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The phylogenetic relationships (based on the ML tree) within Maleae resolved by whole plastid genomes (WPs). Numbers associated with the branches are ML bootstrap value (BS) and BI posterior probabilities (PP). Nodes without numbers are supported by 100/1. BI, Bayesian inference; ML, maximum likelihood.

The phylogenetic relationships (based on the ML tree) within Maleae resolved by whole plastid genomes (WPs). Numbers associated with the branches are ML bootstrap value (BS) and BI posterior probabilities (PP). Nodes without numbers are supported by 100/1. BI, Bayesian inference; ML, maximum likelihood.

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Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea, and Stranvaesia, and 68 species, distributed in Asia and North and Central America. Despite previous efforts to clarify relationships in this group, the generic delimitations have remained unce...

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... ML and BI of WP and CDS resulted in trees with nearly the same topology (Figs. 1, S1), except for the phylogenetic position of Aronia. In each analysis (ML & BI) Photinia-related genera did not form a monophyletic group and they were dispersed in six well-supported clades, Aronia, Heteromeles, Photinia, Pourthiaea, Stranvaesia, and the clade consisting of species of Photinia from Central America. ...
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... this study, we obtained a well-supported phylogeny of Maleae, sampling 81 species in 30 genera, with an emphasis on Photinia and its close allies. Four well-supported clades (clades A, B, C, and D) were recovered within Maleae in the plastid tree (Figs. 1, S1), and this relationship was compatible with the findings by Zhang et al. (2017). The phylogenetic analyses of the Photinia-related genera in the framework of Maleae suggest that the members did not form a monophyletic group. ...
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... phylogenetic analyses of the Photinia-related genera in the framework of Maleae suggest that the members did not form a monophyletic group. Genera of this group are scattered in six clades within Maleae: Aronia, Heteromeles, the Asian Photinia, Pourthiaea, Stranvaesia, and the New World Photinia clade (Figs. 1, 2, S1). The analyses also show additional issues concerning the generic delimitations in Maleae. ...
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... delimitations in Maleae. For example, Amelanchier, Crataegus, Malus, and Sorbus are each shown to be not monophyletic, even though our sampling on these genera is low, suggesting the need for further work on those genera. Furthermore, the phylogenetic position of several unique genera, such as Aronia and Heteromeles, remains uncertain (cf. Figs. 1, 2, ...
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... species of Photinia in Central America (i.e., the Phippsiomeles clade) are shown to be remotely related to the taxa of Photinia in Asia (i.e., the Photinia clade) in both plastome and nrDNA trees (Figs. 1,2, S1). Nevertheless, the position of Phippsiomeles differs in these two trees (Figs. 1,2). It is the basalmost clade of clade A, sister to a large clade of Chaenomeles, Cydonia, Dichotomanthes, Docynia, Eriolobus, Malus, Osteomeles, Pourthiaea, Pseudocydonia, Sorbus, and Torminalis in the WP tree (Fig. 1). Phippsiomeles is the basalmost ...
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... species of Photinia in Central America (i.e., the Phippsiomeles clade) are shown to be remotely related to the taxa of Photinia in Asia (i.e., the Photinia clade) in both plastome and nrDNA trees (Figs. 1,2, S1). Nevertheless, the position of Phippsiomeles differs in these two trees (Figs. 1,2). It is the basalmost clade of clade A, sister to a large clade of Chaenomeles, Cydonia, Dichotomanthes, Docynia, Eriolobus, Malus, Osteomeles, Pourthiaea, Pseudocydonia, Sorbus, and Torminalis in the WP tree (Fig. 1). Phippsiomeles is the basalmost clade in the New World clade, and it is sister to the clade of Amelanchier, Crataegus, ...
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... clade) in both plastome and nrDNA trees (Figs. 1,2, S1). Nevertheless, the position of Phippsiomeles differs in these two trees (Figs. 1,2). It is the basalmost clade of clade A, sister to a large clade of Chaenomeles, Cydonia, Dichotomanthes, Docynia, Eriolobus, Malus, Osteomeles, Pourthiaea, Pseudocydonia, Sorbus, and Torminalis in the WP tree (Fig. 1). Phippsiomeles is the basalmost clade in the New World clade, and it is sister to the clade of Amelanchier, Crataegus, Mespilus, and Hesperomeles in the nrDNA tree (Fig. 2). The results thus strongly support the New World Photinia (Fig. 4) to be delimited as a distinct new genus Phippsiomeles, rather than treating them as members of ...
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... or incomplete lineage sorting, the conflicts in the phylogenetic position of Phippsiomeles between the plastome (WP & CDS: Figs. 1, S1) and nuclear data (nrDNA: Fig. 2) may be explained by a likely origin of the lineage via hybridization between an ancestral lineage of the New World clade (Fig. 2) and one of the ancestral lineages of clade A (Fig. 1). Our data are consistent with a hypothesis that an ancestral lineage of clade A may have served as the maternal parent. The paternal parent may be an ancestral lineage of the New World clade (Fig. 2). Other lines of evidence also support a hybrid origin hypothesis for Phippsiomeles. Intergeneric hybridization is common in Maleae ...
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... results showed that the type species of Stranvaesia, S. nussia, groups with S. oblanceolata and Photinia bodinieri. This clade of three species was then sister to a large clade of Photinia, Heteromeles, Cotoneaster, Eriobotrya, Rhaphiolepis, Sorbus, Pyrus, and Cormus (Fig. 1). However, three species traditionally placed in Stranvaesia, S. amphidoxa, S. davidiana, and S. tomentosa (Lu & Spongberg, 2003), did not form a clade with the clade containing the type species, S. nussia. Even though Stranvaesia has been recently merged with Photinia (Kalkman, 1973, 2004Robertson et al., 1991;Guo et al., 2011), the ...
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... three species traditionally placed in Stranvaesia, S. amphidoxa, S. davidiana, and S. tomentosa (Lu & Spongberg, 2003), did not form a clade with the clade containing the type species, S. nussia. Even though Stranvaesia has been recently merged with Photinia (Kalkman, 1973, 2004Robertson et al., 1991;Guo et al., 2011), the clade of Stranvaesia with its type species is not sister to or nested within Photinia (Figs. 1, 2). Photinia is sister to a clade of Cotoneaster and Heteromeles in the plastome tree ( Fig. 1), but it forms a clade with Pyracantha in the nrDNA tree (Fig. 2). ...
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... the type species, S. nussia. Even though Stranvaesia has been recently merged with Photinia (Kalkman, 1973, 2004Robertson et al., 1991;Guo et al., 2011), the clade of Stranvaesia with its type species is not sister to or nested within Photinia (Figs. 1, 2). Photinia is sister to a clade of Cotoneaster and Heteromeles in the plastome tree ( Fig. 1), but it forms a clade with Pyracantha in the nrDNA tree (Fig. 2). In spite of the topological conflicts between plastid and rDNA trees, the Stranvaesia clade containing the type species is distinct from Photinia (Figs. 1, 2). Only Stranvaesia davidiana is grouped with Photinia; but S. amphidoxa and S. tomentosa form a clade with ...
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... is sister to a clade of Cotoneaster and Heteromeles in the plastome tree ( Fig. 1), but it forms a clade with Pyracantha in the nrDNA tree (Fig. 2). In spite of the topological conflicts between plastid and rDNA trees, the Stranvaesia clade containing the type species is distinct from Photinia (Figs. 1, 2). Only Stranvaesia davidiana is grouped with Photinia; but S. amphidoxa and S. tomentosa form a clade with Pourthiaea, suggesting the need to exclude these three taxa from Stranvaesia. ...
