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In Rosaceae, the replacement of the traditional four-subfamily division (Amygdaloideae or Prunoideae, Maloideae, Rosoideae, and Spiraeoideae) by the three-subfamily division (Dryadoideae, Rosoideae, and Amygdaloideae), the circumscription, systematic position, and phylogeny of genera in Maleae need to be reconsidered. The study aimed to circumscribe Maleae, pinpoint its systematic position, and evaluate the status of all generally accepted genera in the tribe using complete chloroplast genome data. Results indicated that Maleae consisted of pome-bearing genera that belonged to Maloideae as well as four genera ( Gillenia , Kageneckia , Lindleya , and Vauquelinia ) that were formerly considered to be outside Maloideae. The tribe could be subdivided into four subtribes: Gilleniinae ( Gillenia ), Lindleyinae ( Kageneckia and Lindleya ), Vaugueliniinae ( Vauquelinia ), and Malinae (all other genera; the core Maleae). Among the 36 recognized genera, Aria , Docyniopsis , Chamaemespilus , and Mespilus were not considered distinct and more research is needed to determine the taxonomic status of Rhaphiolepis from Eriobotrya . Within the core Maleae, five groups were revealed, whereas Sorbus L. was split as its members belonged to different groups.

Genus Filipendula (Rosoideae, Rosaceae) comprises about 15 species and mainly distributed in Northern Hemisphere. The phylogenetic relationships based on the nrITS marker are not consistent with the traditional taxonomic systems of the genus. Here, we first analysed the complete chloroplast (cp) genomes of seven Filipendula species (including two varieties of F. palmate ). Our results indicated that the cp genomes of Filipendula species had few changes in size, ranging from 154,205 bp to 154,633 bp and the average of 36.63% GC content. A total of 126 annotated genes had the identical order and orientation, implying that the cp genome structure of Filipendula species was rather conserved. However, the cp genomes of Filipendula species exhibited structural differences, including gene loss, transposition and inversion when compared to those of other genera of Rosoideae. Moreover, SSRs with the different number were observed in the cp genome of each Filipendula species and sequence divergence mainly occurred in noncoding regions, in which four mutational hotspots were identified. In contrast, only two positive selection genes ( matK and rps8 ) were found. Phylogenetic and molecular-dating analysis indicated that Filipendula species were divergent from other genera of Rosoideae at about 82.88 Ma. Additionally, Filipendula species from East Asia were split at about 9.64 Ma into two major clades. These results provide a basis for further studying the infrageneric classification of Filipendula .

This paper updates earlier reviews of polyploidy and reproductive biology in the Rosaceae, and does so with a focus on hybridization in relation to polyploidy and (facultative) gametophytic apomixis. Taking data mainly from tribe Maleae, it also seeks to point out evidence for a potential role for fertilization of infrequent unreduced gametes in diploid-diploid crosses in producing autopolyploids. Apomixis may originate in these autopolyploids, and spread as they cross with diploids and other polyploids.

The four-subfamily subdivision of Rosaceae has been recently replaced by a three-subfamily scheme. The re-circumscribed Rosoideae lacks a solid and well-resolved phylogeny on which a classification can be based. In this study, we sampled 56 genera presumably belonging to Rosoideae and 10 genera belonging to other subfamilies or families and used 12 chloroplast regions ( mat K, rbc L, trn L, trn L–F, ndh F, ycf 1, trn C– ycf 6, trn S–G, trn S, psb A– trn H, rpo C1 and trn S– ycf 9) to reconstruct their phylogeny. Our results confirmed (1) the exclusion of Rhodotypos and Kerria from Rosoideae and their inclusion in the subfamily Amygdaloideae and (2) the exclusion of Chamaebatia , Cercocarpus , Dryas and Purshia (including Cowania ) from Rosoideae and their inclusion in Dryadoideae, the sister subfamily of Rosoideae. Within Rosoideae, there are six strongly supported lineages that correspond to six tribes: Ulmarieae, Colurieae, Rubeae, Roseae, Agrimonieae and Potentilleae. We dated the divergence of Rosoideae back to approximately 69.77 million years ago (Mya; 95% HPD = 61.28–78.33 Mya) and that of the tribes within Rosoideae to from 10.42 to 40.02 million years ago (Mya; 95% HPD = 4.73–59.08 Mya). The subfamily is probably of North American and Asian origin and thrives in the northern hemisphere, especially in Asia. After re-circumscriptions of several genera, there are 36 genera recognized in Rosoideae.

Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants. Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BAMM) and ancestral character and area reconstructions (Mesquite). It is inferred that African Alchemilla species originated following long-distance dispersal to tropical East Africa, but that the evolution of dwarf shrubs occurred in Ethiopia and in tropical East Africa independently. Establishing a timeframe is challenging given inconsistencies in age estimates, but it seems likely that they originated in the Pleistocene, or at the earliest in the late Miocene. The adaptation to alpine-like environments in the form of dwarf shrubs has apparently not led to enhanced diversification rates. Ancestral reconstructions indicate reversals in Alchemilla from plants with a woody base to entirely herbaceous forms, a transition that is rarely reported in angiosperms. Alchemilla is a clear example of in situ tropical alpine speciation. The dwarf shrub life form typical of African Alchemilla has evolved twice independently, further indicating its selective advantage in these harsh environments. However, it has not influenced diversification, which, although recent, was not rapid.

Background Meligethes are pollen-beetles associated with flowers of Rosaceae as larvae. This genus currently consists of 63 known species in two subgenera, Meligethes and Odonthogethes, predominantly occurring in the eastern Palaearctic. We analyzed 74 morphological and ecological characters (169 states) of all species, as well as of 11 outgroup species from 7 Meligethinae genera (including Brassicogethes ), to investigate their phylogeny. We also conducted a parallel molecular analysis on 9 Meligethes , 9 Odonthogethes , 3 Brassicogethes and 2 Meligethinus species based on DNA sequence data from mitochondrial (COI, 16S) and nuclear (CAD) genes. Results Morphological phylogenetic reconstructions supported the monophyly of the whole genus and clades corresponding to purported subgenera Meligethes s.str. and Odonthogethes. Main species-groups were mostly confirmed, however some unresolved polytomies remained. Molecular data placed members of Brassicogethes (including 42 mostly W Palearctic species associated with Brassicaceae) as sister to Odonthogethes, with this clade being sister to Meligethes s.str. This phylogenetic scenario suggests that monophyletic Meligethes s.str., Odonthogethes and Brassicogethes should be regarded alternatively as three subgenera of a monophyletic Meligethes , or three genera in a monophyletic genus-complex, with mutually monophyletic Brassicogethes and Odonthogethes . Molecular analyses estimated the origin of this lineage at ca. 14–15 Mya from a common stem including Meligethinus . Conclusions We hypothesize that the ancestor of Meligethes specialized on Rosaceae in the Middle Miocene (likely in Langhian Age) and subsequently radiated during Late Miocene and Plio-Pleistocene maintaining a trophic niche on this plant family. This radiation was primarily due to geographic isolation in E Asiatic mountain systems. Combined evidence from morphology, ancestral state parsimony reconstruction of host-plant associations and molecular evidence suggested that Rosoideae ( Rosa spp.) represented the ancestral hosts of Meligethes s.str., followed by an independent shift of ancestral Odonthogethes (ca. 9–15 Mya) on Rubus (Rosoideae) and members of Rosaceae Spiraeoideae. Other ancestral Odonthogethes probably shifted again on the unrelated plant family Brassicaceae (maybe 8–14 Mya in S China), allowing a rapid westward radiation of the Brassicogethes clade.

Terpenes are organic compounds and play important roles in plant development and stress response. Terpene synthases (TPSs) are the key enzymes for the biosynthesis of terpenes. For Rosaceae species, terpene composition represents a critical quality attribute, but limited information is available regarding the evolution and expansion occurring in the terpene synthases gene family. Here, we selected eight Rosaceae species with sequenced and annotated genomes for the identification of TPSs, including three Prunoideae, three Maloideae, and two Rosoideae species. Our data showed that the TPS gene family in the Rosaceae species displayed a diversity of family numbers and functions among different subfamilies. Lineage and species-specific expansion of the TPSs accompanied by frequent domain loss was widely observed within different TPS clades, which might have contributed to speciation or environmental adaptation in Rosaceae. In contrast to Maloideae and Rosoideae species, Prunoideae species owned less TPSs, with the evolution of Prunoideae species, TPSs were expanded in modern peach. Both tandem and segmental duplication significantly contributed to TPSs expansion. Ka/Ks calculations revealed that TPSs genes mainly evolved under purifying selection except for several pairs, where the divergent time indicated TPS-e clade was diverged relatively anciently. Gene function classification of TPSs further demonstrated the function diversity among clades and species. Moreover, based on already published RNA-Seq data from NCBI, the expression of most TPSs in Malus domestica, Prunus persica, and Fragaria vesca displayed tissue specificity and distinct expression patterns either in tissues or expression abundance between species and TPS clades. Certain putative TPS-like proteins lacking both domains were detected to be highly expressed, indicating the underlying functional or regulatory potentials. The result provided insight into the TPS family evolution and genetic information that would help to improve Rosaceae species quality.

