Draft Genome Sequence of Seven Pigmented Strains of Xanthomonas citri pv. anacardii, the Causal Agent of Cashew Angular Spot.

Cashew (Anacardium occidentale) angular leaf spot is caused by pigmented and non-pigmented strains of Xanthomonas citri pv. anacardii, which have been isolated from infected plants in Brazil. The disease symptoms can be observed in leaves, stems, and fruits. Given that infection in young fruits results in fruits unsuitable for commercialization, angular leaf spot represents a serious threat to the cashew crop in Brazil. Here, we report the genomic sequencing of seven pigmented strains of X. citri pv. anacardii, obtained from the leaves of cashew trees from São Paulo state, Brazil, in 2009. The construction of the libraries was carried out according to the manufacturer, and whole-genome sequencing was performed using the Illumina HiSeq 2500 platform. Genome size, number of coding sequences, largest contig length, and N50 ranged from 4,996,984 to 5,003,485 bp, 4,621 to 4,643 bp, 212,513 to 362,232 bp, and 113,582 to 141,003 bp, respectively. GC content and RNA numbers were 64.68% and 54, respectively, for all strains. ANIm and dDDH analyses showed values above 99.5 and 92.1% among these strains and the non-pigmented pathotype strain of X. citri pv. anacardii (IBSBF2579PT). A maximum likelihood tree built with 2,708 core genes grouped all X. citri pv. anacardii strains in the same clade, with a 100% bootstrap. These resources will contribute in a relevant way to help understand the ecological, taxonomic, evolutionary, pathogenicity, and virulence aspects of X. citri pv. anacardii, which will be useful for the study and development of techniques for managing cashew angular leaf spot.

Full-fat corn germ in diets for dairy cows as an alternative to ground corn.

The experiments reported in this research paper address the effects of replacing ground corn (GC) with full-fat corn germ (FFCG) on nutrient intake and digestibility, nitrogen utilization efficiency, performance, and predicted methane production in dairy cows fed cactus cladodes and sugarcane. We hypothesized that the inclusion of FFCG in the diet would not alter the performance of lactating cows but would reduce the predicted methane production in vivo. Ten multiparous Holstein cows at 90 ± 10 d of lactation and yielding 24.2 ± 3.5 kg milk/d were assigned to dietary treatments consisting of different levels of replacement of GC by FFCG (0; 25; 50; 75 and 100% of diet dry matter) in a replicated 5 × 5 Latin square design with 21-d periods. Methane production was predicted using an automated gas in vitro production system. Except for ether extract intake, which increased, the intake of all nutrients decreased linearly with the replacement of GC by FFCG. The digestibility of dry matter, organic matter and neutral detergent fiber reduced, whereas the digestibility of ether extract increased linearly with FFCG. There were no changes in the digestibility of crude protein. The nitrogen intake and daily excretion in urine and feces decreased, while nitrogen use efficiency increased linearly. There was no significant effect of diets on nitrogen balance or microbial protein synthesis and efficiency. The yield of protein, lactose and total solids in milk showed a quadratic behavior. On the other hand, milk fat yield and energy-corrected milk yield decreased linearly with the replacement of GC by FFCG. No effect on pH or ammonia nitrogen was observed. The production of methane (CH4, g/kg DM) and total CH4 (g/d), and CH4 intensity decreased linearly with the replacement of GC by FFCG. In conclusion, FFCG has been shown to be an effective source of fat to reduce methane production in dairy cows, partially supporting our initial hypothesis. However, as it decreases milk fat production, it is not recommended to replace more than 50% of GC by FFCG for lactating cows fed cactus cladodes and sugarcane.

Partially replacing sorghum silage with cactus (Opuntia stricta) cladodes in a soybean oil-supplemented diet markedly increases trans-11 18:1, cis-9, trans-11 CLA and 18:2 n-6 contents in cow milk.

