Structural and Functional Genome Annotation

The CNRGV team is pleased to announce the launch of a new service dedicated to genome annotation. This fully operational service covers the entire annotation pipeline — from RNA extraction to functional annotation — providing comprehensive support for your genome characterization projects.

1. RNA Extraction

Starting from high-quality plant material, we are able to extract RNA from various plant tissues such as roots, leaves, stems, flowers, etc.

2. Kinnex Library Preparation

From the extracted RNA, we prepare sequencing libraries using Pacific Biosciences’ Kinnex technology. This method, based on MAS-Seq (fragment concatenation), combined with HiFi sequencing and the Revio system, enables the recovery of full-length transcript sequences while significantly increasing data output — up to 16 times more than traditional methods using Sequel II.

3. High-Quality Isoform Generation

The Kinnex analysis pipeline produces only full-length, high-quality isoforms, ideal for accurate and robust genome annotation.

4. Structural and Functional Annotation

• The Eugene pipeline * ( http://eugene.toulouse.inrae.fr/) is used to perform structural annotation. It integrates transcriptomic data (RNA-seq or Isoseq/Kinnex) and proteomic data to predict genes structure.
• For functional annotation, we have developed a flexible pipeline that relies on complementary tools and diverse databases to provide the most comprehensive annotation possible.
• To annotate transposable elements, we recommend contacting URGI (Unit Resource Genomics-Info). URGI is an INRAE unit that offers TE annotation services and is recognized for its expertise in the field :  https://urgi.versailles.inrae.fr/Annotation/Service-offering

With this complete solution, we support your project from plant material to functional genome annotation.

* Sallet E., Gouzy J., Schiex T. (2019) EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes. Methods in Molecular Biology.