Genetics, Plant Science, Molecular Biology, Biochemistry, Genetics and Molecular Biology
19
Scopus Publications
Scopus Publications
A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution Gaetan Droc, Delphine Giraud, Caroline Belser, Karine Labadie, Simone Duprat, et al. Plant Biotechnology Journal, 2026 The main genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa whose radiation occurred in allopatry. In such context, GWAS analysis, genome diversity and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super‐pangenome for cultivated citrus, established with de novo assemblies of C. medica , C. reticulata and C. micrantha , released for the first time alongside a published chromosome‐scale assembly of C. maxima . Repetitive element annotation revealed that half of each genome consisted of transposable elements or DNA‐satellites. The new genome assemblies display strong synteny and collinearity, while discrepancies are observed with the C. maxima assembly. Resequencing information from 55 accessions helped to explore the intra‐ and interspecific diversity of the ancestral taxa and their relationships with horticultural groups. Diagnostic SNPs of the ancestral taxa revealed interspecific introgressions in several representative accessions of C. reticulata , C. maxima and C. medica as well as insights into the origin and phylogenomic structures of horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa. Diagnostic PAV analysis uncovered a large chloroplastic introgression in C. medica chromosome 4. The analysis of the functional enrichment and species‐specific adaptations in the citrus super‐pangenome revealed distinct functional specialisations. This highlights the evolutionary paths that have shaped species, contributing to the diversity in the citrus super‐pangenome while maintaining a shared foundation of essential biological processes. We established a Genome Hub, offering a platform for continuous genomic research.
Azospirillum brasilense as a Bioinoculant to Alleviate the Effects of Salinity on Quinoa Seed Germination Jose David Apaza-Calcina, Milagros Ninoska Munoz-Salas, Flavio Lozano-Isla, Rachel Passos Rezende, Raner José Santana Silva Plants, 2025 Quinoa (Chenopodium quinoa Willd.) is valued for its resilience to abiotic stress; however, germination and seedling establishment remain highly sensitive to salinity. While its salt tolerance at later growth stages has been well studied, strategies to improve early development under high salinity are limited, and the role of halotolerant plant growth-promoting bacteria (PGPB) in quinoa has not been systematically investigated. This study assessed the ability of three Azospirillum brasilense strains (BR-11001, BR-11002, and BR-11005) to increase the germination and seedling performance of the cultivar ‘BRS Piabiru’ under saline stress. A 3 × 4 factorial design with three bacterial treatments and four NaCl concentrations (0, 150, 300, and 450 mM) was conducted in a completely randomized arrangement, with four replicates per treatment. Seeds were surface sterilized, inoculated, and incubated at 18 °C under constant light for 10 days. Elevated salinity (≥300 mM NaCl) drastically reduced germination and seedling vigor in the controls. Inoculation with BR-11002 significantly alleviated salinity-induced damage, sustaining over 84% germination at 450 mM and increasing seedling biomass at 300 mM. These findings highlight the potential of halotolerant A. brasilense, particularly BR-11002, as bioinoculants to promote quinoa establishment in salt-affected soils, supporting sustainable agriculture and food system resilience.
Long-term unsustainable patterns of development rather than recent deforestation caused the emergence of Orthocoronavirinae species Sérvio P. Ribeiro, Debmalya Barh, Bruno Silva Andrade, Raner José Santana Silva, Diogo Henrique Costa‐Rezende, et al. Environmental Microbiology, 2022 We investigated whether a set of phylogeographical tracked emergent events of Orthocoronavirinae were related to developed, urban and polluted environments worldwide. We explored coronavirus records in response to climate (rainfall parameters), population density, CO2 emission, Human Developmental Index (HDI) and deforestation. We contrasted environmental characteristics from regions with spillovers or encounters of wild Orthocoronavirinae against adjacent areas having best‐preserved conditions. We used all complete sequenced CoVs genomes deposited in NCBI and GISAID databases until January 2021. Except for Deltacoronavirus, concentrated in Hong Kong and in birds, the other three genera were scattered all over the planet, beyond the original distribution of the subfamily, and found in humans, mammals, fishes and birds, wild or domestic. Spillovers and presence in wild animals were only reported in developed/densely populated places. We found significantly more occurrences reported in places with higher HDI, CO2 emission, or population density, along with more rainfall and more accentuated seasonality. Orthocoronavirinae occurred in areas with significantly higher human populations, CO2 emissions and deforestation rates than in adjacent locations. Intermediately disturbed ecosystems seemed more vulnerable for Orthocoronavirinae emergence than forested regions in frontiers of deforestation. Sadly, people experiencing poverty in an intensely consumerist society are the most vulnerable.
