Biology subjects

Garcia de la Torre, V. S.

Publications and source records attributed to Garcia de la Torre, V. S..

4 recordsLinked to original sources

bioRxiv2025

Gain and loss of gene function shaped the nickel hyperaccumulation trait in Noccaea caerulescens

Nickel hyperaccumulation is an extreme adaptation to ultramafic soils observed in more than 500 plant species. However, our understanding of the molecular mechanisms underlying the evolution of this trait remains limited. To shed light on these mechanisms, we have generated a high-quality genome assembly of the metal hyperaccumulator Noccaea caerulescens. We then used this genome as reference to conduct comparative intraspecific and interspecific transcriptomic analyses using various accessions of N. caerulescens and the non-accumulating relative Microthlaspi perfoliatum, to identify genes associated with nickel hyperaccumulation. Our results suggest a correlation between nickel hyperaccumulation and a decrease in the expression of genes involved in defense responses and the regulation of membrane trafficking. Surprisingly, these analyses did not reveal a significant enrichment of genes involved in the regulation of metal homeostasis. However, we found that the expression levels of selected metal transporters, namely NcHMA3, NcHMA4 and NcIREG2, is consistently elevated in N. caerulescens accessions hyperaccumulating nickel. Furthermore, our analyses identified frameshift mutations in NcIRT1 associated with the loss of nickel hyperaccumulation in a few accessions. We further showed that the expression of a functional NcIRT1 in roots of the La Calamine accession increases nickel accumulation in shoots. Our results demonstrate that NcIRT1 participate in nickel hyperaccumulation in N. caerulescens. They also suggest that nickel hyperaccumulation is an ancient trait in N. caerulescens that has evolved from the high and constitutive expression of few metal transporters including NcIREG2 and that the trait was subsequently lost in a few accessions due to mutations in NcIRT1.

plant biology↗

bioRxiv2022

Detection of orthologous genes with expression shifts linked to nickel hyperaccumulation across Eudicots

The remarkable capacity of plants to tolerate and accumulate tremendous amount of nickel is a complex adaptative trait that appeared independently in more than 700 species distributed in about fifty families. Nickel hyperaccumulation is thus proposed as a model to investigate the evolution of complex traits in plants. However, the mechanisms involved in nickel hyperaccumulation are still poorly understood in part because comparative transcriptomic analyses struggle to identify genes linked to this trait from a wide diversity of species. In this work, we have implemented a methodology based on the quantification of the expression of orthologous groups and phylogenetic comparative methods to identify genes which expression is correlated to the nickel hyperaccumulation trait. More precisely, we performed de novo transcriptome assembly and reads quantification for each species on its own transcriptome using available RNA-Seq datasets from 15 nickel hyperaccumulator and non-accumulator species. Assembled contigs were associated to orthologous groups built using proteomes predicted from completed plant genome sequences. We then analyzed the transcription profiles of 5953 orthologous groups from distant species using a phylogenetic ANOVA. We identified 31 orthologous groups with an expression shift associated with nickel hyperaccumulation. These orthologous groups correspond to genes that have been previously implicated in nickel accumulation, and to new candidates involved in this trait. We thus believe that this method can be successfully applied to identify genes linked to other complex traits from a wide diversity of species.

plant biology↗

bioRxiv2018

Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants

The Anthropocene epoch is associated with the spreading of metals in the environment increasing oxidative and genotoxic stress on living organisms1,2. Once regarded as a curiosity, plants hyperaccumulating metals are now envisioned as an opportunity to remediate metal contaminated soils. About 500 plant species adapted to metalliferous soils acquired the capacity to hyperaccumulate (>0.1% of dry weight) nickel in their shoot3. The phylogenetic distribution of these hyperaccumulators in 50 families suggest that this complex trait evolved multiple times independently from basic mechanisms involved in metal homeostasis. However, the exact nature of these mechanisms and whether they are shared between various lineages is not known. Here, using cross-species transcriptomic analyses in different plant families, we have identified convergent functions that may represent major nodes in the evolution of nickel hyperaccumulation. In particular, our data point out that constitutive high expression of IREG/Ferroportin transporters recurrently emerged as a mechanism involved in nickel hyperaccumulation.

plant biology↗

bioRxiv2018

Vacuolar iron stores gated by NRAMP3 and NRAMP4 are the primary source of iron in germinating seeds

During seed germination, iron (Fe) stored in vacuoles is exported by the redundant NRAMP3 and NRAMP4 transporter proteins. A double nramp3 nramp4 mutant is unable to mobilize Fe stores and does not develop in the absence of external Fe. We used RNA sequencing to compare gene expression in nramp3 nramp4 and wild type during germination and early seedling development. Even though sufficient Fe was supplied, the Fe-responsive transcription factors bHLH38, 39, 100 and 101 and their downstream targets FRO2 and IRT1 mediating Fe uptake were strongly upregulated in the nramp3 nramp4 mutant. Activation of the Fe deficiency response was confirmed by increased ferric chelate reductase activity in the mutant. At early stages, genes important for chloroplast redox control (FSD1, SAPX), Fe homeostasis (FER1, SUFB) and chlorophyll metabolism (HEMA1, NYC1) were downregulated, indicating limited Fe availability in plastids. In contrast, expression of FRO3, encoding a ferric reductase involved in Fe import into the mitochondria, was maintained and Fe-dependent enzymes in the mitochondria were unaffected in nramp3 nramp4. Together these data show that a failure to mobilize Fe stores during germination triggered Fe deficiency responses and strongly affected plastids but not mitochondria.

plant biology↗