Chado Controller: advanced annotation management with a community annotation system

Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl

GnpAnnot community annotation system: features, qualifiers, values

International audienceIn January 2009, 991 complete genomes have been already published and 3376 genome sequencing projects are ongoing, leading to an explosion of data that needs to be stored, curated and analyzed. GnpAnnot is a project on green genomics which intends to develop a system of structural and functional annotation supported by comparative genomics and dedicated to plant and bio-aggressor genomes allowing both automatic predictions and manual curations of genomic objects. The core of GnpAnnot is a community annotation system (CAS) based on GMOD components: Chado / GBrowse / Apollo / Artemis. The system should also enable to browse comparative genomics results, to build queries and to export sets of gene lists and gene reports in various formats. The system should allow the annotation reconciliation, history, integrity, consistency and update and the management of public and private projects. To facilitate the work of the curators, four steps are crucial: 1. To provide homogeneous features, qualifiers and values for genomic objects; 2. To share a strong CAS: run high quality combiners / pipelines to predict automatically genomic objects which are stored in a relational database management system and then available from graphical and textual fast browsers and powerful editors; 3. To define annotation rules, train the annotators and organize annotation jamborees; 4. To submit the results in public sequence knowledge bases in an easy way. In this work we focus on the first and third steps. A mapping between different known sources: sequence ontology, DDBJ / EMBL / GenBank feature definition, GFF3, Chado, gene nomenclatures, transposable element classification and annotation guidelines from various genome project consortia is described. Homogeneous feature keys, qualifiers and value format with a maximum of controlled vocabularies for genes and transposable elements are proposed. Rules to annotate, in a coherent way, the structure and the function of genes and the structure and the classification of transposable elements are proposed. These rules could be useful both for automatic predictions and manual curation. Examples of annotations on a BAC sequence of a monocot are presented

Data from: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3, 4. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence

Gene trees and alignments for Musa gene orthogroups

These are the orthogroup gene trees and alignments that were used to phylogenetically place the polyploidy events suggested by the Musa acuminata genome. See the README files for a complete description

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3, 4. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence