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The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent “tuning knobs” in the genome adaptive landscapes of given species.

Aims The rhizosheath is defined as the weight of soil adhering strongly to roots on excavation, and current interest in this trait as a potential tolerance mechanism to abiotic stress has prompted us to explore the extent of its occurrence throughout the angiosperm phylogeny. Methods Here we describe a robust, novel method which was used to screen species for the presence/absence and strength of a rhizosheath. We correlate the latter with root hair length to provide insight into some of the factors affecting its formation. We go on to compare experimental data with previous observations in the literature. Results Results of a glasshouse screen demonstrate that rhizosheaths exist in species from many angiosperm orders, and the frequency of their occurrence and their strength and size are related. No correlation between root hair length and rhizosheath size was found, except when root hairs were extremely short, but the presence of root hairs was required for rhizosheath formation. Conclusions The rhizosheath is present in species from many angiosperm orders. Potential to enhance the trait is likely to exist in a range of crop species and could help contribute to future agricultural sustainability.

• Organismal phylogeny provides a crucial evolutionary framework for many studies and the angiosperm phylogeny has been greatly improved recently, largely using organellar and rDNA genes. However, low‐copy protein‐coding nuclear genes have not been widely used on a large scale in spite of the advantages of their biparental inheritance and vast number of choices. • Here, we identified 1083 highly conserved low‐copy nuclear genes by genome comparison. Furthermore, we demonstrated the use of five nuclear genes in 91 angiosperms representing 46 orders (73% of orders) and three gymnosperms as outgroups for a highly resolved phylogeny. • These nuclear genes are easy to clone and align, and more phylogenetically informative than widely used organellar genes. The angiosperm phylogeny reconstructed using these genes was largely congruent with previous ones mainly inferred from organellar genes. Intriguingly, several new placements were uncovered for some groups, including those among the rosids, the asterids, and between the eudicots and several basal angiosperm groups. • These conserved universal nuclear genes have several inherent qualities enabling them to be good markers for reconstructing angiosperm phylogeny, even eukaryotic relationships, further providing new insights into the evolutionary history of angiosperms.

Increasingly robust understanding of angiosperm phylogeny allows more secure reconstruction of the flower in the most recent common ancestor of extant angiosperms and its early evolution. The surprising emergence of several extant and fossil taxa with simple flowers near the base of the angiosperms—Chloranthaceae, Ceratophyllum, Hydatellaceae, and the Early Cretaceous fossil Archaefructus (the last three are water plants)—has brought a new twist to this problem. We evaluate early floral evolution in angiosperms by parsimony optimization of morphological characters on phylogenetic trees derived from morphological and molecular data. Our analyses imply that Ceratophyllum may be related to Chloranthaceae, and Archaefructus to either Hydatellaceae or Ceratophyllum. Inferred ancestral features include more than two whorls (or series) of tepals and stamens, stamens with protruding adaxial or lateral pollen sacs, several free, ascidiate carpels closed by secretion, extended stigma, extragynoecial compitum, and one or several ventral pendent ovule(s). The ancestral state in other characters is equivocal: e.g., bisexual vs. unisexual flowers, whorled vs. spiral floral phyllotaxis, presence vs. absence of tepal differentiation, anatropous vs. orthotropous ovules. Our results indicate that the simple flowers of the newly recognized basal groups are reduced rather than primitively simple.

The term rheophyte describes a biological group of flood‐tolerant plants that are confined to the beds of swift‐running streams and rivers in nature and grow up to flood level, but not beyond the reach of regularly occurring flash floods. Although over 35 yr have passed since the first global census of rheophytes, no updates have been recorded regarding the number of taxa in this biological group in seed plants. Therefore, the present work aimed to (1) review the main topics associated with rheophytism (e.g., morphological characteristics, genetic studies, geographic distribution, conservation, and evolutionary aspects); (2) provide an updated checklist of rheophytes distributed around the world considering the two main groups in seed plants (gymnosperms and angiosperms); (3) demonstrate the distribution of rheophytism in the angiosperm phylogeny; and (4) estimate the geographical distribution and richness of selected taxa on the world map for the first time. All data compiled for the present study originated from a search of peer‐reviewed articles, secondary literature (theses, dissertations, reports, books, and floras), and electronic facilities. We compiled a data set composed of four taxa in gymnosperms (Podocarpaceae family) and 1,368 taxa (including obligate, facultative, and unclassified rheophytes) distributed in 114 families and 508 genera in angiosperms. Most of the studied taxa belong to eudicotyledons (72.81%), while 1.46% belong to magnoliids, and 25.73% belong to monocotyledons. The families with the highest number of taxa in descending order are Podostemaceae, Araceae, Myrtaceae, Rubiaceae, Asteraceae, Apocynaceae, Arecaceae, Fabaceae, Phyllanthaceae, and Poaceae. Of the 114 families plotted in angiosperm phylogeny, at least 80 harbor obligate rheophytes. The geographical distribution of rheophytes in angiosperms, as expected based on the first census of this biological group, is mainly in the tropical and subtropical regions. The high richness of rheophytic taxa was mostly found in southern Mexico, southern China, Borneo, and northern and eastern Australia. In contrast, the geographical distribution of rheophytes in gymnosperms is restricted to New Caledonia and Tasmania. The present study will help to advance knowledge regarding the diversity of rheophytes in angiosperms and gymnosperms while drawing attention to this biological group, which has often been overlooked. There are no copyright restrictions. Please cite this data paper when the data are used in publications and teaching events.