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... the basalmost clade of Photinia, Stranvaesia davidiana is more closely related to Photinia rather than to Stranvaesia (Figs. 1, S1). Morphologically, S. davidiana and Photinia both lack stone cells in the flesh of pomes (Iketani & Ohashi, 1991b), while the species of Stranvaesia clade as redefined here possess stone cells in the flesh of pomes. ...
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... characterized by spines on the stems and black-purple fruits, Photinia bodinieri was hypothesized to be of hybrid origin between Photinia and another genus of Pyrinae (currently the tribe Maleae) also with spines on the stem (Guo et al, 2011). Our results showed that P. bodinieri was sister to Stranvaesia oblanceolata, and then together sister to S. nussia in both the plastome (WP & CDS: Figs. 1, S1) and nuclear (nrDNA: Fig. 2) trees. ...
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... fruits, Photinia bodinieri was hypothesized to be of hybrid origin between Photinia and another genus of Pyrinae (currently the tribe Maleae) also with spines on the stem (Guo et al, 2011). Our results showed that P. bodinieri was sister to Stranvaesia oblanceolata, and then together sister to S. nussia in both the plastome (WP & CDS: Figs. 1, S1) and nuclear (nrDNA: Fig. 2) trees. This congruent relationship in both data sets does not support the hybrid origin hypothesis of Photinia ...
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... phylogenetic result showed that Stranvaesia amphidoxa and S. tomentosa were nested within the Pourthiaea clade (Figs. 1, 2, S1). In the plastome trees (WP & CDS: Figs. 1, S1), S. amphidoxa was sister with P. pilosicalyx, then together sister with all other taxa in Pourthiaea; S. tomentosa was sister with a large clade of P. arguta, P. blinii, P. sorbifolia, and P. zhejiangensis while S. tomentosa was sister with P. pilosicalyx, and then together formed a clade with S. amphidoxa in the nuclear (nrDNA) tree (Fig. 2). ...
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... phylogenetic result showed that Stranvaesia amphidoxa and S. tomentosa were nested within the Pourthiaea clade (Figs. 1, 2, S1). In the plastome trees (WP & CDS: Figs. 1, S1), S. amphidoxa was sister with P. pilosicalyx, then together sister with all other taxa in Pourthiaea; S. tomentosa was sister with a large clade of P. arguta, P. blinii, P. sorbifolia, and P. zhejiangensis while S. tomentosa was sister with P. pilosicalyx, and then together formed a clade with S. amphidoxa in the nuclear (nrDNA) tree ...
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... we herein formally transfer Stranvaesia amphidoxa and S. tomentosa to Pourthiaea. The incongruence of the position of Stranvaesia tomentosa has been shown between the plastome (WP & CDS) and the nuclear (nrDNA) trees (Figs. 1, 2). One possible explanation for this topological conflict is that the ancestral lineage of S. tomentosa originated via hybridization between Pourthiaea pilosicalyx and a large clade of P. arguta, P. blinii, P. sorbifolia, and P. zhejiangensis (Fig. 1). ...
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... tomentosa has been shown between the plastome (WP & CDS) and the nuclear (nrDNA) trees (Figs. 1, 2). One possible explanation for this topological conflict is that the ancestral lineage of S. tomentosa originated via hybridization between Pourthiaea pilosicalyx and a large clade of P. arguta, P. blinii, P. sorbifolia, and P. zhejiangensis (Fig. 1). Our data support that an ancestor of P. pilosicalyx may have served as the maternal parent, and its chloroplast was captured by the ancestor of S. tomentosa via introgression. Based on our data, the paternal parent is likely to be an ancestor of a member of the clade ...
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... and fruits of Aronia are indistinguishable from those of Photinia. But our phylogenetic analyses support recognizing Aronia as a distinct genus. Aronia, nevertheless, has an uncertain position, either sister to the clade of Cydonia and Dichotomanthes (CDS: S1), or with a large clade of Eriolobus, Malus, Pourthiaea, Sorbus, and Torminalis (WP: Fig. 1), or sister to a larger clade as shown in the nrDNA tree (nrDNA : Fig. 2); however, all of the phylogenetic positions are only weakly supported. Based on a combined data (six nuclear (18 S, GBSSI-1, GBSSI-2, ITS, pgip, and ppo) and four chloroplast (matK, ndhF, rbcL, and trnL-trnF) regions), Potter et al. (2007) also showed an uncertain ...
