Allioideae

Abstract: Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus-Allium-is vast, comprising about a thousand species. Allium species (as well as other members of the Amaryllidaceae) are widespread and diversified, they are adapted to a wide range of habitats from shady forests to open habitats like meadows, steppes, and deserts. The genes present in chloroplast genomes (plastomes) play fundamental roles for the photosynthetic plants. Plastome traits could thus be associated with geophysical abiotic characteristics of habitats. Most chloroplast genes are highly conserved and are used as phylogenetic markers for many families of vascular plants. Nevertheless, some studies revealed signatures of positive selection in chloroplast genes of many plant families including Amaryllidaceae. We have sequenced plastomes of the following nine Allium (tribe Allieae of Allioideae) species: A. zebdanense, A. moly, A. victorialis, A. macleanii, A. nutans, A. obliquum, A. schoenoprasum, A. pskemense, A. platyspathum, A. fistulosum, A. semenovii, and Nothoscordum bivalve (tribe Leucocoryneae of Allioideae). We compared our data with previously published plastomes and provided our interpretation of Allium plastome genes' annotations because we found some noteworthy inconsistencies with annotations previously reported. For Allium species we estimated the integral evolutionary rate, counted SNPs and indels per nucleotide position as well as compared pseudogenization events in species of three main phylogenetic lines of genus Allium to estimate whether they are potentially important for plant physiology or just follow the phylogenetic pattern. During examination of the 38 species of Allium and the 11 of other Amaryllidaceae species we found that rps16, rps2, infA, ccsA genes have lost their functionality multiple times in different species (regularly evolutionary events), while the pseudogenization of other genes was stochastic events. We found that the "normal" or "pseudo" state of rps16, rps2, infA, ccsA genes correlates well with the evolutionary line of genus the species belongs to. The positive selection in various NADH dehydrogenase (ndh) genes as well as in matK, accD, and some others were found. Taking into account known mechanisms of coping with excessive light by cyclic electron transport, we can hypothesize that adaptive evolution in genes, coding subunits of NADH-plastoquinone oxidoreductase could be driven by abiotic factors of alpine habitats, especially by intensive light and UV radiation.

Abstract: The genus Leucocoryne (Amaryllidaceae) comprises approximately 15 species and is the only genus of the tribe Ipheieae endemic to the western region of Chile in sclerophyll and arid winter-rainfall biomes in the Andes. To better understand the karyotype diversification of this genus, nine species of Leucocoryne were analyzed in terms of their chromosome number and morphology, CMA and DAPI heterochromatic bands, distribution of rDNA sites, and their molecular phylogenetic relationships. Based on phylogenetic analyses Leucocoryne was divided in four clades: I (L. alliacea and L. conferta); II (L. dimorphopetala and L. narcisoides); III (L. coquimbensis, L. macropetala, L. appendiculata, L. talinensis, L. angustipetala, L. purpurea, and L. violacescens); and IV (L. vittata, L. ixioides, L. foetida, and L. pauciflora). The species were diploids with 2n = 10 (6M + 4A) or tetraploids with 2n = 18 (14M + 4A)/2n = 19 (13M + 6A). 45S rDNA sites were co-localized with CMA+/DAPI− bands on the short arms of acrocentric chromosomes in all species. 5S rDNA sites were observed on one, two, or four pairs of metacentric chromosomes per species. Estimations of the ancestral karyotype suggest that 2n = 10 (6M + 2A) with one 5S rDNA site per monoploid complement was the plesiomorphic condition of the genus Leucocoryne. Increases in number of 5S rDNA sites in the same species associated with biome shifts from sclerophyll to arid winter-rainfall region occurred independently in clade II and clade III. The two species of clade II retained the six fertile stamens (plesiomorphic condition) in contrast to the other Leucocoryne species that reduced to only three functional stamens. Based on these findings, we discuss the role of environmental change on the diversification of this group.

Abstract: Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, matK, ndhF, and rbcL to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum, Miersia, Solaria, and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere ('out-of-India' hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution.