In silico prediction and analysis of transmembrane-coiled-coil resistance gene analogues in 27 Brassicaceae species

The Brassicaceae family is composed of a broad range of species, including the economically important crops from Brassica, Raphanus, Camelina and Sinapis genera. The production of Brassicaceae species, particularly the crop members, is threatened by major diseases. However, the impact of diseases can be minimized or even negated by improving disease resistance. Transmembrane-coiled-coil (TM-CC) genes are a type of resistance gene analogue (RGA) that have been proven to play specific roles in resistance to several diseases. Here, TM-CCs have been predicted in 27 genomes from Brassicaceae genera including Arabidopsis, Arabis, Barbarea, Boechera, Brassica, Camelina, Capsella, Cardamine, Eutrema, Leavenworthia, Lepidium, Raphanus, Sinapis, Sisymbrium, Schrenkiella and Thlaspi. The number of TM-CCs varies throughout the studied genomes, as well as between genera, diploids and polyploids, and Brassica genomes and subgenomes. In total, 6788 TM-CCs were identified, with 708 of them predicted with signalling function, 172 colocalized with previously known disease resistance regions and 70 phylogenetically related to cloned resistance genes, indicating the possible functional involvement of TM-CCs in resistance. This study provides a resource for the identification of functional Brassicaceae TM-CCs along with their clustering and duplication patterns and provides a benchmark for further studies investigating TM-CCs.