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September 18, 2023
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JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Publicated to: Nucleic Acids Research. 51 (16): 8383-8401 - 2023-09-08 51(16), DOI: 10.1093/nar/gkad616

Authors:

Sreedasyam, A; Plott, C; Hossain, MS; Lovell, JT; Grimwood, J; Jenkins, JW; Daum, C; Barry, K; Carlson, J; Shu, SQ; Phillips, J; Amirebrahimi, M; Zane, M; Wang, M; Goodstein, D; Haas, FB; Hiss, M; Perroud, PF; Jawdy, SS; Yang, YG; Hu, RB; Johnson, J; Kropat, J; Gallaher, SD; Lipzen, A; Shakirov, E; Weng, XY; Torres-Jerez, I; Weers, B; Conde, D; Pappas, MR; Liu, LF; Muchlinski, A; Jiang, H; Shyu, C; Huang, P; Sebastian, J; Laiben, C; Medlin, A; Carey, S; Carrell, AA; Chen, JG; Perales, M; Swaminathan, K; Allona, I; Grattapaglia, D; Cooper, EA; Tholl, D; Vogel, JP; Weston, DJ; Yang, XH; Brutnell, TP; Kellogg, EA; Baxter, I; Udvardi, M; Tang, YH; Mockler, TC; Juenger, TE; Mullet, J; Rensing, SA; Tuskan, GA; Merchant, SS; Stacey, G; Schmutz, J
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Affiliations

BASF Corp, Durham, NC USA - Author
Bayer Crop Sci, St Louis, MO USA - Author
Clemson Univ, Adv Plant Technol Program, Clemson, SC USA - Author
Clemson University - Author
Donald Danforth Plant Sci Ctr, St Louis, MO USA - Author
Donald Danforth Plant Science Center - Author
EMBRAPA Recursos Genet & Biotecnol, Lab Genet Vegetal, EPQB Final W5 Norte, Brasilia, Brazil - Author
Embrapa Recursos Geneticos e Biotecnologia - Author
Firmenich, San Diego, CA USA - Author
GSK Vaccines GmbH, Emil von Behring Str, Marburg, Germany - Author
Guardant Hlth Inc, 3100 Hanover St, Palo Alto, CA USA - Author
HudsonAlpha Inst Biotechnol, Huntsville, AL 35806 USA - Author
HudsonAlpha Institute for Biotechnology - Author
HudsonAlpha Institute for Biotechnology , U.S. Department of Energy Joint Genome Institute - Author
Indian Inst Sci Educ & Res, Dept Biol Sci, Berhampur IISER BPR, Berhampur, Odisha, India - Author
Lawrence Berkeley Natl Lab, Environm Genom & Syst Biol, Berkeley, CA USA - Author
Lawrence Berkeley Natl Lab, Joint Genome Inst, Berkeley, CA 94720 USA - Author
Marshall Univ, Dept Biol Sci, Huntington, WV USA - Author
Max Planck Inst Biol Tubingen, Dept Algal Dev & Evolut, Tubingen, Germany - Author
McClintock LLC, St Louis, MO USA - Author
Noble Res Inst, Ardmore, OK USA - Author
Noble Research Institute - Author
Oak Ridge National Laboratory - Author
Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA - Author
Oak Ridge Natl Lab, Ctr Bioenergy Innovat, Oak Ridge, TN USA - Author
Philipps-Universität Marburg - Author
Propper Asset Management, 17 Res Pk Dr, St Charles, MO USA - Author
Saginaw High Sch, 800 N Blue Mound Rd, Saginaw, TX USA - Author
Texas A&M University - Author
Texas A&M AgriLife Res, College Stn, TX USA - Author
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX USA - Author
Texas A&M Univ, Dept Soil & Crop Sci, College Stn, TX USA - Author
The University of Texas at Austin - Author
U.S. Department of Energy Joint Genome Institute - Author
Univ Calif Berkeley, Dept Mol & Cell Biol, QB3, Berkeley, CA USA - Author
Univ Calif Berkeley, Dept Plant & Microbial Biol, QB3, Berkeley, CA USA - Author
Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA USA - Author
Univ Calif Los Angeles, Inst Genom & Prote, Los Angeles, CA USA - Author
Univ Freiburg, Fac Chem & Pharm, Freiburg, Germany - Author
Univ Marburg, Fac Biol, Plant Cell Biol, Karl von Frisch Str, Marburg, Germany - Author
Univ Missouri, Div Plant Sci & Technol, CS Bond Life Sci Ctr, Columbia, MO USA - Author
Univ North Carolina Charlotte, Dept Bioinformat & Genom, Charlotte, NC USA - Author
Univ Paris Saclay, Inst Jean Pierre Bourgin IJPB, INRAE, AgroParisTech, Versailles, France - Author
Univ Politecn Madrid, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA C, Madrid, Spain - Author
Univ Politecn Madrid, Escuela Tecn Super Ingn Agron Alimentaria & Biosis, Dept Biotecnol Biol Vegetal, Madrid, Spain - Author
Univ Queensland, Ctr Crop Sci, Queensland Alliance Agr & Food Innovat, Brisbane, Australia - Author
Univ Texas Austin, Dept Integrat Biol, Austin, TX USA - Author
Universidad Politécnica de Madrid - Author
University of California, Los Angeles - Author
University of Missouri - Author
Virginia Polytechnic Institute and State University - Author
Virginia Tech, Dept Biol Sci, Blacksburg, VA USA - Author
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Abstract

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
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Keywords

arabidopsisgrowth-stagesnetwork analysissorghum-bicolorsucrosetoleranceAtlases as topicExpression atlasGene expression regulation, plantGenes, plantGenome, plantPhylogenySoftwareTranscriptome

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nucleic Acids Research due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2023, it was in position 6/313, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemistry & Molecular Biology. Notably, the journal is positioned above the 90th percentile.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 3.19. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 13, 2025)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 4.52 (source consulted: FECYT Mar 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-12-21, the following number of citations:

  • WoS: 21
  • Scopus: 28
  • Google Scholar: 8
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-12-21:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 55.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 56 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 45.
  • The number of mentions on the social network X (formerly Twitter): 68 (Altmetric).
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Australia; Brazil; France; Germany; India; United States of America.

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