Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with ∼10% missing, 10–25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.

Asexual reproduction is expected to reduce the adaptive potential to novel or changing environmental conditions, restricting or altering the ecological niche of asexual lineages. Asexual lineages of plants and animals are typically polyploid, an attribute that may influence their genetic variation, plasticity, adaptive potential, and niche breadth. The genus Boechera (Brassicaceae) represents an ideal model to test the relative ecological and biogeographic impacts of reproductive mode and ploidy because it is composed of diploid sexual and both diploid and polyploid asexual (i.e., apomictic) lineages. Here, we demonstrate a strong association between a transcriptionally conserved allele and apomictic seed formation. We then use this allele as a proxy apomixis marker in 1,649 accessions to demonstrate that apomixis is likely to be a common feature across the Boechera phylogeny. Phylogeographic analyses of these data demonstrate (i) species-specific niche differentiation in sexuals, (ii ) extensive niche conservation between differing reproductive modes of the same species, (iii) ploidy-specific niche differentiation within and among species, and (iv) occasional niche drift between apomicts and their sexual ancestors. We conclude that ploidy is a substantially stronger and more common driver of niche divergence within and across Boechera species although variation in both traits may not necessarily lead to niche evolution on the species scale.Boechera | UPGRADE2 | APOLLO | geographic parthenogenesis | niche conservation

The genetic mechanisms causing seed development by gametophytic apomixis in plants are predominantly unknown. As apomixis is consistently associated with hybridity and polyploidy, these confounding factors may either A) be the underlying mechanism for the expression of apomixis, or B) obscure the genetic factors which cause apomixis. To distinguish between these hypotheses, we analyzed the population genetic patterns of diploid and triploid apomictic lineages and their sexual progenitors in the genus Boechera (Brassicaceae). We find that while triploid apomixis is associated with hybridization, the majority of diploid apomictic lineages are likely the product of intra-specific crosses. We then show that these diploid apomicts are more likely to sire triploid apomictic lineages than conspecific sexuals. Combined with flow cytometric seed screen phenotyping for male and female components of apomixis, our analyses demonstrate that hybridization is an indirect correlate of apomixis in Boechera. KeywordsBoechera; Apomixis; Apomeiosis; Hybridization; Polyploidy Sexual, outcrossing reproduction is the ancestral state of embryo development in flowering plants (Karron et al. 2012). This breeding system has generated much of the biodiversity on earth and provides species with the potential to adapt to changing conditions, thus improving the chance for long term survival. Despite these advantages, many groups of plants have independently evolved asexual methods to produce seed (van Dijk and Vijverberg 2005;Carman 1997). Among these mechanisms, gametophytic apomixis (hereon "apomixis") is one of the most common (Hörandl and Hojsgaard 2012 requires the coordination of several independent phenotypes including the formation of an unreduced embryo sac (female apomeiosis) and embryo development from an unfertilized and unreduced egg cell (parthenogenesis). Other traits, including the production of unreduced pollen (male apomeiosis) and the development of functional endosperm (e.g. pseudogamy) are typical of apomictic genotypes (Mogie 1992;Bicknell and Koltunow 2004). Considering that apomixis evolves from sexuality, the expression of any one of these traits alone would be deleterious. For example, female apomeiosis without parthenogenesis would lead to ploidy increases after each generation (although see Van Dijk & Vijverberg, 2005). The evolutionary mechanism causing the simultaneous establishment of these traits is the foremost debate in the apomixis literature.Many authors have suggested that the genome-wide affects of hybridization and polyploidy may induce apomixis (Carman 1997;Comai et al. 2003;Madlung et al. 2002;Sharbel et al. 2010; Wang et al. 2004) as evidenced by the nearly uniform pattern of hybridity and polyploidy in apomictic lineages (Pongratz et al. 1997;Bicknell and Koltunow 2004;Mogie 1986; Asker and Jerling 1992;Nelson-Jones et al. 2002). However, this correlation may be indirect: since apomictic lineages are expected to accumulate mutations through time (Hopf et al. 1988;Kondrashov 1985), hybridity ...

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Pollen size is often used as a biological parameter to estimate the ploidy and viability of mature pollen grains. In general, pollen size quantification is performed one- or two-dimensionally using image-based diameter measurements. As these approaches are elaborate and time consuming, alternative approaches that enable a quick, reliable analysis of pollen size are highly relevant for plant research. In this study, we present the volume-based particle size analysis technique as an alternative method to characterize mature pollen. Based on a comparative assay using different plant species (including tomato, oilseed rape, kiwifruit, clover, among others), we found that volume-based pollen size measurements are not biased by the pollen shape or position and substantially reduce non-biological variation, allowing a more accurate determination of the actual pollen size. As such, volume-based particle size techniques have a strong discriminative power in detecting pollen size differences caused by alterations in the gametophytic ploidy level and therefore allow for a quick and reliable estimation of the somatic ploidy level. Based on observations in Arabidopsis thaliana gametophytic mutants and differentially reproducing Boechera polyantha lines, we additionally found that volume-based pollen size analysis provides quantitative and qualitative data about alterations in male sporogenesis, including aneuploid and diploid gamete formation. Volume-based pollen size analysis therefore not only provides a quick and easy methodology to determine the somatic ploidy level of flowering plants, but can also be used to determine the mode of reproduction and to quantify the level of diplogamete formation.