Sushma Naithani

Sushma Naithani
Oregon State University | OSU · Department of Botany and Plant Pathology

Ph.D. (Botany; Plant Molecular Biology)

About

95
Publications
13,811
Reads
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3,251
Citations
Introduction
Sushma Naithani, an Associate Professor (Senior Research) in the Dept. of Botany & Plant Pathology at Oregon State University. Naithani has a Ph.D. in Botany and worked as a postdoc at Iowa State University and Cornell University. Her research interests include the curation of plant pathways (e.g. Plant Reactome, VitisCyc, FragariaCyc, MaizeCyc, etc.), modeling of gene-networks, organelle biogenesis, photosynthesis, self-incompatibility and cell signaling mechanisms in plants. She currently serv
Additional affiliations
August 2006 - June 2007
Cornell University
Position
  • Lecturer
Description
  • Courses: PLBR 2010: From where our food comes from? PLBR 2250: Introduction to Plant Breeding and Genetics.
June 2002 - August 2006
Cornell University
Position
  • Research Associate
October 1999 - May 2002
Cornell University
Position
  • PostDoc Position

Publications

Publications (95)
Article
Full-text available
Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest p...
Article
Full-text available
The highly polymorphic S-locus receptor kinase (SRK) is the stigma determinant of specificity in the self-incompatibility response of the Brassicaceae. SRK spans the plasma membrane of stigma epidermal cells, and it is activated in an allele-specific manner on binding of its extracellular region (eSRK) to its cognate pollen coat-localized S-locus c...
Article
Full-text available
FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on the Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the add...
Article
Full-text available
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study...
Article
Full-text available
Professor Krishna K. Tewari (1937-2017) was a pioneer in plant molecular biology and biochemistry. He was a professor and served as the Chairman of the Department of Molecular Biology and Biochemistry at the University of California, Irvine, and was the founder-director of the International Centre for Genetic Engineering and Biotechnology, New Delh...
Data
Table of Contents
Chapter
Plant Reactome (https://plantreactome.gramene.org) and PubChem (https://pubchem.ncbi.nlm.nih.gov) are two reference data portals and resources for curated plant pathways, small molecules, metabolites, gene products, and macromolecular interactions. Plant Reactome knowledgebase, a conceptual plant pathway network, is built by biocuration and integra...
Book
History and Science of Cultivated Plants narrates how humans transitioned from foragers to farmers and have arrived at present-day industrial agriculture-based civilization. It entails myths, historical accounts, and scientific concepts to describe how human efforts have shaped and produced easier to grow, larger, tastier, and more nutritious fruit...
Article
Full-text available
Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, a...
Article
Full-text available
Lectins are ubiquitous proteins that reversibly bind to specific carbohydrates and, thus, serve as readers of the sugar code. In photosynthetic organisms, lectin family proteins play important roles in capturing and releasing photosynthates via an endogenous lectin cycle. Often, lectin proteins consist of one or more lectin domains in combination w...
Article
Full-text available
Chia (Salvia hispanica L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information available in the public domain for this crop are scanty, which hinders an understanding of its growth and developm...
Article
Full-text available
Johannes Manjrekar (1957–2020) was a well-known molecular biologist and a faculty member at the Department of Microbiology and Biotechnology Centre, Maharaja Sayajirao University of Baroda, India. He was an extremely popular professor among his students and offered help to anyone who needed it. He was also an avid reader, a writer, polyglot, and a...
Article
Full-text available
The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S -locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus...
Book
हम सभी का खानपान से बेहद अंतरंग और प्राथमिक सम्बंध है. हम दुनिया के किसी भी हिस्से में हो, खानपान सम्बंधी चिंता हमारे मन में चाहे-अनचाहे बनी रहती है. बाज़ार से आटा, दाल, चावल, आलू, प्याज़, फल-सब्ज़ी, चाय, चीनी, कॉफ़ी आदि उठाते समय हम सोचते रहते हैं कि अमुक चीज़ स्वास्थ्य पर कैसा असर डालेगी; उसमें पौष्टिक तत्वों की मात्रा कितनी है; किसे विलास में और...
Preprint
Full-text available
Chia ( Salvia hispanica L.), now a popular superfood, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids. At present, the genomic and genetic information available in the public domain for this crop is scanty, which hinders understanding its growth and developmental processes and impedes genet...
Article
Full-text available
Lalit Mohan Srivastava (1931–2012) was a well-known plant developmental biologist. He was an authority on the molecular basis of the action of gibberellins and on the physiology, and biochemistry of the seaweeds. Here, we honor him by presenting a glimpse of his life and research; he had authored more than 60 research papers, of which we mention on...
Article
Full-text available
Gramene (http://www.gramene.org), a knowledge-base founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases...
Article
Full-text available
Plant Reactome (https://plantreactome.gramene. org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework....
Article
Full-text available
We pay tribute to Donald J. Armstrong, who passed away at age 82 on June 13, 2019 in Corvallis, Oregon, USA. He was both an excellent teacher and a respected scientist. His research spanned more than 40 years and ranged from studying cytokinin structure and activity, to secondary metabolism, to inhibition of seed germination. He is fondly remembere...
