Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Jan 17, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

20.5K

PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.

Jingjing Zhai1, Aaron Gokaslan2, Sheng-Kai Hsu1

  • 1Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853.

Biorxiv : the Preprint Server for Biology
|September 15, 2025
PubMed
Summary

Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

20.5K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
20.5K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.9K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.9K
DNA as a Genetic Template02:05

DNA as a Genetic Template

27.4K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
27.4K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.6K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.6K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

15.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
15.3K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.6K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The Vertebrate Genomes Project Phase I: A global reference genome resource.

bioRxiv : the preprint server for biology·2026
Same author

Decoding RNA N6-Methyladenosine Methylome of Wheat Using Machine Learning and Nanopore Direct RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same author

Translating functional molecular knowledge into crop-breeding success.

Nature reviews. Genetics·2026
Same author

Observational epidemiological studies can mitigate genetic confounding with a genetic relatedness matrix.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Phenotypic complexity determines the predictability of molecular convergence.

bioRxiv : the preprint server for biology·2026
Same author

Discovery of additional ancient genome duplications in yeasts.

Current biology : CB·2026
This summary is machine-generated.

PlantCAD2 is a new DNA language model for plants that accurately predicts genomic functions. It outperforms existing models in evolutionary conservation and regulatory architecture tasks, aiding plant genomics research.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Understanding DNA sequence function is a key biological challenge.
  • Flowering plants (angiosperms) possess complex genomes, diverse species, and variable genome sizes.
  • These features necessitate specialized models for plant genomics.

Purpose of the Study:

  • Introduce PlantCAD2, a plant-specific DNA language model.
  • Evaluate its performance on plant genomic tasks.
  • Demonstrate its capability in capturing evolutionary conservation and regulatory functions.

Main Methods:

  • Pre-trained PlantCAD2 on 65 angiosperm genomes with single-nucleotide resolution and an 8,192bp context window.
  • Conducted comprehensive zero-shot and fine-tuning evaluations on public benchmarks.

More Related Videos

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.9K
mRNA Interactome Capture from Plant Protoplasts
12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

9.6K

Related Experiment Videos

Last Updated: Jan 17, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

20.5K
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.9K
mRNA Interactome Capture from Plant Protoplasts
12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

9.6K
  • Compared PlantCAD2 against Evo2 and AgroNT models.

    • Main Results:

    • PlantCAD2 (676M parameters) surpassed Evo2 (7B parameters) in 10 of 12 tasks for evolutionary conservation.
    • Fine-tuned PlantCAD2 outperformed AgroNT (1B parameters) in seven cross-species tasks.
    • The long context window significantly improved accessible chromatin prediction in maize genomes.

    Conclusions:

    • PlantCAD2 is a powerful and efficient foundation model for plant genomics.
    • It enables accurate genome annotation across diverse angiosperm species.
    • Highlights the importance of long-range genomic context for regulatory modeling.