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... is a monotypic genus restricted to California and Baja California in western North America (Fig. 4; Phipps, 2014). The genus is characterized by 10 stamens, nearly free carpels, well defined carpellary walls (even though they may be quite soft in fruit), and moderately soft testa (Phipps, 1992). Heteromeles forms a clade with Cotoneaster, and then together sister to the clade Eriobotrya and Rhaphiolepis in the plastome tree (Figs. 1, S1); ...
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... genus is characterized by 10 stamens, nearly free carpels, well defined carpellary walls (even though they may be quite soft in fruit), and moderately soft testa (Phipps, 1992). Heteromeles forms a clade with Cotoneaster, and then together sister to the clade Eriobotrya and Rhaphiolepis in the plastome tree (Figs. 1, S1); however, the position of Heteromeles is uncertain and has weak support in the nrDNA tree (Fig. 2). Other lines of evidence also suggested the close relationship between Heteromeles and Cotoneaster. ...

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... It has long been difficult to classify the genera of the Maleae tribe, which may be due to polyploidy events, rapid radiations, frequent hybridizations, and/or ancient diversification among some clades (Wolfe and Wehr, 1988;Robertson et al., 1991;Vamosi and Dickinson, 2006;Campbell et al., 2007;Dickinson et al., 2007;Li et al., 2012;Lo and Donoghue, 2012;Xiang et al., 2016;Liu et al., 2019). The latest research also shows that multiple ancient hybridization and chloroplast capture events within Eriobotrya in the Yunnan-Guizhou Plateau (Chen et al., 2021). ...
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... Genome skimming has often been used to target the highcopy fractions of genomes, including plastomes, mitochondrial genomes (mitogenomes), and nuclear ribosomal DNA (nrDNA) repeats (Straub et al., 2012;Dodsworth, 2015;Zhang et al., 2015;Thode et al., 2020), and these data sets have been widely used for inferring phylogenies in many recent studies. For example, the plastome has been widely utilized for inferring the phylogenetic relationships at various levels (Bock et al., 2014;Zhang et al., 2015;Valcárcel & Wen, 2019;Zhang et al., 2019;Wang et al., 2020), clarifying generic and species delimitations (Wen et al., 2018a;Liu et al., 2019Liu et al., , 2020aLiu et al., , 2020b, as well as acting as an ultra-barcode in plants (Kane et al., 2012;Hollingsworth et al., 2016). The uniparental (mostly maternal, rarely paternal) inheritance and nonrecombinant nature of the plastomes make them the ideal marker for tracking the maternal (rarely paternal) history, providing useful evidence to untangle hybridization events in plants (Rieseberg & Soltis, 1991;Sun et al., 2015;Folk et al., 2017;Vargas et al., 2017;Morales-Briones et al., 2018). ...
... Some regions of the nrDNA repeat, especially the internal transcribed spacer (ITS) and sometimes also the external transcribed spacer (ETS) have been widely used for lower-level phylogenetic reconstruction in flowering plants (Baldwin et al., 1995;Álvarez & Wendel, 2003;Soltis et al., 2008). Recently, the entire nrDNA repeats, including ETS, 18S, ITS1, 5.8S, ITS2, and 26S regions, have been assembled from genome skimming data, and depending on the region of the repeat that has been utilized, have also been effective in providing phylogenetic resolution at shallow evolutionary levels (e.g., in the Rosaceae: Liu et al., 2019Liu et al., , 2020aLiu et al., , 2020b. Hence, genome skimming has been a valuable approach for providing genomic data for phylogenetic inferences. ...
