Biology subjects

Bamba, M.

Publications and source records attributed to Bamba, M..

8 recordsLinked to original sources

bioRxiv2025

Chromosome-level genome assembly of the gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies

Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida, which was developed through hybridization of two wild species. Sequencing was performed using a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). The total span of the nuclear genome assembly is 2.32 gigabases, and 99.3% of the sequence assembled into 25 scaffolds, consistent with the known chromosome number. Genome annotation of the nuclear genome identified 36,160 protein-coding genes and 11,572 non-coding transcripts. The mitochondrial genome had 363,511 bp and contains 36 protein-coding genes, 3 rRNAs, and 21 tRNAs, while the chloroplast genome is 151,898 bp in length and includes 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.

plant biology↗

bioRxiv2025

Cyclophilin A-mediated cis/trans isomerization modulates RIN4 to control intracellular rhizobial infection in legumes

In most legume-rhizobium symbioses, rhizobial colonization occurs through host-derived intracellular infection threads, which enable recruitment of compatible rhizobia while presumably modulating the host immune system to prevent rejection. To investigate how legumes regulate immune responses through post-translational mechanisms during the infection, we focused on Cyclophilin A (CyPA), a peptidyl-prolyl cis/trans isomerase. The model legume Lotus japonicus encodes three canonical CyPA genes. Among them, LjCyPA1 was characterized through CRISPR/Cas9-mediated knockout analysis and shown to be important for normal intracellular infection of compatible rhizobia. A gain-of-function LjCyPA1 variant in a soybean cultivar was able to promote symbiosis with not only compatible but also incompatible rhizobia. Structural modeling followed by genetic analysis demonstrated a functional interaction between LjCyPA1 and the immune hub protein LjRIN4. The cis conformation of LjRIN4 promoted intracellular rhizobial infection, while the trans conformation suppressed it. LjCyPA1 acted with the rhizobial type III secretion system (T3SS) which exhibited a cooperative role between host and symbiont in facilitating infection. Phylogenomic analysis showed that conservation of the CyPA1 orthologue is correlated with the trait of intracellular infection in legumes. Our results contribute to the understanding of how legumes accept symbiotic partners while balancing immune responses.

plant biology↗

bioRxiv2023

Species Composition and Distribution of Anopheles gambiae Complex Circulating in Kinshasa

Understanding the distribution of Anopheles species in a region is an important task in the planning and implementation of malaria control programmes. This study was proposed to evaluate the composition and distribution of cryptic species of the main malaria vector, Anopheles gambiae complex, circulating in different districts of Kinshasa. To study the distribution of members of the An. gambiae complex, Anopheles were sampled by CDC light trap and larva collection across the four districts of Kinshasa city between July 2021 and June 2022. After morphological identification, an equal proportion of Anopheles gambiae s.l. sampled per site were subjected to polymerase chain reaction (PCR) for identification of cryptic An. gambiae complex species. The Anopheles gambiae complex was widely identified in all sites across the city of Kinshasa, with a significant difference in mean density, captured by CDC light, inside and outside households in Kinshasa (p=0.002). Two species of this complex circulate in Kinshasa: Anopheles gambiae (82.1%) and Anopheles coluzzii (17.9%). In all study sites, Anopheles gambiae was the most prevalent species. Anopheles coluzzii was very prevalent in Tshangu district. No hybrids (Anopheles coluzzii/Anopheles gambiae) were identified. Two cryptic species of the Anopheles gambiae complex circulate in Kinshasa. Anopheles gambiae s.s., present in all districts and Anopheles coluzzii, with a limited distribution. Studies on the ecology of the larval sites are essential to better understand the factors influencing the distribution of members of the An. gambiae complex in this megalopolis.

