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Cinnamomum is among the largest genera of the Lauraceae, including species from tropical to temperate Asia and from tropical to subtropical America. However, previous studies indicated that Cinnamomum might not be monophyletic in its current circumscription. We therefore re‐investigated the genus and possible relatives with an increased taxon sample, particularly of the Neotropical species. Our results, based on sequences of the nuclear ITS region and the chloroplast spacers psbA‐trnH and trnG‐trnS, show that the Neotropical Cinnamomum species indeed do not form a monophyletic group with the Paleotropical species. Instead, the American species form a clade in which most species of the Neotropical genus Aiouea are nested within several subclades. According to the ITS data the Aiouea/Cinnamomum clade is sister to the likewise predominantly Neotropical Ocoteacomplex, rather than the two Paleotropical Cinnamomum clades. Therefore, Cinnamomum cannot be upheld in its cur‐rent circumscription. As the type C. verum, is from Asia, the Neotropical species need to be placed in a different genus. We decided to transfer them to Aiouea here, because this is the oldest generic name in the Aiouea/Cinnamomum clade, and the only character separating Aiouea from Neotropical Cinnamomum is the number of pollen sacs per anther (di‐ vs. tetrasporangiate), a feature that is known to be variable within several other genera as well. This transfer requires 42 new combinations and two nomina nova. In addition, six species described in the unpublished Ph.D. thesis of one of the authors (FLH) are validated in Aioueahere, and the only species of the genus Mocinnodaphne is transferred to Aiouea as well.

Short-sequence fragments ('DNA barcodes') used widely for plant identification and inventorying remain to be applied to complex biological problems. Host-herbivore interactions are fundamental to coevolutionary relationships of a large proportion of species on the Earth, but their study is frequently hampered by limited or unreliable host records. Here we demonstrate that DNA barcodes can greatly improve this situation as they (i) provide a secure identification of host plant species and (ii) establish the authenticity of the trophic association. Host plants of leaf beetles (subfamily Chrysomelinae) from Australia were identified using the chloroplast trnL(UAA) intron as barcode amplified from beetle DNA extracts. Sequence similarity and phylogenetic analyses provided precise identifications of each host species at tribal, generic and specific levels, depending on the available database coverage in various plant lineages. The 76 species of Chrysomelinae included-more than 10 per cent of the known Australian fauna-feed on 13 plant families, with preference for Australian radiations of Myrtaceae (eucalypts) and Fabaceae (acacias). Phylogenetic analysis of beetles shows general conservation of host association but with rare host shifts between distant plant lineages, including a few cases where barcodes supported two phylogenetically distant host plants. The study demonstrates that plant barcoding is already feasible with the current publicly available data. By sequencing plant barcodes directly from DNA extractions made from herbivorous beetles, strong physical evidence for the host association is provided. Thus, molecular identification using short DNA fragments brings together the detection of species and the analysis of their interactions.

• Premise of the study: Noncoding chloroplast DNA (NC-cpDNA) sequences are the staple data source of low-level phylogeographic and phylogenetic studies of angiosperms. We followed up on previous papers (tortoise and hare II and III) that sought to identify the most consistently variable regions of NC-cpDNA. We used an exhaustive literature review and newly available whole plastome data to assess applicability of previous conclusions at low taxonomic levels.• Methods: We aligned complete plastomes of 25 species pairs from across angiosperms, comparing the number of genetic differences found in 107 NC-cpDNA regions and matK. We surveyed Web of Science for the plant phylogeographic literature between 2007 and 2013 to assess how NC-cpDNA has been used at the intraspecific level.• Key results: Several regions are consistently the most variable across angiosperm lineages: ndhF-rpl32, rpl32-trnL(UAG), ndhC-trnV(UAC), 5′rps16-trnQ(UUG), psbE-petL, trnT(GGU)-psbD, petA-psbJ, and rpl16 intron. However, there is no universally best region. The average number of regions applied to low-level studies is ∼2.5, which may be too little to access the full discriminating power of this genome.• Conclusions: Plastome sequences have been used successfully at lower and lower taxonomic levels. Our findings corroborate earlier works, suggesting that there are regions that are most likely to be the most variable. However, while NC-cpDNA sequences are commonly used in plant phylogeographic studies, few of the most variable regions are applied in that context. Furthermore, it appears that in most studies too few NC-cpDNAs are used to access the discriminating power of the cpDNA genome.

