A chromosome-level genome of mango exclusively from long-read sequence data

Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome-level mango genome using only PacBio high-fidelity (HiFi) long reads. HiFi reads at high coverage (204x) resulted in the assembly of 17 chromosomes, each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs, with telomeres at one end and ribosomal repeats at the other end. Analyzing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere but with ribosomal repeats of uncertain length. The assembled genome was 365 Mb with 100% completeness as assessed by Benchmarking Universal Single-Copy Orthologs analysis. The haplotypes assembled demonstrated extensive structural differences. This approach using very high genome coverage may be useful for assembling high-quality genomes for many other plants.

The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool

Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica. This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars.

The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality

BACKGROUND

Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency.

RESULTS

This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar 'Tommy Atkins'. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins', supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between 'Tommy Atkins' x 'Kensington Pride' was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the 'Tommy Atkins' x 'Kensington Pride' mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population.

CONCLUSIONS

The availability of the complete 'Tommy Atkins' mango genome will aid global initiatives to study mango genetics.

Genetic Map of Mango: A Tool for Mango Breeding

Mango (Mangifera indica) is an economically and nutritionally important tropical/subtropical tree fruit crop. Most of the current commercial cultivars are selections rather than the products of breeding programs. To improve the efficiency of mango breeding, molecular markers have been used to create a consensus genetic map that identifies all 20 linkage groups in seven mapping populations. Polyembryony is an important mango trait, used for clonal propagation of cultivars and rootstocks. In polyembryonic mango cultivars, in addition to a zygotic embryo, several apomictic embryos develop from maternal tissue surrounding the fertilized egg cell. This trait has been associated with linkage group 8 in our consensus genetic map and has been validated in two of the seven mapping populations. In addition, we have observed a significant association between trait and single nucleotide polymorphism (SNP) markers for the vegetative trait of branch habit and the fruit traits of bloom, ground skin color, blush intensity, beak shape, and pulp color.

Cell and humoral immunity in endemic pemphigus foliaceus

A study was conducted on 16 patients with pemphigus foliaceus, ten of them with the localized form (group G1) and six with the disseminated form (group G2). These patients were submitted to full blood counts, quantitation of mononuclear cell subpopulations by monoclonal antibodies, study of blastic lymphocyte transformation, and quantitation of circulating antibodies by the indirect immunofluorescence test, in order to correlate their clinical signs and symptoms and laboratory data with their immunological profile, and to determine the relationship between circulating autoantibody titers and lesion intensity and course of lesions under treatment. Leucocytosis was observed especially in group G2. All patients showed decreased relative CD3+ and CD4+ values and a tendency to decreased relative values of the CD8+ subpopulation. Blastic lymphocyte transformation indices in the presence of phytohemagglutinin were higher in patients (group G1 + G2) than in controls. The indirect immunofluorescence test was positive in 100% of G2 patients and in 80% of G1 patients. The median value for the titers was higher in group G2 than in group G1. Analysis of the results as a whole permits us to conclude that cell immunity was preserved and that there was a relationship between antibody titers detected by the direct immunofluorescence test and extent of skin lesions.

Evaluation of nutritional status in patients with endemic pemphigus foliaceus

Sixteen patients with endemic pemphigus foliaceus were submitted to nutritional evaluation. Ten had the localized form of the disease (Group G1) and six the disseminated form (Group G2). The patients were submitted to anthropometric measurements (weight, height, Quetelét index, tricipital skin fold, subscapular skin fold, arm circumference, arm muscle circumference, arm area, arm muscle area, and arm adipose area) and to laboratory evaluation by protein electrophoresis. Arm circumference, arm area and arm muscle area showed lower values in G2 than in G1. Weight and arm muscle circumference tended to the lower in G2 than in G1. Protein electrophoresis showed decreased albumin levels in both groups, with lower values in G2. Overall analysis of the results permits us to conclude that patients with endemic pemphigus foliaceus present signs and symptoms of protein, but not calorie, malnutrition and that this malnutrition is more marked in patients with disseminated pemphigus foliaceus.

