CapBase

Capsella is a small genus in the Brassicaceae family and an excellent model system for investigating the genomic and epigenomic consequences of mating-system transitions from outbreeding to inbreeding. The genus includes the obligate outcrosser Capsella grandiflora and two predominantly self-fertile species, Capsella rubella and Capsella orientalis. Compared with more distantly related systems such as Arabidopsis thaliana and its outcrossing relatives, Capsella offers a short evolutionary distance among species and relatively recent, repeated transitions to self-fertilization. These features make Capsella especially powerful for studying how the breakdown of self-incompatibility affects genome architecture, transposable element dynamics, gene evolution, and epigenomic regulation. However, previous Capsella genome assemblies were fragmented and incomplete, particularly in repetitive regions, limiting comparative studies of transposable elements and genome evolution.

The Mosher Lab therefore (1) de novo assembled the genomes for these three Capsella species, leveraging PacBio long-read sequencing and Hi-C data; (2) created high-quality annotations for protein-coding genes and transposable elements (TEs); and (3) built the Capsella Database (CapBase) to maintain genetic and genomic data for these model plants. Data available from CapBase includes near-gapless genomes along with high-quality gene structure and TE annotations. CapBase also offers several command-free bioinformatic tools for Capsella research, including built-in genome browsers, locus searching for both genes and TEs, ortholog searching, and related comparative-genomics utilities.

CapBase is maintained by the Mosher Lab at the Department of Biology, University of Oxford. This database is supported by the Plant Genome Research Program (PGRP), U.S. National Science Foundation. CapBase is free for academic use only. For any commercial use, please get in touch with us for commercial licensing terms.