Biology subjects

Facchiano, A.

Publications and source records attributed to Facchiano, A..

4 recordsLinked to original sources

bioRxiv2024

The mitochondrial orf125 affects male fertility of Solanum tuberosum (+) S. commersonii somatic hybrids and participates in the onset of ''Tuberosum''-Type CMS and evolution of common potato

Cytoplasmic male sterility (CMS) is an agronomically significant trait and a powerful tool to study interactions between nuclear and cytoplasmic genomes. In this study, the chondriomes of two isonuclear male-fertile and sterile somatic hybrids (SH9A and SH9B, respectively) between the common potato (Solanum tuberosum Group Tuberosum, tbr) and the wild species S. commersonii (cmm), were sequenced and compared to those of parental species to identify mitochondrial genes involved in the expression of male sterility. A putative novel gene (orf125) was found only in tbr and in male-sterile hybrids. Two approaches, a physical or functional deletion of orf125 by mtDNA editing in SH9B and its allotopic expression in SH9A, clearly demonstrate that orf125 affects male fertility. To trace the origin of orf125 and hypothesize its role in the evolution of common potato, we searched it in tbr varieties, tuber-bearing potato relatives and other Solanaceae. The organization of the mitochondrial genome region implicated in CMS remained consistent across all common potato accessions in GenBank. An identical tbr copy of orf125 was also detected in all six accessions belonging to the S. berthaultii complex (ber) analyzed. Such findings corroborate the hypothesis that ber accessions with T/{beta} cytoplasm crossed as female with Andean potato (S. tuberosum Group Andigenum, adg), giving rise to the differentiation of the Chilean potato (S. tuberosum Group Chilotanum), and highlights the origin of mitochondrial factors contributing to genic-cytoplasmic male sterility in tbr x adg (or some wild species) hybrids.

plant biology↗

bioRxiv2022

In Silico Analysis Of The Effects Of Omicron Spike Amino Acid Changes On The Interactions With Human ACE2 Receptor And Structurally Characterized Complexes With Human Antibodies

The new SARS-CoV-2 variant Omicron is characterised, among others, by more than 30 amino acid changes (including 4 deletions and 1 insertion) occurring on the spike glycoprotein. We report a comprehensive analysis of the effects of the Omicron spike amino acid changes in the interaction with human ACE2 receptor or with human antibodies, obtained by analysing the publicly available resolved 3D structures. Our analysis predicts that amino acid changes occurring on amino acids interacting with the ACE2 receptor may increase Omicron transmissibility. The interactions of Omicron spike with human antibodies can be both negatively and positively affected by amino acid changes, with a predicted total loss of interactions only in few complexes. We believe that such an approach can be used to better understand SARS-CoV-2 transmissibility, detectability, and epidemiology, especially when extended to other than spike proteins.

bioinformatics↗

bioRxiv2021

On the capacity of putative plant odorant-binding proteins to bind volatile plant isoprenoids

Plants use odors not only to recruit other organisms for symbioses, but to talk to each other. Volatile organic compounds (VOCs) from "emitting" plants inform the "receiving" (listening) plants of impending stresses or simply of their presence. However, the receptors that allow receivers to perceive the volatile cue are elusive. Most likely, plants (as animals) have odorant bind proteins (OBPs), and in fact few OBPs are known to bind "stress-induced" plant VOCs. We investigated whether OBPs may bind volatile constitutive and stress-induced isoprenoids, the most emitted plant VOCs, with well-established roles in plant communication. First, we performed a data base search that generated a list of candidate plant OBPs. Second, we investigated in silico the ability of the identified candidate plant OBPs to bind VOCs by molecular simulation experiments. Our results show that monoterpenes can bind the same OBPs that were described to bind other stress-induced VOCs. Whereas, the constitutive hemiterpene isoprene does not bind any investigated OBP and may not have an info-chemical role. We conclude that, as for animal, plant OBPs may bind different VOCs. Despite being generalist and not specialized, plant OBPs may play an important role in allowing plants to eavesdrop messages sent by neighboring plants.

plant biology↗

bioRxiv2018

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites.

BackgroundCapsicum is one of the major vegetable crops grown world-wide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Fruits broad variability has been driven by breeding programs and has been mainly studied by linkage analysis.\n\nResultsWe discovered 746k variable sites by sequencing 1.8% of the genome in a collection of 373 accessions belonging to 11 Capsicum species from 51 countries. We describe genomic variation at population-level, confirm major subdivision in clades and species, and show that the known subdivision of C. annuum in two groups separates large and bulky fruits form small ones. In C. annuum, we identify four novel loci associated with phenotypes determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g16080).\n\nConclusionsOur collection covers all the economically important species of Capsicum widely used in breeding programs, and represent the widest and largest study so far in terms of the number of species and genetic variants analyzed. We identified a large set of markers that can be used for population genetic studies and genetic association analyses. Our results foster fine genetic association studies and foresee genomic variability at population-level.

genetics↗