... Because the nrDNA copies are arranged in tandem repeats, we tentatively treated the complete nrDNA as circular in order to use the plastome assembly software (NOVOPlasty) for the nrDNA assembly, and the steps we used were nearly the same as the assembly procedure of plastomes as described above. The detailed procedure has been described in several recent studies (Zhang et al., 2015;Liu et al., 2019Liu et al., , 2020aLiu et al., , 2020bWang et al., 2020). All the assembled plastomes and nrDNA repeats have been submitted to GenBank with the accession numbers listed in Tables S1 and S2. ...
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With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage in silico. We tested the performance of four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus level and Vitaceae at the family level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, coupled with incredibly low sequencing costs, we showcase that deep genome skimming (DGS) is as effective for capturing large datasets of SCNs as the widely used Hyb-Seq approach, in addition to capturing plastomes, mtDNA, and entire nrDNA repeats. DGS may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach. This article is protected by copyright. All rights reserved.
... Interestingly, within GAW Clade, Glycyrrhizinae occupies quite different habitats (xeric temperate region) from that of Adinobotrys and Wisterieae (mainly tropical/subtropical forests), possibly corresponding to the theory that introgressive progenies may have become the founding groups for expanding distributions as they adapt to their particular environment (Rieseberg, 1995). Such a chloroplast capture scenario can also be seen in other plant taxa (Acosta and Premoli, 2010;Yi et al., 2015;Duan et al., 2016;Liu et al., 2019Liu et al., , 2020. Likewise within CCH Clade, common ancestors of the tribes Hedysareae (♂) and Chesneyeae (♀) provided chloroplast and nuclear genomes to Caraganeae, respectively (Fig. 1). ...
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The inverted repeat-lacking clade (IRLC) is one of the most derived clades within the subfamily Papilionoideae of the legume family, and includes various economically important plants, e.g., chickpeas, peas, liquorice, and the largest genus of angiosperms, Astragalus. Tribe Wisterieae is one of the earliest diverged groups of the IRLC, and its generic delimitation and spatiotemporal diversification need further clarifications. Based on genome skimming data, we herein reconstruct the phylogenomic framework of the IRLC, and infer the inter-generic relationships and historical biogeography of Wisterieae. We redefine tribe Caraganeae to contain Caragana only, and tribe Astragaleae is reduced to the Erophaca-Astragalean clade. The chloroplast capture scenario was hypothesized as the most plausible explanation of the topological incongruences between the chloroplast CDSs and nuclear ribosomal DNA trees in both the Glycyrrhizinae-Adinobotrys-Wisterieae clade and the Chesneyeae-Caraganeae-Hedysareae clade. A new name, Caragana lidou L.Duan & Z.Y.Chang, is proposed within Caraganeae. Thirteen genera are herein supported within Wisterieae, including a new genus, Villosocallerya L.Duan, J.Compton & Schrire, segregated from Callerya. Our biogeographic analyses suggest that Wisterieae originated in the late Eocene and its most recent common ancestor (MRCA) was distributed in continental southeastern Asia. Lineages of Wisterieae remained in the ancestral area from the early Oligocene to the early Miocene. By the middle Miocene, Whitfordiodendron and the MRCA of Callerya-Kanburia-Villosocallerya Clade became disjunct between the Sunda area and continental southeastern Asia, respectively; the MRCA of Wisteria migrated to North America via the Bering land bridge. The ancestor of Austrocallerya and Padbruggea migrated to the Wallacea-Oceania area, which split in the early Pliocene. In the Pleistocene, Wisteria brachybotrys, W. floribunda and Wisteriopsis japonica reached Japan, and Callerya cinerea dispersed to South Asia. This study provides a solid tribal-level phylogenetic framework for further evolutionary/biogeographic/systematic investigations on the ecologically diverse and economically important IRLC legumes.
