Chloroplast genomes provide important insights into plant phylogeny, genome evolution, and molecular marker development. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of two endemic species from Uzbekistan, Astragalus nuratensis and Oxytropis pseudorosea. Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively. The chloroplast genomes were 122,316 bp in A. nuratensis and 122,708 bp in O. pseudorosea. Both genomes encoded 110 unique genes, including 76 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Consistent with members of the inverted repeat-lacking clade of Fabaceae, both species lacked the typical inverted repeat regions, resulting in a single-copy genome structure. Phylogenetic analysis based on 119 complete chloroplast genomes resolved major lineages within Astragalus and related genera with strong support. Astragalus nuratensis was placed within the Phaca clade, while Oxytropis pseudorosea formed part of a distinct Oxytropis lineage. These results provide new genomic resources for understanding evolutionary relationships and plastome evolution in Central Asian legumes.

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Premise With over 3100 species, Astragalus L. (Fabaceae) has long fascinated botanists as the largest genus of flowering plants. With an origin in the Middle Miocene, Astragalus has one of the highest diversification rates known in flowering plants. Comprehensive taxonomic treatments exist, and the genus is currently subdivided into 136 sections in the eastern hemisphere and 93 sections in the western hemisphere based on morphological characters. Despite considerable efforts, a comprehensive and well-resolved phylogeny of the genus is still lacking. Methods Here, we reconstruct the backbone phylogeny of Astragalus using a custom bait set capturing 819 loci specifically designed for a target enrichment approach in the Astragalean clade. We carefully selected a set of 107 taxa representing all major clades currently recognized in Astragalus. Of those, 80 newly sequenced taxa were obtained from herbarium specimens as old as 110 years. Results We retrieved all the targeted loci and additional off-target plastome sequences for all samples, including the 80 herbarium specimens. Our phylogenetic analysis reinforced the currently accepted backbone phylogeny of Astragalus with high support and novel details, additionally providing insights into cytonuclear phylogenetic conflicts in the genus. Evidence for potential reticulate evolution was found, providing a possible explanation for the conflicts observed. Conclusions This work represents an important milestone in obtaining a comprehensive, herbarium-based phylogeny of Astragalus, which will constitute the base to study a wealth of relevant biological questions, for example, the still unanswered question of what drove the rapid diversification of Astragalus, with important repercussions on our understanding of diversification in natural contexts.

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Phlomoides , with 150-170 species, is the second largest and perhaps most taxonomically challenging genus within the subfamily Lamioideae (Lamiaceae). With about 60 species, China is one of three major biodiversity centers of Phlomoides . Although some Phlomoides species from China have been included in previous molecular phylogenetic studies, a robust and broad phylogeny of this lineage has yet to be completed. Moreover, given the myriad new additions to the genus, the existing infrageneric classification needs to be evaluated and revised. Here, we combine molecular and morphological data to investigate relationships within Phlomoides , with a focus on Chinese species. We observed that plastid DNA sequences can resolve relationships within Phlomoides better than nuclear ribosomal internal and external transcribed spacer regions (nrITS and nrETS). Molecular phylogenetic analyses confirm the monophyly of Phlomoides , but most previously defined infrageneric groups are not monophyletic. In addition, morphological analysis demonstrates the significant taxonomic value of eight characters to the genus. Based on our molecular phylogenetic analyses and morphological data, we establish a novel section Notochaete within Phlomoides , and propose three new combinations as well as three new synonyms. This study presents the first molecular phylogenetic analyses of Phlomoides in which taxa representative of the entire genus are included, and highlights the phylogenetic and taxonomic value of several morphological characters from species of Phlomoides from China. Our study suggests that a taxonomic revision and reclassification for the entire genus is necessary in the future.

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Phlomoides is one of the largest genera of Lamiaceae with approximately 150-170 species distributed mainly in Eurasia. In this study, we describe and illustrate a new species, P.henryi , which was previously misidentified as P.bracteosa , from Yunnan Province, southwest China. Molecular phylogenetic analyses revealed that P.henryi is found within a clade in which most species lack basal leaves. In this clade, the new species is morphologically distinct from P.rotata in having an obvious stem and, from the rest, by having transparent to white trichomes inside the upper corolla lip. In addition, micro-features of trichomes on the calyx and leaf epidermis can differentiate the new species from other species grouped in the same clade and a key, based on trichome morphology for these species, is provided. The findings demonstrate that the use of scanning electron microscopy can reveal inconspicuous morphological affinities amongst morphologically similar species and play an important role in the taxonomic study of the genus Phlomoides .

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The Astragalus subgenus Hypoglottis Bunge, which consists of several sections, is one of the taxonomically most complicated groups in the genus. The Astragalus section Stereothrix Bunge belongs to this subgenus and is a significant element of the Irano-Turanian floristic region. A molecular phylogenetic analysis of this section and its closely related taxa using nuclear ribosomal DNA internal transcribed spacers (ITS) and external transcribed spacer (ETS) regions as well as plastid mat K sequences were conducted. Parsimony analyses and Bayesian phylogenetic inference revealed that the section is not monophyletic in its current form, as some taxa belonging to closely related sections such as Hypoglottidei DC. and the Malacothrix Bunge group within the sect. Stereothrix render it paraphyletic. Moreover, species groups belonging to sect. Stereothrix are placed in different clades within the phylogenetic tree of subgenus Hypoglottis , which indicates polyphyly, i.e., multiple independent origins of taxa placed in the sect. Stereothrix . Molecular dating of the group estimated an age of 3.62 (1.73-5.62) My for this assemblage with the major diversification events happening during the last 2 My. Many species groups separated only within the last 0.5 to 1 My. Based on morphological and molecular data, we discuss the phylogenetic relationships of the groups and synonymy of species. In addition, the included taxa of sect. Hypoglottidei are not monophyletic and include species belonging to sects. Hololeuce , Koelziana , Malacothrix , Onobrychoideae, and Ornithodpodium group within the sect. Stereothrix taxa. We conclude that only an analysis including all groups and nearly all species of the sections within the Hypoglottis clade can finally result in an new evolutionary-based system for these taxa.

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