Article
Full-text available
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree...
Article
Full-text available
This is an editorial article for a special issue of Current Plant Biology journal on Plant Genomics and Bioinformatics.
Article
Full-text available
Biocuration plays a crucial role in building databases and complex systems-level platforms required for processing, annotating and analyzing ‘Big Data’ in biology. However, biocuration efforts cannot keep pace with a dramatic increase in the production of omics data; this presents one of the bottlenecks in genomics. In two pathway curation jamboree...
Article
Full-text available
The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are p...
Article
Full-text available
The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are pr...
Article
Full-text available
On March 9, 2018, 5 years have passed since Prasanna K. Mohanty, an extraordinary student of photosynthesis, plant biologist par excellence, a pioneer of Light Regulation of Photosynthesis, a renowned mentor, and a friend of a vast international community of scientists had left us. Many of us who knew him, miss him dearly and cherish his fond memor...
Chapter
The goal of Gramene database (www.gramene.org) is to empower plant research community in conducting comparative genomics studies across model plants and crops by employing a phylogenetic framework and orthology-based projections. Gramene database (release #49) provides resources for comparative plant genomics including well-annotated plant genomes...
Chapter
The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to variou...
Article
Full-text available
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, a...
Chapter
Seed formation is a plant’s long-term evolutionary strategy for surviving in extreme conditions of temperature and dehydration during long, extended periods. On arrival of the favorable season, seeds germinate and give rise to new plants. As an archetype seed retains elements of plant’s response to abiotic stresses and recovery from it. Here we rev...
Article
Full-text available
Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and pro...
Article
Full-text available
Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biolo...
Data
RNA-Seq expression data used for Omics Viewer analysis. This is a subset of publicly available data from F. vesca (Kang et al., 2013) that represent differential expression of 16,316 genes across 10 samples: ovule1 and cortex1 were from open flower prior to fertilization, ovule2 and cortex2 are from pollinated flowers just after fertilization, whil...
Data
Differential expression of genes using absolute RPKM values (cutoff = 50) associated with gibberellin (B), jasmonic acid (C), and brassinosteroid (D), biosynthesis pathway during fruit development in three tissues: ovule, embryo, and cortex. A common color scale shown (A) depicts the expression level of genes belonging to pathways (B–D). The sample...
Article
Full-text available
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform...
Article
Full-text available
We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload,...
Article
As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages, and compared these with transcriptomes of diverse vegetative tissues, including leaves, roots, and stems.A subse...
Article
Full-text available
Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two...
Article
Full-text available
Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum mo...
Data
The goal of a novel model plant genomics resource database is to provide a community resource that allows researchers to build their research models by making use of data derived from one or more approaches, for example the forward and reverse genetics, comparative genomics, in silico predictions etc. This resource can be built for a given plant sp...
Article
Full-text available
Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to i...
Article
Full-text available
A framework for understanding the synthesis and catalysis of metabolites and other biochemicals by proteins is crucial for unraveling the physiology of cells. To create such a framework for Zea mays L. subsp. mays (maize), we developed MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary plant p...
Article
Full-text available
The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Her...
Article
Full-text available
The goal of a novel model plant genomics resource database is to provide a community resource that allows researchers to build their research models by making use of data derived from one or more approaches, for example the forward and reverse genetics, comparative genomics, in silico predictions, etc. This resource can be built for a given plant s...
Article
The goal of a novel model plant genomics resource database is to provide a community resource that allows researchers to build their research models by making use of data derived from one or more approaches, for example the forward and reverse genetics, comparative genomics, in silico predictions etc. This resource can be built for a given plant sp...
Chapter
This chapter describes the 5-locus cysteine-rich protein SCR, which is also known as SP11. It is identified in members of the Brassicaceae that exhibit self-incompatibility (SI). SCR is genetically and physically tightly linked to the gene for its receptor, the S-locus receptor kinase (SRK) gene. These two genes comprise the SI specificity-determin...
Article
The genome of the cyanobacterium Synechocystis sp. PCC 6803 contains genes identified as menD and menE, homologs of Escherichia coli genes that code for 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase and O-succinylbenzoic acid-CoA ligase in the menaquinone biosynthetic pathway. In cyanobacteria, the product of this pathway...