Greenhouse Core Lab

Permanent URI for this collection


Recent Submissions

Now showing 1 - 5 of 7
  • Preprint

    Learning from the expert: studying Salicornia to understand salinity tolerance

    (Cold Spring Harbor Laboratory, 2023-04-23) 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; Biological and Environmental Science and Engineering (BESE) Division; Greenhouse Core Lab; Center for Desert Agriculture; Growth Chambers and Facilities; Marine Science Program; Red Sea Research Center (RSRC); Bioscience Program; Plant Science

    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.

  • Bioproject

    LeafGo - Eucalyptus and Peanut genome sequencing

    (NCBI, 2020-11-05) Driguez, Patrick; Bougouffa, Salim; Carty, Karen; Putra, Alexander; Jabbari, Kamel; Reddy, Muppala P.; Soppe, Richard Willem Otto; Cheung, Ming Sin; Fukasawa, Yoshinori; Ermini, Luca; Bioinformatics; Bioscience Core Lab; Center for Desert Agriculture; Greenhouse Core Lab; Plant Growth Core Lab; Plant Growth Facility; Sanger and Third Generation Sequencing

    The sequencing and the assembly of chromosome-level genomes following the LeafGo protocol using a single long read technology.

  • Article

    LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology.

    (Springer Science and Business Media LLC, 2021-09-03) Driguez, Patrick; Bougouffa, Salim; Carty, Karen; Putra, Alexander; Jabbari, Kamel; Reddy, Muppala P.; Soppe, Richard Willem Otto; Cheung, Ming Sin; Fukasawa, Yoshinori; Ermini, Luca; Bioinformatics; Bioscience Core Lab; Center for Desert Agriculture; Core Labs; Greenhouse Core Lab; Plant Growth Core Lab; Plant Growth Facility; Sanger and Third Generation Sequencing

    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.

  • Preprint

    A diversity of traits contributes to salinity tolerance of wild Galapagos tomatoes seedlings

    (Cold Spring Harbor Laboratory, 2019-05-20) Pailles, Yveline; Awlia, Mariam; Julkowska, Magdalena M.; Passone, Luca; Zemmouri, Khadija; Negrão, Sónia; Schmoeckel, Sandra Manuela; Tester, Mark A.; Biological and Environmental Science and Engineering (BESE) Division; Center for Desert Agriculture; Earth Science and Engineering Program; Greenhouse Core Lab; Physical Science and Engineering (PSE) Division; Plant Science; The Salt Lab

    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.

  • Article

    Isolation and sequence characterization of DNA-A genome of a new begomovirus strain associated with severe leaf curling symptoms of Jatropha curcas L.

    (Elsevier BV, 2018-04-22) Chauhan, Sushma; Rahman, Hifzur; Mastan, Shaik G.; Sudheer, Pamidimarri D.V.N.; Reddy, Muppala P.; Greenhouse Core Lab; Plant Stress Genomics Research Lab; Department of Chemical and Biochemical Engineering, Dongguk University–Seoul, Seoul 100-715, Republic of Korea; Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003, India; Department of Biotechnology, Aditya Degree and PG college, Adikavinannaya University, Laxminarayana Nagar, Kakinada 533003, Andhra Pradesh, India; Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, Gyeonggi-do, Republic of Korea

    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.