldwide. Accurate identification and quantification of X. albilineans is a prerequisite for successful management of this disease. A sensitive and robust quantitative PCR (qPCR) assay was developed in this study for detection and quantification of X. albilineans using TaqMan probe and primers targeting a putative adenosine triphosphate-binding cassette (ABC) transporter gene (abc). The novel qPCR assay was highly specific to the 43 tested X. albilineans strains belonging to different pulsed-field gel electrophoresis groups. The detection thresholds were 100 copies/µl of plasmid DNA, 100 fg/µl of bacterial genomic DNA, and 100 CFU/ml of bacterial suspension prepared from pure culture. This qPCR assay was 100 times more sensitive than a conventional PCR assay. The pathogen was detected by qPCR in 75.1% (410/546) of symptomless stalk samples, whereas only 28.4% (155/546) of samples tested positive by conventional PCR. Based on qPCR data, population densities of X. albilineans in symptomless stalks of the same varieties differed between two sugarcane production areas in China, Beihai (Guangxi Province) and Zhanjiang (Guangdong Province), and no significant correlation between these populations was identified. Furthermore, no relationship was found between these populations of the pathogen in asymptomatic stalks and the resistance level of the sugarcane varieties to leaf scald. The newly developed qPCR assay proved to be highly sensitive and reliable for the detection and quantification of X. albilineans in sugarcane stalks.

[From boots on the ground to nucleotides in the sequencer: a century of advances in the study of the plant virus ecology]. / De la paire de bottes à la paire de bases : de l'intérêt d'étudier l'écologie des viromes de plantes.

Plant virus ecology began to be explored at the end of the 19th century. Since then, major advances have revealed complex virus-host-vector interactions in a variety of environments. These advances have been accelerated by development of new technologies for virus detection and characterization, the latest of which being high-throughput sequencing (HTS). HTS technologies have proved to be effective for non-targeted characterization of all or nearly all viruses present in a sample without requiring prior information about virus identity, as would be needed for virus-targeted tests. Phytoviromic studies have thus made important advances, including characterization of the complex interactions between phytovirus dynamics and the structure of multi-species host communities, and documentation of the effects of anthropogenic ecosystem simplification on plant virus emergence and diversity. However, such studies must overcome challenges at every stage, from plant sampling to bioinformatics analysis. This review summarizes major advances in plant virus ecology, in association with technological developments, and presents key considerations for use of HTS in the study of the ecology of phytovirus communities.

Weather-Based Predictive Modeling of Orange Rust of Sugarcane in Florida.

Epidemics of sugarcane orange rust (caused by Puccinia kuehnii) in Florida are largely influenced by prevailing weather conditions. In this study, we attempted to model the relationship between weather conditions and rust epidemics as a first step toward development of a decision aid for disease management. For this purpose, rust severity data were collected from 2014 through 2016 at the Everglades Research and Education Center, Belle Glade, Florida, by recording percentage of rust-affected area of the top visible dewlap leaf every 2 weeks from three orange rust susceptible cultivars. Hourly weather data for 10- to 40-day periods prior to each orange rust assessment were evaluated as potential predictors of rust severity under field conditions. Correlation and stepwise regression analyses resulted in the identification of nighttime (8 PM to 8 AM) accumulation of hours with average temperature 20 to 22°C as a key predictor explaining orange rust severity. The five best regression models for a 30-day period prior to disease assessment explained 65.3 to 76.2% of variation of orange rust severity. Prediction accuracy of these models was tested using a case control approach with disease observations collected in 2017 and 2018. Based on receiver operator characteristic curve analysis of these two seasons of test data, a single-variable model with the nighttime temperature predictor mentioned above gave the highest prediction accuracy of disease severity. These models have potential for use in quantitative risk assessment of sugarcane rust epidemics.

Field Infection of Virus-Free Sugarcane by Sugarcane Yellow Leaf Virus and Effect of Yellow Leaf on Sugarcane Grown on Organic and on Mineral Soils in Florida.

Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf, is widespread in Florida. Two field trials were set up, one on organic soil and one on mineral soil, to investigate the rate and timing of sugarcane infection by SCYLV under field conditions and the effect of the virus on yield. Each trial consisted of plots planted with healthy or SCYLV-infected seed cane of two commercial cultivars. Virus prevalence varied from 83 to 100% in plots planted with infected seed cane regardless of cultivar, location, and crop season. On organic soil, plants of virus-free plots became progressively infected in plant cane and first ratoon crops. On mineral soil, healthy sugarcane became initially infected in the first ratoon crop. After three crop seasons, the highest SCYLV prevalence rates were 33 and 7% on organic and mineral soils, respectively. No significant negative effect of SCYLV on yield was found in plant cane crop regardless of cultivar and soil type. However, yield reductions in ratoon crops varied from nonsignificant to 27% depending on cultivar and soil type. Low virus prevalence observed after three crop seasons suggested that planting virus-free seed cane should limit the impact of SCYLV on sugarcane production in Florida.

Comparison of Progress of Brown Rust and Orange Rust and Conditions Conducive for Severe Epidemic Development During the Sugarcane Crop Season in Florida.

Brown rust (caused by Puccinia melanocephala) and orange rust (caused by P. kuehnii) are two major diseases of sugarcane in Florida. To better understand the epidemiology of these two rusts, disease severity and weather variables were monitored for two seasons in cultivars CL90-4725 (susceptible to brown rust and resistant to orange rust) and CL85-1040 (susceptible to orange rust and resistant to brown rust). Brown rust was most severe during mid-May to mid-July, whereas orange rust severity peaked during two periods: mid-May to early August and then November to December. Overall, disease severity was higher for orange rust than for brown rust. Maximum disease severity was correlated with the number of hours at night with an average temperature of 20 to 22.2°C for brown rust one season and orange rust both seasons. Slightly higher correlation was obtained when relative humidity above 90% was included in the number of hours at night with an average temperature of 20 to 22.2°C for brown rust but not orange rust, suggesting that leaf wetness is not a limiting factor for either disease in Florida. Epidemics of brown rust began at lower night temperatures (16.7 to 22.2°C) in one season, but epidemics of orange rust lasted longer under higher temperatures. The correlation of rust severity on recently emerged leaves with conducive temperatures recorded in 10-, 20-, or 30-day windows starting 7 days before disease assessment suggested that earlier inoculum production is needed to create severe epidemics that result in yield loss.

Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans.

Sugarcane (Saccharum spp. hybrids) is a major source of sugar and renewable bioenergy crop worldwide and suffers serious yield losses due to many pathogen infections. Leaf scald caused by Xanthomonas albilineans is a major bacterial disease of sugarcane in most sugarcane-planting countries. The molecular mechanisms of resistance to leaf scald in this plant are, however, still unclear. We performed a comparative transcriptome analysis between resistant (LCP 85-384) and susceptible (ROC20) sugarcane cultivars infected by X. albilineans using the RNA-seq platform. 24 cDNA libraries were generated with RNA isolated at four time points (0, 24, 48, and 72 h post inoculation) from the two cultivars with three biological replicates. A total of 105,783 differentially expressed genes (DEGs) were identified in both cultivars and the most upregulated and downregulated DEGs were annotated for the processes of the metabolic and single-organism categories, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the 7612 DEGs showed that plant-pathogen interaction, spliceosome, glutathione metabolism, protein processing in endoplasmic reticulum, and plant hormone signal transduction contributed to sugarcane's response to X. albilineans infection. Subsequently, relative expression levels of ten DEGs determined by quantitative reverse transcription-PCR (qRT-PCR), in addition to RNA-Seq data, indicated that different plant hormone (auxin and ethylene) signal transduction pathways play essential roles in sugarcane infected by X. albilineans. In conclusion, our results provide, for the first time, valuable information regarding the transcriptome changes in sugarcane in response to infection by X. albilineans, which contribute to the understanding of the molecular mechanisms underlying the interactions between sugarcane and this pathogen and provide important clues for further characterization of leaf scald resistance in sugarcane.

The gyrase inhibitor albicidin consists of p-aminobenzoic acids and cyanoalanine.