Key messageUpon loss of either its chloroplast or mitochondrial target, a uniquely dual-targeted factor for C-to-U RNA editing in angiosperms reveals low evidence for improved molecular adaptation to its remaining target.RNA-binding pentatricopeptide repeat (PPR) proteins specifically recognize target sites for C-to-U RNA editing in the transcriptomes of plant chloroplasts and mitochondria. Among more than 80 PPR-type editing factors that have meantime been characterized, AEF1 (or MPR25) is a special case given its dual targeting to both organelles and addressing an essential mitochondrial (nad5eU1580SL) and an essential chloroplast (atpFeU92SL) RNA editing site in parallel in Arabidopsis. Here, we explored the angiosperm-wide conservation of AEF1 and its two organelle targets. Despite numerous independent losses of the chloroplast editing site by C-to-T conversion and at least four such conversions at the mitochondrial target site in other taxa, AEF1 remains consistently conserved in more than 120 sampled angiosperm genomes. Not a single case of simultaneous loss of the chloroplast and mitochondrial editing target or of AEF1 disintegration or loss could be identified, contrasting previous findings for editing factors targeted to only one organelle. Like in most RNA editing factors, the PPR array of AEF1 reveals potential for conceptually “improved fits” to its targets according to the current PPR-RNA binding code. Surprisingly, we observe only minor evidence for adaptation to the mitochondrial target also after deep losses of the chloroplast target among Asterales, Caryophyllales and Poales or, vice versa, for the remaining chloroplast target after a deep loss of the mitochondrial target among Malvales. The evolutionary observations support the notion that PPR-RNA mismatches may be essential for proper function of editing factors.

The colors of fleshy fruits are considered to be a signal to seed-dispersing animals, but their diversity remains poorly understood. Using an avian color space to derive a sensory morphospace for fruit color, we tested four hypotheses of fruit color diversity: fruit colors occupy a limited area of the color space; they are less diverse than flower colors; fruit colors within localities are similar to each other; and fruit color diversity reflects phylogeny. The global fruit color diversity of 948 primarily bird-dispersed plant species and the color diversity of localities were compared with null models of random, unconstrained evolution of fruit color. Fruit color diversity was further compared with the diversity of 1300 flower colors. Tests of phylogenetic effects on fruit color were used to assess the degree of correspondence with phylogeny. Global and local fruit color diversity was limited compared with null models and fruits have achieved only half the color diversity of flowers. Interestingly, we found little indication of phylogenetic conservatism. Constraints resulting from the chemical properties of pigments probably limit global fruit and flower color diversity. Different types of selection on fruits and flowers may further explain the smaller color diversity of fruits.

Recent studies indicate that both key innovations and available area influence species richness in angiosperms. Available area has been observed to have the greatest effect, however, and appears to alter the \"carrying capacity\" of a lineage rather than alter diversification rates. Here, we review and weigh the evidence of predictors of angiosperm diversification and further dissect how area can place ecological limits on diversification of angiosperms, specifically addressing the following: (1) theoretical mechanisms by which particular intrinsic and extrinsic traits may affect diversification in angiosperm families; (2) evidence that the amount of available area determines the ecological limits on lineages; and (3) geographical distribution of diversification hotspots in angiosperms, concentrating on the effects of zygomorphy, noncontiguous area, and latitude. While we found that dispersal to numerous noncontiguous areas is most important in spurring diversification, diversification of tropical and zygomorphic families appears to be elevated by the generation of more species per given area.