Recent Submissions

  • Learning from the expert: studying Salicornia to understand salinity tolerance

    Salazar Moya, Octavio Ruben; Chen, Ke; Melino, Vanessa J.; Reddy, Muppala P.; Hřibová, Eva; Čížková, Jana; Beránková, Denisa; Aranda, Manuel; Jaremko, Lukasz; Jaremko, Mariusz; Fedoroff, Nina V.; Tester, Mark A.; Schmoeckel, Sandra Manuela (Cold Spring Harbor Laboratory, 2023-04-23) [Preprint]
    Salinity remains a major inhibitor of crop production in irrigated and marginal lands. The identification of genes involved in salinity tolerance has been predominantly limited to model plants and crop species. However, plants naturally adapted to highly saline environments can provide key insights into mechanisms of salinity tolerance. Plants of the genus Salicornia grow in coastal salt marshes, and their growth is even stimulated by NaCl – much can be learnt from them. We generated genome sequences of two Salicornia species and studied the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Through the generation of subcellular membrane proteomes, we found that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, where it could be involved in mediating Na+ translocation into the vacuole to prevent toxicity in the cytosol. We identified 11 proteins of interest which, when expressed in yeast, altered salinity tolerance. One of these proteins, SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR showed it to be an intrinsically disordered protein and to localize to the endoplasmic reticulum in planta, where it could interact with ribosomes and RNA, potentially stabilizing or protecting them during salt stress. The study and understanding of the molecular mechanisms providing high salinity tolerance in S. bigelovii is likely to provide significant insights for improving salinity tolerance of crop plants.
  • LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology.

    Driguez, Patrick; Bougouffa, Salim; Carty, Karen; Putra, Alexander; Jabbari, Kamel; Reddy, Muppala P.; Soppe, Richard Willem Otto; Cheung, Ming Sin; Fukasawa, Yoshinori; Ermini, Luca (Genome biology, Springer Science and Business Media LLC, 2021-09-03) [Article]
    Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.
  • LeafGo - Eucalyptus and Peanut genome sequencing

    Driguez, Patrick; Bougouffa, Salim; Carty, Karen; Putra, Alexander; Jabbari, Kamel; Reddy, Muppala P.; Soppe, Richard Willem Otto; Cheung, Ming Sin; Fukasawa, Yoshinori; Ermini, Luca (NCBI, 2020-11-05) [Bioproject, Dataset]
    The sequencing and the assembly of chromosome-level genomes following the LeafGo protocol using a single long read technology.
  • A diversity of traits contributes to salinity tolerance of wild Galapagos tomatoes seedlings

    Pailles, Yveline; Awlia, Mariam; Julkowska, Magdalena M.; Passone, Luca; Zemmouri, Khadija; Negrão, Sónia; Schmoeckel, Sandra Manuela; Tester, Mark A. (Cold Spring Harbor Laboratory, 2019-05-20) [Preprint]
    AbstractTraits of modern crops have been heavily selected in agriculture, causing the commercial lines to be more susceptible to harsh conditions, which their wild relatives are naturally better able to withstand. Understanding the developed mechanisms of tolerance present in wild relatives can enhance crop performance under stress. In this study, salinity tolerance traits of two species of wild tomato endemic to the Galapagos Islands, Solanum cheesmaniae and Solanum galapagense, were investigated. Since these tomatoes grow well despite being constantly splashed with seawater, they could be a valuable genetic resource for improving salinity tolerance in commercial tomatoes. To explore their potential, over 20 traits reflecting plant growth, physiology and ion content were recorded in 67 accessions of S. cheesmaniae and S. galapagense and two commercial tomato lines of Solanum lycopersicum. Salt treatments of 200 mM NaCl were applied for ten days, using supported hydroponics. Great natural variation was evident in the responses of the Galapagos tomatoes to salt stress and they also displayed greater tolerance to salt stress than the commercial lines tested, based on multivariate trait analyses. Although Galapagos tomatoes in general exhibited better tolerance to salt stress than the commercial lines tested, the accessions LA0317, LA1449 and LA1403 showed particularly high salinity tolerance based on growth maintenance under stress. Thus, Galapagos tomatoes should be further explored using forward genetic studies to identify and investigate the genes underlying their high tolerance and be used as a resource for increasing salinity tolerance of commercial tomatoes. The generated data, along with useful analysis tools, have been packaged and made publicly available via an interactive online application ( to facilitate trait selection and the use of Galapagos tomatoes for the development of salt tolerant commercial tomatoes.
  • Isolation and sequence characterization of DNA-A genome of a new begomovirus strain associated with severe leaf curling symptoms of Jatropha curcas L.

    Chauhan, Sushma; Rahman, Hifzur; Mastan, Shaik G.; Sudheer, Pamidimarri D.V.N.; Reddy, Muppala P. (Gene, Elsevier BV, 2018-04-22) [Article]
    Begomoviruses belong to the family Geminiviridae are associated with several disease symptoms, such as mosaic and leaf curling in Jatropha curcas. The molecular characterization of these viral strains will help in developing management strategies to control the disease. In this study, J. curcas that was infected with begomovirus and showed acute leaf curling symptoms were identified. DNA-A segment from pathogenic viral strain was isolated and sequenced. The sequenced genome was assembled and characterized in detail. The full-length DNA-A sequence was covered by primer walking. The genome sequence showed the general organization of DNA-A from begomovirus by the distribution of ORFs in both viral and anti-viral strands. The genome size ranged from 2844 bp–2852 bp. Three strains with minor nucleotide variations were identified, and a phylogenetic analysis was performed by comparing the DNA-A segments from other reported begomovirus isolates. The maximum sequence similarity was observed with Euphorbia yellow mosaic virus (FN435995). In the phylogenetic tree, no clustering was observed with previously reported begomovirus strains isolated from J. curcas host. The strains isolated in this study belong to new begomoviral strain that elicits symptoms of leaf curling in J. curcas. The results indicate that the probable origin of the strains is from Jatropha mosaic virus infecting J. gassypifolia. The strains isolated in this study are referred as Jatropha curcas leaf curl India virus (JCLCIV) based on the major symptoms exhibited by host J. curcas.
  • TDZ-Induced Plant Regeneration in Jatropha curcas: A Promising Biofuel Plant

    Kumar, Nitish; Bhatt, Vacha D.; Mastan, Shaik G.; Reddy, Muppala P. (Thidiazuron: From Urea Derivative to Plant Growth Regulator, Springer Nature, 2018-03-24) [Book Chapter]
    In recent years, Jatropha curcas has pronounced attention due to its capacity of production of biodiesel. Uniform large-scale propagation of J. curcas is one of the significant keys that will eventually decide victory. Direct regeneration is one of the methods which help in the production of uniform and homogenous plant, and TDZ plays an important role in the production of plantlets by direct organogenesis in several number of plant species including J. curcas. Measuring the economical importance of J. curcas and the role of TDZ in shoot regeneration, the present book chapter briefly reviews the impact of TDZ on shoot bud induction from various explants of J. curcas.
  • Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

    Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira Santillán, María José; Fusi, Marco; Bariselli, Paola; Reddy, Muppala P.; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele (Frontiers in Microbiology, Frontiers Media SA, 2016-08-22) [Article]
    Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.