Albicidin is a potent DNA gyrase inhibitor produced by the sugarcane pathogenic bacterium Xanthomonas albilineans. Here we report the elucidation of the hitherto unknown structure of albicidin, revealing a unique polyaromatic oligopeptide mainly composed of p-aminobenzoic acids. In vitro studies provide further insights into the biosynthetic machinery of albicidin. These findings will enable structural investigations on the inhibition mechanism of albicidin and its assessment as a highly effective antibacterial drug.

Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion.

BACKGROUND: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. METHODS: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. RESULTS: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion. CONCLUSIONS: As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

Prevalence of Sugarcane yellow leaf virus in Sugarcane-Producing Regions in Kenya Revealed by Reverse-Transcription Loop-Mediated Isothermal Amplification Method.

Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conventional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane 'C132-81' and 'SP71-6163', respectively. Additionally, 68 sugarcane samples that tested negative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicating high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5' and 3' genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clustered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.

Molecular evolutionary history of Sugarcane yellow leaf virus based on sequence analysis of RNA-dependent RNA polymerase and putative aphid transmission factor-coding genes.

RNA-dependent RNA polymerase (RdRp) encoded by ORF2 and putative aphid transmission factor (PATF) encoded by ORF5 of Sugarcane yellow leaf virus (SCYLV) were detected in six sugarcane cultivars affected by yellow leaf using RT-PCR and real-time RT-PCR assays. Expression of both genes varied among infected plants, but overall expression of RdRp was higher than expression of PATF. Cultivar H87-4094 from Hawaii yielded the highest transcript levels of RdRp, whereas cultivar C1051-73 from Cuba exhibited the lowest levels. Sequence comparisons among 25 SCYLV isolates from various geographical locations revealed an amino acid similarity of 72.1-99.4 and 84.7-99.8 % for the RdRp and PATF genes, respectively. The 25 SCYLV isolates were separated into three (RdRp) and two (PATF) phylogenetic groups using the MEGA6 program that does not account for genetic recombination. However, the SCYLV genome contained potential recombination signals in the RdRp and PATF coding genes based on the GARD genetic algorithm. Use of this later program resulted in the reconstruction of phylogenies on the left as well as on the right sides of the putative recombination breaking points, and the 25 SCYLV isolates were distributed into three distinct phylogenetic groups based on either RdRp or PATF sequences. As a result, recombination reshuffled the affiliation of the accessions to the different clusters. Analysis of selection pressures exerted on RdRp and PATF encoded proteins revealed that ORF 2 and ORF 5 underwent predominantly purifying selection. However, a few sites were also under positive selection as assessed by various models such as FEL, IFEL, REL, FUBAR, MEME, GA-Branch, and PRIME.

Leaf Surface Colonization of Sugarcane by Xanthomonas albilineans and Subsequent Disease Progress Vary According to the Host Cultivar.

Spread of leaf scald in modern sugarcane cultivars in Guadeloupe occurs through aerial dissemination of Xanthomonas albilineans. However, the importance of host genotype on the foliar spread of leaf scald has never been investigated. To explore this, we followed two trials used to screen sugarcane cultivars for resistance to leaf scald under natural inoculum pressure. Leaf scald epidemic characteristics were studied by measuring epiphytic populations of X. albilineans, leaf symptom incidence and severity, and the number of infected stalks. In both trials, epiphytic X. albilineans populations and incidence of foliar symptoms varied between sugarcane cultivars (P < 0.001 in each trial for both traits) and differences in stalk infection between cultivars was also observed (P < 0.002 and P < 0.07 for trials A and B, respectively). Part of the cultivar resistance that minimizes epiphytic bacterial populations is correlated to resistance to internal leaf tissue infection as expressed by leaf symptoms. No correlation was found between epiphytic X. albilineans populations of cultivar and the incidence of stalk infection. However, foliar symptom incidence was inconsistently correlated with stalk infection. Resistance of sugarcane to leaf scald appears to involve several traits, including limiting size of epiphytic X. albilineans populations and limiting the capacity of the pathogen to produce leaf necrotic symptoms by invading the leaf vascular system or to move from the leaf into the stalk.