Based on low 18:0 contents observed in milk fat of cows fed cactus cladodes (CC), we hypothesized that including Opuntia stricta cladodes in a soybean oil (SO)-supplemented diet would promote incomplete rumen biohydrogenation of supplemental PUFA, leading to increased trans-11 18:1 and cis-9, trans-11 CLA contents in milk. Twelve Holstein cows were used in a two-period study: (a) Baseline: all cows received a total mixed ration (TMR) composed of sorghum silage (SS) and a concentrate containing no SO for 14 days; (b) Treatment: cows received one of the following SO-supplemented diets for 21 days: (1) SS-TMR: a TMR composed of SS and a SO-enriched concentrate, (2) CC-TMR: a TMR containing CC as a partial substitute for SS plus the SO-enriched concentrate, and (3) CC-PMR: same diet as in treatment 2, but CC were mixed with the SO-enriched concentrate and fed as a partial mixed ration (PMR). Both CC diets increased relative abundances of trans-11 18:1, cis-9, trans-11 CLA, and 18:2 n-6 in milk fat, whereas opposite effects were observed on 18:0 and cis-9 18:1. Proportion of 18:2 n-6 increased, and cis-9, trans-11 CLA tended to increase with CC-PMR as compared to CC-TMR, whereas 18:3 n-3 was higher with CC-PMR than with SS-TMR. Proportions of several odd- and branched-chain fatty acids, certain 18:1 isomers, and trans-9, cis-11 CLA changed with CC diets, notably with CC-PMR. Milk yield and intake of most nutrients (except fibre) increased or tended to increase with the CC diets, whereas gross milk composition was unaltered. Stearoyl-CoA desaturase-1 index for C18 (SCD18 ) was higher with CC-PMR than with SS-TMR, and milk n-6:n-3 FA ratio and apparent transfer of 18:2 n-6 to milk increased with CC diets. These results indicate that Opuntia stricta cladodes can be a valuable feed ingredient for improving the nutraceutical value of milk fat.

Conjugated linoleic acid-enriched butter improved memory and up-regulated phospholipase A2 encoding-genes in rat brain tissue.

Reduced phospholipase A2 (PLA2) activity has been reported in blood cells and in postmortem brains of patients with Alzheimer disease (AD), and there is evidence that conjugated linoleic acid (CLA) modulates the activity of PLA2 groups in non-brain tissues. As CLA isomers were shown to be actively incorporated and metabolized in the brains of rats, we hypothesized that feeding a diet naturally enriched in CLA would affect the activity and expression of Pla 2 -encoding genes in rat brain tissue, with possible implications for memory. To test this hypothesis, Wistar rats were trained for the inhibitory avoidance task and fed a commercial diet (control) or experimental diets containing either low CLA- or CLA-enriched butter for 4 weeks. After this period, the rats were tested for memory retrieval and killed for tissue collection. Hippocampal expression of 19 Pla 2 genes was evaluated by qPCR, and activities of PLA2 groups (cPLA2, iPLA2, and sPLA2) were determined by radioenzymatic assay. Rats fed the high CLA diet had increased hippocampal mRNA levels for specific PLA2 isoforms (iPla 2 g6γ; cPla 2 g4a, sPla 2 g3, sPla 2 g1b, and sPla 2 g12a) and higher enzymatic activity of all PLA2 groups as compared to those fed the control and the low CLA diet. The increment in PLA2 activities correlated significantly with memory enhancement, as assessed by increased latency in the step-down inhibitory avoidance task after 4 weeks of treatment (rs = 0.69 for iPLA2, P < 0.001; rs = 0.81 for cPLA2, P < 0.001; and rs = 0.69 for sPLA2, P < 0.001). In face of the previous reports showing reduced PLA2 activity in AD brains, the present findings suggest that dairy products enriched in cis-9, trans-11 CLA may be useful in the treatment of this disease.

Nutritional Quality of Milk Fat from Cows Fed Full-Fat Corn Germ in Diets Containing Cactus Opuntia and Sugarcane Bagasse as Forage Sources.

We evaluated the performance, milk composition, and milk fatty acid profile of cows fed diets composed of cactus cladodes (Opuntia stricta [Haw.] Haw), sugarcane bagasse and increasing levels of full-fat corn germ (FFCG). We hypothesized that ground corn can be effectively replaced by FFCG when cactus cladodes and sugarcane bagasse are used as forage sources. The cows were randomly distributed into two 5 × 5 Latin Squares and fed five diets in which ground corn was progressively replaced with full-fat corn germ (FFCG; 0%, 25%, 50%, 75%, or 100% of substitution). Adding FFCG to the diet increased milk production and milk fat content and reduced milk protein content. Overall, FFCG reduced the proportion of saturated FAs and increased mono- and polyunsaturated FAs in milk, including CLA isomers. In addition, activity indices of stearoyl-CoA desaturase were reduced by increasing levels of FFCG. We conclude that the substitution of corn for FFCG in diets based on cactus cladodes and sugarcane bagasse positively modifies the FA profile of milk and could add commercial value to milk products (e.g., CLA-enriched milk). In addition, the milk fat response indicates that the basal diet was favorable to the rumen environment, preventing the trans-10 shift commonly associated with milk fat depression.

Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin.

