Biology subjects

Lijavetzky, D.

Publications and source records attributed to Lijavetzky, D..

5 recordsLinked to original sources

bioRxiv2024

Transcriptomic regulation of juvenile-to-adult vegetative phase transition in grapevine

Plants go through two distinct stages in their vegetative phase, with the juvenile stage being characterized by a lack of maturity to respond to flowering induction stimuli and the adult stage marked by the presence of this capacity. Phase transition has been extensively analysed in herbaceous species such as Arabidopsis and maize, where the sequential activity of miR156 and miR172 in the control of the juvenile to adult phase transition has been determined. Contrarily, little is known about most woody perennial crops, where phase transition appears to be dissociated, with a first transition from juvenile to adult vegetative state in the first year and a subsequent induction to flower in later years under flowering-inductive environmental conditions. This significantly extended vegetative phase makes fruit production depend on the grafting of adult vegetative materials. A particular aspect of grapevine vegetative phase transition is that it is marked by the differentiation of tendrils, a modified sterile reproductive organ adapted to climbing, which is continuously generated with different patterns in different Vitis species. When the grapevine plant reaches flowering inductive condition in later years, it produces inflorescences in place of some tendrils. As a first step to understand the regulation of phase change in grapevine, we have performed a detailed gene expression analysis of the juvenile-to-adult phase transition during the development of grapevine plantlets grown from seeds. The RNA-seq analysis demonstrated that miR156 was significantly repressed in the grapevines adult phase, where the appearance of tendrils acts as a marker of the transition. Consistent with the results reported in other species, we observed the activation of several SPL genes, known to be targets of miR156, providing evidence for the conservation of the miR156-SPLs regulatory module in grapevine. However, no variation was detected in the expression of miR172 and TPS genes were found downregulated, two key determinants in the transition to flowering in other species. This could be explained considering that grapevines do not flower during the first years of growth. Interestingly, we were able to observe the overexpression of several genes known to be involved in the establishment of flower meristem identity, which in the case of grape had also been detected along tendril development, consistent with the proposed common ontogenetic origin of tendrils and inflorescences in the Vitaceae family.

plant biology↗

bioRxiv2024

Birnaviral Hijacking of Endosomal Membranes

Birnaviruses are a group of double-stranded RNA (dsRNA) viruses infecting birds, fish and insects. Early endosomes (EE) constitute the platform for viral replication. Here, we study the mechanism of birnaviral targeting of EE membranes. Using the Infectious Bursal Disease Virus (IBDV) as a model, we validate that the viral protein 3 (VP3) binds to phosphatidylinositol-3-phosphate (PI3P) present in EE membranes. We identify the domain of VP3 involved in PI3P-binding, named P2 and localized in the core of VP3, and establish the critical role of the arginine at position 200 (R200), conserved among all known birnaviruses. Mutating R200 abolishes viral replication. Moreover, we propose a two-stage modular mechanism for VP3 association with EE. Firstly, the carboxy-terminal region of VP3 adsorbs on the membrane, and then the VP3 core reinforces the membrane engagement by specifically binding PI3P through its P2 domain, additionally promoting PI3P accumulation. Significance StatementBirnaviruses are a family of viruses unique among the group of dsRNA viruses. Here, we show that VP3 seizes the endosomes by anchoring to the PI3P lipids in the luminal side of the EE membrane, in order to organize the viral replication factory. We propose a two-stage modular mechanism for VP3 association with PI3P-enriched EE. The significance of this work resides in the biochemical and biophysical insights on the mechanism of association of VP3 with EE and its role in the viral life cycle, which represents a substantial contribution toward understanding the replication strategy of these "non-canonical" viruses.

microbiology↗

bioRxiv2023

Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

1.To preserve their varietal attributes, established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines, and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with very low haplotype switch-error rate (<0.025). The haplophases alignment identified >25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated to abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and to unveil the molecular bases of clonal phenotypic variation.

genomics↗

bioRxiv2020

Clonal propagation history shapes the intra-cultivar genetic diversity in Malbec grapevines

Grapevine (Vitis vinifera L.) cultivars are clonally propagated to preserve their varietal attributes. However, novel genetic variation still accumulates due to somatic mutations. Aiming to study the potential impact of clonal propagation history on grapevines intra-cultivar genetic diversity, we have focused on Malbec. This cultivar is appreciated for red wines elaboration, it was originated in Southwestern France and introduced into Argentina during the 1850s. Here, we generated whole-genome resequencing data for four Malbec clones with different historical backgrounds. A stringent variant calling procedure was established to identify reliable clonal polymorphisms, additionally corroborated by Sanger sequencing. This analysis retrieved 941 single nucleotide variants (SNVs), occurring among the analyzed clones. Based on a set of validated SNVs, a genotyping experiment was custom-designed to survey Malbec genetic diversity. We successfully genotyped 214 samples and identified 14 different clonal genotypes, that clustered into two genetically divergent groups. Group-Ar was driven by clones with a long history of clonal propagation in Argentina, while Group-Fr was driven by clones that have longer remained in Europe. Findings show the ability of such approaches for clonal genotypes identification in grapevines. In particular, we provide evidence on how human actions may have shaped Malbec extant genetic diversity pattern.

genomics↗

bioRxiv2020

Identification and functional prediction of anthocyanin biosynthesis regulatory long non-coding RNAs (lncRNAs) in carrot

Carrot (Daucus carota L.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical roles in regulating gene expression of various biological processes in plants. In this study, we used a high throughput stranded RNA-seq to identify and analyze the expression profiles of lncRNAs in phloem and xylem root samples using two genotypes with a strong difference in anthocyanin production. We discovered and annotated 8484 new genes, including 2095 new protein-coding and 6373 non-coding transcripts. Moreover, we identified 639 differentially expressed lncRNAs between the phenotypically contrasted genotypes, including certain only detected in a particular tissue. We then established correlations between lncRNAs and anthocyanin biosynthesis genes in order to identify a molecular framework for the differential expression of the pathway between genotypes. A specific natural antisense transcript (NAT) linked to the DcMYB7 key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.

genomics↗