Cupuassu (Theobroma grandiflorum [Willd. ex Sprengel] Schumann) Fruit Development: Key Genes Involved in Primary Metabolism and Stress Response Lucas Ferraz dos Santos, Raner José Santana Silva, Loeni Ludke Falcão, Rafael Moyses Alves, Lucilia Helena Marcellino, et al. Agronomy, 2022 Cupuassu (Theobroma grandiflorum [Willd. ex Sprengel] Schumann) seeds constitute the raw material for oil extraction and fabrication of cupulate (product similar to chocolate). However, fungal diseases such as witches’ broom caused by Moniliophthora perniciosa have interfered with the large-scale development of cupuassu plantations. Cupuassu genetic breeding programmes focus on a variety of biotechnological tools or approaches to select genes related to quality or resistance mechanisms. In this study, we used expression and interactomics analyses of preselected genes involved in fruit quality and/or resistance to better understand the molecular and physiological mechanisms associated with these plant processes. It was found that (i) resistant and susceptible cupuassu genotypes showed different pulp characteristics as well as gene expression patterns; (ii) monosaccharide and carbohydrate transport pathways were enhanced during fruit maturation; (iii) sugar accumulation participated in signal transduction associated with fruit development and stress response in maturing fruits; and (iv) maturing pulp and seeds showed increased phospholipid metabolism and translocation, as well as immune system activation. The TgSTP1, TgWRKY33, TgCZF1, and TgUBA1 genes in cupuassu and the orthologues of DIN10, CNI1, and TET8 identified by the interactomics approach may be good candidates for marker-assisted selection in breeding programmes focusing on both fruit quality and resistance/tolerance to biotic/abiotic stress.
An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2 Sk. Sarif Hassan, Vaishnavi Kodakandla, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, et al. Peerj, 2022 Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
Genomic Designing for Biotic Stress Resistant Cocoa Tree Fredson dos Santos Menezes, Jonathan Javier Mucherino-Muñoz, Cláusio Antônio Ferreira, Saulo Fabrício da Silva Chaves, Ceslaine Barbosa, et al. Genomic Designing for Biotic Stress Resistant Technical Crops, 2022
Structural and functional genomics of the resistance of cacao to phytophthora palmivora Jonathan Javier Mucherino Muñoz, Cláusio Antônio Ferreira de Melo, Raner José Santana Silva, Edna Dora Martins Newman Luz, Ronan Xavier Corrêa Pathogens, 2021 Black pod disease, caused by Phytophthora spp., is one of the main diseases that attack cocoa plantations. This study validated, by association mapping, 29 SSR molecular markers flanking to QTL (Quantitative Trait Loci) associated with Phytophthora palmivora Butler (Butler) (PP) resistance, in three local ancient varieties of the Bahia (Comum, Pará, and Maranhão), varieties that have a high potential in the production of gourmet chocolate. Four SSR loci associated with resistance to PP were detected, two on chromosome 8, explaining 7.43% and 3.72% of the Phenotypic Variation (%PV), one on chromosome 2 explaining 2.71%PV and one on chromosome 3 explaining 1.93%PV. A functional domains-based annotation was carried out, in two Theobroma cacao (CRIOLLO and MATINA) reference genomes, of 20 QTL regions associated with cocoa resistance to the pathogen. It was identified 164 (genome CRIOLLO) and 160 (genome MATINA) candidate genes, hypothetically involved in the recognition and activation of responses in the interaction with the pathogen. Genomic regions rich in genes with Coiled-coils (CC), nucleotide binding sites (NBS) and Leucine-rich repeat (LRR) domains were identified on chromosomes 1, 3, 6, 8, and 10, likewise, regions rich in Receptor-like Kinase domain (RLK) and Ginkbilobin2 (GNK2) domains were identified in chromosomes 4 and 6.