zoology↗

bioRxiv2023

Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo

Arbovirus epidemics (e.g. Chikungunya, dengue, West Nile, Yellow Fever, and Zika), are a growing threat in Africa in areas where Aedes (Ae.) aegypti and A. albopictus are present. The lack of complete sampling of these two vectors limits our ability to understand their propagation dynamics in areas at risk from arboviruses. Here, we describe for the first time the geographical distribution of two arbovirus vectors (Ae. aegypti and Ae. albopictus) in a chikungunya post-epidemic zone in the provincial city of Kinshasa, Democratic Republic of Congo between 2020 and 2022. In total 6,943 observations were reported using larval capture and human capture on landing methods. These data are published in the public domain as a Darwin Core archive in the Global Biodiversity Information Facility. The results of this study potentially provide important information for further basic and advanced studies on the ecology and phenology of these vectors, as well as on vector dynamics after an epidemic period. Subject AreasEcology, Biodiversity, Taxonomy Data description

zoology↗

bioRxiv2022

Receptor-like kinases FER and SRK mediate Lotus japonicus freezing tolerance and climate adaptation

Many plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Here, we show that two of these, the FERONIA-receptor like kinase (LjFER) and a novel S-receptor-like kinase (LjSRK) are required for non-acclimated freezing tolerance and show haplotype-dependent cold-responsive expression. Our work demonstrates that recruiting a conserved growth regulator, FER, and a novel receptor-like kinase, SRK, into the set of cold-responsive genes has contributed to freezing tolerance and local climate adaptation in L. japonicus, offering new functional genetic insight into perennial herb evolution.

plant biology↗

bioRxiv2022

Genotype by microbiome interactions have large effects on growth in Lotus japonicus

Biological interactions between plants and their root microbiomes are pivotal for plant growth. Even though the plant genotype [G], soil microbiome [C], and growth conditions (environment) [E] are core factors shaping the root microbiome, their relationships remain unclear. We disentangled the effects of G, C, E, and their interactions on the Lotus root microbiome and plant growth using a cross-inoculation approach that reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. We found that a large proportion of the root microbiome composition was determined by C and E and that G-related (G, G x C, and G x E) effects were significant but small. In contrast, the interactions between G and C had a more pronounced effect on plant shoot growth than C alone. Our findings indicate that most microbiome variations controlled by C have little effect on the plant phenotype, whereas G x C interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention in efforts to optimize crop yield and resilience.

plant biology↗

bioRxiv2021

A photoactivable natural product with broad antiviral activity against enveloped viruses including highly pathogenic coronaviruses

The SARS-CoV-2 outbreak has highlighted the need for broad-spectrum antivirals against coronaviruses (CoVs). Here, pheophorbide a (Pba) was identified as a highly active antiviral molecule against HCoV-229E after bioguided fractionation of plant extracts. The antiviral activity of Pba was subsequently shown for SARS-CoV-2 and MERS-CoV, and its mechanism of action was further assessed, showing that Pba is an inhibitor of coronavirus entry by directly targeting the viral particle. Interestingly, the antiviral activity of Pba depends on light exposure, and Pba was shown to inhibit virus-cell fusion by stiffening the viral membrane as demonstrated by cryo-electron microscopy. Moreover, Pba was shown to be broadly active against several other enveloped viruses, and reduced SARS-CoV-2 and MERS-CoV replication in primary human bronchial epithelial cells. Pba is the first described natural antiviral against SARS-CoV-2 with direct photosensitive virucidal activity that holds potential for COVID-19 therapy or disinfection of SARS-CoV-2 contaminated surfaces.

microbiology↗

bioRxiv2020

Massive rhizobial genomic variations associated with partner quality in Lotus-Mesorhizobium symbiosis

In diverse mutualistic relationships, genetic variations in impact on the growth of interacting partners--variations in partner quality--are common, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variations. Here, we investigated how variations in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variations in the core genome and the contrastingly similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using nine sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variations represented by plant growth phenotypes, including genotype-by-genotype interactions. Quality variations were not associated with the presence/absence variations of known symbiosis-related genes in the symbiosis island, but rather, showed significant correlations with the core genome variations, supported by SNP- and kinship matrix-based association analyses. These findings highlight the novel role of HGT of symbiosis islands, which indirectly supply mutations of core genomes into L. japonicus-associated bacteria, thereby contributing to the maintenance of variations in partner quality.

evolutionary biology↗