Two putative novel Burkholderia cenocepacia lineages found in the semi-arid region of north-east Brazil causing onion sour skin were studied using genomic approaches to determine their taxonomic position. Four strains belonging to one novel lineage (CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171) and one strain (CCRMBC51) belonging to another novel lineage had their whole genome sequenced to carry out taxogenomic analyses. The phylogenomic tree built using the type (strain) genome server (TYGS) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 into the same clade, while grouped the strain CCRMBC51 separately. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analysis showed values above 99.21 % and 93.2 %, respectively, among the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171, while ANI and dDDH values between these strains and the strain CCRMBC51 were below 94.49 % and 56.6 %, respectively. All these strains showed ANI and dDDH values below 94.78 % and 58.8 % concerning type strains of the B. cepacia complex (Bcc) species. The phylogenetic maximum likelihood tree constructed based on the multilocus sequence analysis of core genes (cMLSA) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 and the strain CCRMBC51 in two exclusive clades, which did not cluster with any known species of the Bcc. Therefore, combined data from TYGS, ANI, dDDH, and cMLSA demonstrated that the strains represent two novel species of the Bcc, which we classified as Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., and proposed the strains CCRMBC74T (=IBSBF 3371 T = CBAS 905 T) and CCRMBC51T (=IBSBF3370T = CBAS 904 T) as type strains, respectively.

Polyphasic Characterization of Pigmented Strains of Xanthomonas Pathogenic to Cashew Trees.

The export of cashew (Anacardium occidentale) nuts generates millions of dollars for the Brazilian economy annually. However, production may be limited by the occurrence of diseases that affect cashew trees, such as Xanthomonas spot and angular leaf spot, which are caused by pigmented strains of Xanthomonas and Xanthomonas citri pv. anacardii, respectively. Thirty-one pigmented strains of Xanthomonas were characterized for phenotypic, pathogenic, and molecular attributes. These strains were similar to X. citri pv. anacardii in phenotypical characteristics, sensitivity to antibiotics and copper compounds used in agriculture, epidemiology, and repetitive sequence-based polymerase chain reaction (rep-PCR) profiles. When inoculated into Brazilian pepper, cashew, mango, and hog plum seedlings, the pigmented strains of Xanthomonas and X. citri pv. anacardii produced similar symptoms. However, the pigmented strains of Xanthomonas were more aggressive toward cashew plants than toward the other hosts tested, which confirms their specificity. We conclude that pigmented strains of Xanthomonas are very aggressive on cashew trees and should not be considered casual pathogens of these hosts. Moreover, based on our results from rep-PCR and IS1595-PCR amplification, we suggest that these strains constitute a variant of X. citri pv. anacardii.

Xanthomonas citri pv. viticola Affecting Grapevine in Brazil: Emergence of a Successful Monomorphic Pathogen.

The pathovar viticola of Xanthomonas citri causes bacterial canker of grapevine. This disease was first recorded in India in 1972, and later in Brazil in 1998, where its distribution is currently restricted to the northeastern region. A multilocus sequence analysis (MLSA) based on seven housekeeping genes and a multilocus variable number of tandem repeat analysis (MLVA) with eight loci were performed in order to assess the genetic relatedness among strains from India and Brazil. Strains isolated in India from three related pathovars affecting Vitaceae species and pathogenic strains isolated from Amaranthus sp. found in bacterial canker-infected vineyards in Brazil were also included. MLSA revealed lack of diversity in all seven genes and grouped grapevine and Amaranthus strains in a monophyletic group in X. citri. The VNTR (variable number of tandem repeat) typing scheme conducted on 107 strains detected 101 haplotypes. The total number of alleles per locus ranged from 5 to 12. A minimum spanning tree (MST) showed that Brazilian strains were clearly separated from Indian strains, which showed unique alleles at three loci. The two strains isolated from symptomatic Amaranthus sp. presented unique alleles at two loci. STRUCTURE analyses revealed three groups congruent with MST and a fourth group with strains from India and Brazil. Admixture among populations were observed in all groups. MST, STRUCTURE and e-BURST analyses showed that the strains collected in 1998 belong to two distinct groups, with predicted founder genotypes from two different vineyards in the same region. This suggest that one introduction of grape planting materials contaminated with genetically distinct strains took place, which was followed by pathogen adaptation. Genome sequencing of one Brazilian strain confirmed typical attributes of pathogenic xanthomonads and allowed the design of a complementary VNTR typing scheme dedicated to X. citri pv. viticola that will allow further epidemiological survey of this genetically monomorphic pathovar.

Complete Genome Sequence of Xanthomonas campestris pv. viticola Strain CCRMXCV 80 from Brazil.

Here, we report the complete 5.3-Mb genome sequence of Xanthomonas campestris pv. viticola (CCRMXCV 80), which causes grapevine (Vitis vinifera L.) bacterial canker. Genome data will improve our understanding of the strain's comparative genomics and epidemiology, and help to further define plant protection and quarantine procedures.