The holly genus, Ilex L., in the monogeneric Aquifoliaceae, is the largest woody dioecious genus (>664 spp.), with a near‐cosmopolitan distribution in mesic environments. We constructed a phylogeny based on two nuclear genes, representing 177 species spread across the geographical range, and dated using macrofossil records. The five main clades had a common ancestor in the early Eocene, much earlier than previously suggested. Ilex originated in subtropical Asia and extant clades colonized South America by 30 Ma, North America by 23 Ma, Australia by 8 Ma, Europe by 6 Ma, and Africa by 4 Ma. South and North America were colonized multiple times. Ilex also reached Hawaii (10 Ma) and other oceanic islands. Macrofossil and pollen records show the genus has tracked mesic climates through time and space, and had a wider distribution before late Miocene global cooling. Our phylogeny provides a framework for studies in comparative ecology and evolution.

The hollies (Ilex L., Aquifoliaceae) form a large (>669 spp.) genus of forest trees and shrubs, which is almost cosmopolitan in mesic environments but most diverse in subtropical China and montane South America. Throughout the range of the genus, Ilex species have been utilized as beverages, medicines, ornamentals, honey plants, timber, and for various other minor uses. Recent studies on the genomics, evolution, and biogeography of Ilex now make it possible to take a systematic approach to understanding and expanding the economic importance of the genus, but information on existing uses is scattered among numerous published and unpublished sources. We therefore review the existing literature on utilization of Ilex species, supplementing this with information from the grey literature and product websites. We show that, despite the number and diversity of known uses, most Ilex species are not known to be utilized at present, suggesting considerable unrealized potential. We highlight gaps in our knowledge and opportunities for expanded usage. Finally, we discuss how the availability of a new phylogeny and whole genome can assist screening of additional wild species for economic potential and facilitate breeding programs for species already under cultivation.

Background: Transcription factors (TFs) play important roles in plants. Among the major TFs, GATA plays a crucial role in plant development, growth, and stress responses. However, there have been few studies on the GATA gene family in foxtail millet (Setaria italica). The release of the foxtail millet reference genome presents an opportunity for the genome-wide characterization of these GATA genes. Results: In this study, we identified 28 GATA genes in foxtail millet distributed on seven chromosomes. According to the classification method of GATA members in Arabidopsis, SiGATA was divided into four subfamilies, namely subfamilies I, II, III, and IV. Structural analysis of the SiGATA genes showed that subfamily III had more introns than other subfamilies, and a large number of cis-acting elements were abundant in the promoter region of the SiGATA genes. Three tandem duplications and five segmental duplications were found among SiGATA genes. Tissue-specific results showed that the SiGATA genes were mainly expressed in foxtail millet leaves, followed by peels and seeds. Many genes were significantly induced under the eight abiotic stresses, such as SiGATA10, SiGATA16, SiGATA18, and SiGATA25, which deserve further attention. Conclusions: Collectively, these findings will be helpful for further in-depth studies of the biological function of SiGATA, and will provide a reference for the future molecular breeding of foxtail millet.

Southwest China is a plant diversity hotspot. The near-cosmopolitan genus Ilex (c. 664 spp., Aquifoliaceae) reaches its maximum diversity in this region, with many narrow-range and a few widespread species. Divergent selection on widespread species leads to local adaptation, with consequences for both conservation and utilization, but is counteracted by geneflow. Many Ilex species are utilized as teas, medicines, ornamentals, honey plants, and timber, but variation below the species level is largely uninvestigated. We therefore studied the widespread Ilex polyneura, which occupies most of the elevational range available and is cultivated for its decorative leafless branches with persistent red fruits. We assembled a chromosome-scale genome using approximately 100x whole genome long-read and short-read sequencing combined with Hi-C sequencing. The genome is approximately 727.1 Mb, with a contig N50 size of 5 124 369 bp and a scaffold N50 size of 36 593 620 bp, for which the BUSCO score was 97.6%, and 98.9% of the assembly was anchored to 20 pseudochromosomes. Out of 32 838 genes predicted, 96.9% were assigned functions. Two whole genome duplication events were identified. Using this genome as a reference, we conducted a population genomics study of 112 individuals from 21 populations across the elevation range using restriction site-associated DNA sequencing (RADseq). Most populations clustered into four clades separated by distance and elevation. Selective sweep analyses identified 34 candidate genes potentially under selection at different elevations, with functions related to responses to abiotic and biotic stresses. This first high-quality genome in the Aquifoliales will facilitate the further domestication of the genus.

Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome forHelwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels. TheHelwingiagenome consists of 158,362 bp containing a pair of inverted repeat (IR) regions of 25,996 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

Background: The genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages. This suggests a strong positive selection on rbcL, involved in yet unknown adaptations. We therefore investigated positive selection on rbcL in 240 Ilex sequences from across the global range. Results: The rbcL gene shows a much higher rate of positive selection in Ilex than in any other plant lineage studied so far (> 3000 species) by tests in both PAML and SLR. Most positively selected residues are on the surface of the folded large subunit, suggesting interaction with other subunits and associated chaperones, and coevolution between positively selected residues is prevalent, indicating compensatory mutations to recover molecular stability. Coevolution between positively selected sites to restore global stability is common. Conclusions: This study has confirmed the predicted high incidence of positively selected residues in rbcL in Ilex, and shown that this is higher than in any other plant lineage studied so far. The causes and consequences of this high incidence are unclear, but it is probably associated with the similarly high incidence of hybridization and introgression in Ilex, even between distantly related lineages, resulting in large cytonuclear discordance in the phylogenies.