OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.

Chloroplast development, maintenance and function depend on the coordinated expression of chloroplast and nuclear genes. The retrograde chloroplast signals are essential in coordinating nuclear gene expression. Although the sources of signals in chloroplasts have been identified and the associated transcription factors in the nucleus extensively studied, the molecular mechanism that relays chloroplast signals to the nucleus remains a mystery. Here we show that PTm, a chloroplast envelope-bound plant homeodomain (PHD) transcription factor with transmembrane domains, functions in multiple retrograde signal pathways. The proteolytic cleavage of PTm occurs in response to retrograde signals and amino-terminal PTm accumulates in the nucleus, where it activates ABI4 transcription in a PHD-dependent manner associated with histone modifications. These results provide a molecular basis for the critical function of PTm in retrograde chloroplast signaling and shed new light on the mechanism whereby chloroplast signals are transmitted to the nucleus through the cytosol.

a b s t r a c tThe different mechanisms of CO 2 methanation on Ni(111) surfaces have been investigated by density functional theory with and without the formation of CO as an intermediate. The most stable adsorption configurations of all reaction species (O, OH, CO, CH, CH 2 , CH 3 , CH 4 , HCOO, C(OH) 2 , CH 2 O, etc.) in three paths of CO 2 methanation adsorbed on the Ni(111) surface are described. The energy barriers and reaction energies for the overall processes involved in the various paths are presented. The rate-determining steps for the three mechanisms are HCOO→CO + OH for path 1, CO → C + O for path 2 and CO 2 + 2H → C(OH) 2 for path 3 with maximum energy barriers of 306.8 kJ/mol, 237.4 kJ/mol and 292.3 kJ/mol, respectively. Path 2 is therefore the optimum of the three mechanisms. The path starts with CO 2 dissociation into CO and O, CO decomposition into C and O species and C species hydrogenation to form CH 4 : CO 2 → CO + O → C + O + 4H → CH 2 + 2H → CH 3 + H → CH 4 .

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