... Although the nuclear genome can provide a wealth of valuable information for phylogenetic studies (e.g., Ness et al., 2011), their acquisition can be difficult and costly and their complexity can pose analytical and computational challenges. In contrast, plastid genomes are relatively easy to assemble, and provide valuable resources to assess interspecific relationships, especially within unresolved low taxonomic levels with complex morphological characters (Niu et al., 2017;Liu et al., 2019;Song et al., 2019). With the rapid development of high-throughput sequencing, an increasing number of plastomes has been published and used to fully resolve phylogenetic relationships at different taxonomic levels (Song et al., 2015(Song et al., , 2019Wen et al., 2015;Thomson et al., 2018;. ...
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Monochoria is a genus of Pontederiaceae and confined to the Old World, with species mainly distributed in tropical and subtropical Africa, Asia, and Australia. However, phylogenetic relationships and biogeography within Monochoria are yet to be fully resolved. Here, we sequenced 14 Monochoria plastomes, representing around eight of the ~ 10 species of Monochoria, and two plastomes from related genera. We conducted comparative analyses and phylogenetic reconstructions of Monochoria using these and other available sequences. We found the plastomes of Pontederiaceae to be highly conserved in structure, and identified six regions as mutational hotspots among species of Monochoria. Our data strongly support the monophyly of Monochoria and two main clades within the genus. We confirm that Monochoria australasica is sister to the rest of the genus and that M. korsakowii defines the second split within Monochoria. In addition, we inferred the African endemic species M. africana to be closely related to M. plantaginea and an undetermined specimen from Australia (Monochoria sp. AU63). Estimation of divergence times and biogeography implied that the African species M. africana originated in Asia, and the most recent common ancestor of Monochoria was distributed in Australasia/Asia at approximately 15 Ma (million years ago), followed by diversification in Asia during the late Miocene and Pliocene. Long‐distance dispersal, likely mediated by migratory birds, to Africa and Australia during the Pliocene and Pleistocene, may have contributed to the extant transoceanic distribution of the genus. Additionally, based on our phylogenetic results, we revised the description of M. valida here. This article is protected by copyright. All rights reserved.
... Petals in the family Rosaceae are generally showy, and the attractive petals make many species of the family highly valued as ornamental plants, such as roses and cherry blossoms, and the cultivation of several double flowers (Phipps, 2014;Liu et al., 2019). Ronse De Craene (2003) suggested that the petals in Rosaceae are transformed stamens, which arise as the outermost (first-formed) primordia of stamen fascicles that extend with the growth of a hypanthium. ...
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Although the vast majority of Prunus L. (Rosaceae) species have clearly differentiated sepals and petals, two former genera Maddenia and Pygeum have been described as having an undifferentiated perianth. However, floral morphological and morphogenetic data are scarce, and a renewed investigation is essential to understand the evolution of the perianth differentiation. Here, floral morphogenesis in Prunus hypoleuca (Koehne) J.Wen (=Maddenia hypoleuca Koehne) and Prunus topengii (Merr.) J. Wen & L. Zhao (=Pygeum topengii Merr.) were examined with scanning electron microscopy. The floral development demonstrates that the ten perianth parts can be distinguished as five sepals in an external whorl and five petals in an internal whorl. The sepal primordia are broad, crescent‐shaped, and truncate. The petal primordia are rounded and initially resemble the androecium. However, at maturity petals and sepals look much the same in the two species, differing from other Prunus species. The ovule is anatropous and unitegmic, but there is a basal appendage near the ovule of P. hypoleuca which is absent in P. topengii. The direction of development of floral nectaries in the hypanthium is basipetal in P. hypoleuca but acropetal in P. topengii. Perianth segments are differentiated in the two groups and the similarity of the perianth parts is secondarily acquired. Our results support the separation of the Maddenia and Pygeum groups as well as their inclusion in a broader monophyletic Prunus based on molecular phylogenetic studies. We herein provide a new nomenclatural change: Prunus topengii (Merr.) J. Wen & L. Zhao, comb. nov. This article is protected by copyright. All rights reserved.