Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae.

BACKGROUND AND AIMS: The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS: New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS: Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS: Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.

Phylogeny and evolution of plant Phytochrome Interacting Factors (PIFs) gene family and functional analyses of PIFs in Brachypodium distachyon.

KEY MESSAGES: Plant PIFs have been characterized, WGDs contributed to the expansion of class II PIFs; BdPIFs localized in the nucleus; BdPIF4/5C most likely response to high temperature and light stress. Phytochrome interacting factors (PIFs) belong to a small subset of basic helix-loop-helix (bHLH) transcription factors (TFs). As cellular signaling hubs, PIFs integrate multiple external and internal signals to orchestrate the regulation of the transcriptional network, thereby actuating the pleiotropic aspects of downstream morphogenesis. Nevertheless, the origin, phylogeny and function of plant PIFs are not well understood. To elucidate their evolution history and biological function, the comprehensive genomic analysis of the PIF genes was conducted using 40 land plant genomes plus additionally four alga lineages and also performed their gene organizations, sequence features and expression patterns in different subfamilies. In this study, phylogenetic analysis displayed that 246 PIF gene members retrieved from all embryophytes could be divided into three main clades, which were further felled into five distinct classes (Class I-V). The duplications of Class II PIFs were associated specially with whole genome duplication (WGD) events during the plant evolution process. Sequence analysis showed that PIF proteins had a conserved APB motif, and its crucial amino acid residues were relatively high proportion in the average abundance. As expected, subcellular localization analysis revealed that all BdPIF proteins were localized to the nucleus. Especially, BdPIF4/5C showed the highest expression level at high temperature, and the most significant hypocotyl elongation phenotype of overexpression of BdPIFs in Arabidopsis, which was consistent with the function and phenotype of AtPIF4. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant PIFs, and lays a foundation for further investigation on its functions in plant growth and development.