Using DNA sequence data from nuclear ribosomal ITS in combination with plastid trnLF spacer and trnL intron data, we show that Sibbaldia is a polyphyletic assemblage. It falls into five separate clades of Potentilleae, three within Fragariinae and two within Potentilla (Potentillinae sensu Soják). To a large extent, our results are congruent with Soják’s findings based on morphological characters such as anther structure. Four of the Sibbaldia species included in this study remain in Sibbaldia, while S. adpressa is classified in Sibbaldianthe, S. perpusilloides is considered to represent a new genus in Fragariinae, Chamaecallis Smedmark, S. micropetala is nested within the Potentilla anserina clade, and four species belong to a basal clade of Potentilla. The phylogenetic affinity of Sibbaldiopsis is still unsettled, but one of the three species that have been classified in the genus is found to belong inside Sibbaldia, and it should be named Sibbaldia retusa (O.F. Müller) T. Erikss. Further study will show whether the remaining two species, Potentilla cuneifolia and P. miyabei, are more closely related to Sibbaldia, Sibbaldianthe, or if they make up a distinct lineage separate from either of these.

To get a more comprehensive knowledge of oil contents and fatty acid pattern, seed oils from various Rosaceous plants belonging to the subfamilies Maloideae and Rosoideae, respectively, were investigated. For this purpose, isolated seeds of 18 dessert and cider apple ( Malus domestica BORKH.) cultivars of different provenances, pear ( Pyrus communis L.), rose hip ( Rosa canina L.), quince ( Cydonia oblonga Mill.), and red chokeberry ( Aronia arbutifolia L.) were analyzed for their oil content and fatty acid composition. Oil contents varied significantly, not only among the different genera, but also among cultivars of one species, ranging from 0.8 to 29.4 g/100 g dry matter. Qualitatively, the fatty acid profiles of the investigated seed oils showed good agreement in all representatives of the Rosaceae. Their triacylglycerols were uniformly composed of linoleic, oleic, palmitic, stearic, palmitoleic, α-linolenic, arachidic, gondoic, and behenic acids. Quantitation of individual fatty acids revealed the oils to be rich in mono- and diunsaturated oleic acid and linoleic acid, ranging from 15.1 to 33.3 g/100 g and from 32.5 to 49.7 g/100 g, respectively. As expected, contents of saturated fatty acids were 6–10 times lower. Moreover, apple cultivars showed pronounced differences in yields, numbers, and weights of their seeds. As demonstrated by the data obtained from this study, seeds resulting from the processing of apple, pear, quince, chokeberry (Maloideae), and rose hip (Rosoideae) into juices, jellies, and jams may serve as a promising source for the recovery of nutritionally valuable edible oils.

Cultivated strawberry (Fragaria × ananassa) together with other economically important genera such as Rosa (roses) and Rubus (raspberry and blackberry) belongs to the subfamily Rosoideae. There is increasing interest in the development of transferable markers to allow genome comparisons within the Rosaceae family. In this report, 122 new genic microsatellite (SSR) markers have been developed from cultivated strawberry and its diploid ancestor Fragaria vesca. More than 77% of the sequences from which the markers were developed show significant homology to known or predicted proteins and more than 92% were polymorphic among strawberry cultivars, representing valuable markers in transcribed regions of the genome. Sixty-three SSRs were polymorphic in the diploid Fragaria reference population and were bin-mapped together with another five previously reported but unmapped markers. In total, 72 loci were distributed across the seven linkage groups. In addition, the transferability of 174 Fragaria SSRs to the related Rosa and Rubus genera was investigated, ranging from 28.7% for genic-SSRs in rose to 16.1% for genomic-SSRs in raspberry. Among these markers, 33 and 16 were both localized in the diploid Fragaria reference map and cross-amplified in rose and raspberry, respectively. These results indicate that transferability of SSRs across the Rosoideae subfamily is limited. However, we have identified a set of Fragaria markers, polymorphic in the diploid reference population, which cross-amplified in both Rosa and Rubus, which represents a valuable tool for comparative mapping and genetic diversity analyses within the Rosoideae subfamily.