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In natural ecosystems, it has been shown that highly competent plant host species may determine the ecology of virus infection in less competent hosts, in which infection proceeds mostly by 'spill-over' from the most competent host (Power and Mitchell 2004; Cronin et al. 2010).
After an initial round of clustering, we noticed that, unexpectedly, the known AM-related VAPYRIN protein was not found among the trees generated by Hieranoid, although it is believed to generally occur in all AM-competent plants [ 17, 26], whereas it is absent from the Brassicaceae [ 16, 18].
Conceptually, such an approach represents a substractive procedure where the proteomes of non-mycorrhizal plants such as A. thaliana are substracted from a panel of proteomes of AM-competent species to result in a set of proteins that are consistently conserved among AM-competent plants and absent from non-mycorrhizal reference species.
The validity of this approach has been confirmed by the finding that it identified many known AM-related genes from the genomes of AM-competent plant species.
AM-related genes are often conserved among AM-competent plant species, while they are less conserved or even missing in non-mycorrhizal species.
Finally, to focus on conserved constitutively expressed genes (such as the common SYM genes), a proteome blast of the conserved genes to an extended panel of proteomes (including monocots) allowed to perform quantitative statistics on the E-values, hence providing a set of proteins that are significantly more conserved among AM-competent plant species than towards the non-mycorrhizal Brassicaceae.
Such a pattern of conservation was also observed in AM-related genes that are members of large ubiquitous gene families such as the ABC transporters STUNTED ARBUSCULE (STR) and STR2, or the GRAS-type transcription factor REQUIRED FOR ARBUSCULAR MYCORRHIZA1 (RAM1), which both belong to subfamilies which are restricted to AM-competent plant species [ 21, 22].
To evaluate the efficiency of the approach, this list was ordered according to the ratios of E-values between the averaged Brassicaceae and AM-competent dicot plants, respectively (Additional file 14: Table S6).
This vernalized state is epigenetically maintained or 'memorized' in warm rendering plants competent to flower in spring, but is reset in the next generation.
Another feature of many autumn-sown wheats and barleys is the vernalization requirement; the requirement for prolonged exposure to cold to make plants competent to flower.
Meiotically competent cells in plants differentiate late in floral ontogeny.
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