[Outbreak of American cutaneous leishmaniasis in Itaporanga, São Paulo (Brazil)]

An outbreak of cutaneous leishmaniasis in a small rural settlement, located in the Southern of São Paulo State-Brazil was observed. This region has basic agricultural activities, and has no forests. Two hundred and thirty one persons were evaluated, and the following aspects were observed. 1) 67 individuals (29%) had skin lesions, confirmed by histopathologic study and the Montenegro skin test; 2) of these cases, 40 (59.7%) were males; 3) The youngest patients were 2 years (5 cases), and the oldest, 86 (1 case); 4) the following types of cutaneous lesions, were observed: a) 54 cases (80.6%) had ulcers, 13 (19.4%) had nodules, 4 (5.9%) had verrucose lesions, and 3 (4.4%) had typical scars. In all the cases, the parasite identified was Leishmania (Viannia) braziliensis. The vector captured in the region was Lutzomyia intermedia, a strong anthropophilic sandfly very frequently observed in São Paulo. This study shows that apart from the well-known outbreak observed in the forest environments, leishmaniasis can be transmitted within or around dwellings.

[Accidental cutaneous leishmaniasis]

The authors report the 3rd case of cutaneous leishmaniasis due to accidental contamination of a student of biological sciences during laboratory research. The inoculation occurred when amastigotes of Leishmania (Viannia) braziliensis from infected hamsters were injected in healthy animals. At this stage, the student had her glove bitten by a healthy hamster and the infection was probably conveyed by the direct contact of the inoculum with the skin.

[Microsporum nanum. A fourth report of human infection in Brazil]

The authors present the fourth Brazilian case of human Microsporum nanum (M. nanum) infection. A child of nine months old presents cutaneous dorsal lesions compatible with tinea corporis, which appeared one month before. The culture revealed M. nanum. The lesions resolved spontaneously after a month. Epidemiologic investigation in the patient's place of origin identified swine infected by M. nanum, indicating the probable source of the infection.

Delayed results of treatment of paracoccidioidomycosis with amphotericin B plus sulfamides versus amphotericin B alone

A delayed evaluation of two groups of patients with paracoccidioidomycosis was carried out. Both groups were treated with amphotericin B, "but one of them was submitted to maintenance treatment with sulfonamides. Statistical analysis showed that treatment is more effective when patients are maintained with sulfonamide drugs.

Paracoccidioidomycosis: a comparative study of the evolutionary serologic, clinical and radiologic results for patients treated with ketoconazole or amphotericin B plus sulfonamides

A comparative study of two groups of patients with paracoccidioidomycosis was carried out with the objective of comparing the evolutionary serologic, clinical and radiologic results after 6, 12, 15 and 18 months of treatment with ketoconazole (22 patients) or amphotericin B plus sulfonamides (32 patients). The serologic data analyzed as a whole showed a tendency to sharper drops in antibody titers in the patients treated with ketoconazole. Clinically patients treated with ketoconazole fared better but the differences were not statistically significant. No statistical difference was detected between groups in terms of the results of radiologic evolution.

Correlation between cell-mediated immunity and clinical forms of paracoccidioidomycosis

Cellular immune response to specific and non-specific stimulants was investigated, both in vivo and in vitro, in 29 healthy controls and in 53 previously untreated patients with the chronic isolated organic form (CIOF), the chronic mixed form (CMF) and the acute progressive form (APF) of paracoccidioidomycosis. The study included skin tests to Paracoccidioides brasiliensis antigen (PbAg) and phytohaemagglutinin (PHA), DNCB sensitization, determination of T lymphocytes and complement rosette-forming cells, lymphocyte transformation and leucocyte migration inhibition tests using PbAg and PHA. Patients displayed staggered cutaneous response to PHA and to PbAg, with marked decrease in intensity in the APF group. DNCB sensitization test and proliferative response of lymphocytes to PHA and PbAg were severely depressed in most of the patients. Leucocyte migration inhibition indices to PbAg were highly positive, while response to PHA was slightly decreased regardless of the clinical form. The number of T lymphocytes was reduced in most of patients and in them the number of complement-rosette forming cells was normal. The distribution of patients according to a suppression index, based in the results of the tests employed, revealed a tendency towards an increased degree of cellular immunosuppression from the least severe (CIOF) to the most severe (APF) clinical form of the disease. On the whole, the present study demonstrated a gamut of immunological reactivity in paracoccidioidomycosis.

[Microsporum nanum. Report of the 2d case of human infection in Brazil]

É comunicado o segundo caso de infecção humana por Microsporum nanum no Brasil. A investigação epidemiológica visando determinar a fonte de infecção não obteve sucesso. O padrão dermatológico das lesões foi o de Tinea corporis clássica.