“Bioinformatics for Plant Biology”

Applications in Plant Sciences (APPS), the Botanical Society of America’s (BSA) open access journal highlighting new tools and protocols across the plant sciences, is organizing a special issue titled “Bioinformatics for Plant Biology.”

In the past few decades, we have witnessed tremendous advances in plant biology. Numerous genomes and transcriptomes have been sequenced, from both model and non-model species, and the relationships between plants and microorganisms have expanded beyond understanding pathogenicity. Much of this progress has been driven by widely available DNA sequencing methods and other -omics approaches, which has been accompanied by increased access to powerful computational resources, represented in hardware and software.

In light of these advances, the goal of this special issue is to highlight novel bioinformatic tools and methods tailored to plants (i.e., Archaeplastida), as well as comprehensive databases that are making it possible to understand the complexity of their genomes, ploidies, and evolutionary histories. We are interested in such diverse topics as:

  • New tools for addressing challenges in plant bioinformatics
  • Systematic evaluation of the performance and accuracy of existing and new software for assembling, annotating, and analyzing complex plant genomes
  • New databases of plant genome features (e.g., transposable elements, genes, ploidy) that have a general scope, moving beyond model plant species
  • Reviews highlighting the major bioinformatic challenges of working with plants and strategies to deal with such challenges
  • Reviews highlighting the current state of plant genome and transcriptome sequencing, and gaps in sequencing/analysis efforts
  • Protocols for low-cost plant genome and transcriptome sequencing and data analysis aimed at facilitating research in underfunded labs or in the field
  • Development of integrative multi-layered databases (e.g., -omics, phenotype) for plant species or groups.

How to submit:
Authors interested in contributing to this special issue should email a proposal consisting of a tentative title, proposed author list, and a 200–300-word abstract to the APPS editorial office (

The deadline for proposal submission is April 25, 2022. Proposals will be reviewed by the Editor-in-Chief and the special issue editors. Authors will be notified by May 20, 2022, as to whether their proposal was accepted. Proposal submissions from early-career researchers and researchers based in institutions from the global south are particularly encouraged.

Authors whose proposals are accepted should submit their manuscript by September 22, 2022. Note that acceptance of a proposal does not guarantee the eventual acceptance of the manuscript, as all manuscripts will be rigorously peer-reviewed and held to the standards of the journal. The target date for publication of the special issue is mid 2023.

Reduced article publication charges (at the BSA member rate) are available for papers accepted for publication in the special issue. For more details about journal scope, article types, and manuscript preparation, please see the Author Guidelines. Any questions may be sent to the APPS editorial office (

Best wishes,

María Fernanda Torres Jiménez (Vilnius University)
Diego Mauricio Riaño-Pachón (University of São Paulo)
Special Issue Editors

Photo credit: Tatiana Vila, Endemica Studios