Ammopiptanthus nanus (Fabaceae), a nationally protected endangered evergreen shrub endemic to Central Asian deserts, is severely threatened by habitat fragmentation. To conserve its genetic resources, multiple ex situ populations have been established across China. We evaluated conservation efficacy under distinct management strategies across four ex situ populations (n = 114), including a near-site protected area (J), a Forestry and Grassland Administration–managed zone (L), Tazhong Botanical Garden (T), and the Forestry Academy of Sciences (K), using integrated molecular markers: expressed sequence tag–simple sequence repeats (EST-SSRs), chloroplast DNA fragments ( psbA–trnH , trnL–trnF , trnS–trnG ), and nuclear ribosomal ITS (ITS1/ITS4) sequences. The results reveal significant strategy-dependent divergence in genetic conservation efficiency, primarily driven by founder genetic composition and reproductive management protocols. Strategy (J) retained moderate chloroplast diversity but exhibited reduced nuclear diversity and high inbreeding. Strategy (L) maintained moderate nuclear diversity yet limited chloroplast variation. Strategy (T) showed the highest nuclear diversity but minimal maternal lineage preservation. Strategy (K) preserved unique maternal haplotypes and phylogenetic distinctiveness despite constrained nuclear diversity. Critically, all populations displayed high inbreeding coefficients (F > 0.404), indicating genetic bottlenecks and restricted gene flow. To ensure long-term viability, we recommend: (1) diversifying genetic foundations through the introduction of founders from multiple wild sources and expansion of population sizes to mitigate drift; (2) enhancing gene flow via periodic interpopulation transplants and facilitated distant cross-pollination, integrated with long-term monitoring of nuclear and cytoplasmic diversity.

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.

Blepharostoma trichophyllum was found to be a species collectiva formed by several strongly genetically different species. The taxonomic diversity in the group is the possible result of radiation in early stages; then, these taxa likely survived for a long time in similar environmental conditions, which resulted in stasis. Presently, the existing taxa are similar one to another and may be morphologically distinguished with difficulties. The most taxonomically valuable morphological characteristics include oil bodies and cells in the leaf segment features. The most diverse genotypes (the vast majority of which are treated here as distinct species) were found in amphi-Pacific Asia, which may reflect the evolutionary history of the genus or may be the consequence of more profound sampling in the macro-region in comparison with other parts of the Holarctic.

Artemisia subg. Seriphidium is one of the largest groups within Artemisia, encompassing more than one hundred species, some of them having considerable ecological and economical importance. However, the evolution of subg. Seriphidium has received less attention in comparison to other subgenera of Artemisia, probably, apart from the difficulty of sampling throughout its very large distribution area, because of the low molecular and morphological variability observed in previous studies. Here, we use thorough taxonomic sampling within both Artemisia and subg. Seriphidium to reconstruct the evolutionary history of the subgenus, employing nuclear and plastid DNA sequences as well as various phylogenetic, biogeographic and diversification dynamics tools to analyse the data. Our results show that subg. Seriphidium is not monophyletic, but segregated into two main clades: one large monophyletic group corresponding to the formerly recognised sect. Seriphidium and a second, small clade, phylogenetically distant from the first. Biogeographic and diversification analyses indicate that a rapid radiation of species within sect. Seriphidium occurred in Central Asia during the Miocene‐Pliocene transition. The results of our biogeographic analysis suggest that this diversification process started around the Tian‐Shan, Pamir and Hindu Kush mountain ranges, subsequently expanding into the Eurasian continent. Finally, we uncovered numerous incongruences between taxonomic and genetic information in several sect. Seriphidium species, which could be explained by morphological uniformity, hybridisation and/or incomplete lineage sorting processes.

Although the chloroplast genome contains many noncoding regions, relatively few have been exploited for interspecific phylogenetic and intraspecific phylogeographic studies. In our recent evaluation of the phylogenetic utility of 21 noncoding chloroplast regions, we found the most widely used noncoding regions are among the least variable, but the more variable regions have rarely been employed. That study led us to conclude that there may be unexplored regions of the chloroplast genome that have even higher relative levels of variability. To explore the potential variability of previously unexplored regions, we compared three pairs of single-copy chloroplast genome sequences in three disparate angiosperm lineages: Atropa vs. Nicotiana (asterids); Lotus vs. Medicago (rosids); and Saccharum vs. Oryza (monocots). These three separate sequence alignments highlighted 13 mutational hotspots that may be more variable than the best regions of our former study. These 13 regions were then selected for a more detailed analysis. Here we show that nine of these newly explored regions (rpl32-trnL⁽UAG⁾, trnQ⁽UUG⁾-5'rps16, 3'trnV⁽UAC⁾-ndhC, ndhF-rpl32, psbD-trnT⁽GGU⁾, psbJ-petA, 3'rps16-5'trnK⁽UUU⁾, atpI-atpH, and petL-psbE) offer levels of variation better than the best regions identified in our earlier study and are therefore likely to be the best choices for molecular studies at low taxonomic levels.

Although China and India are the two largest tea-producing countries, the domestication origin and breeding history of the tea plant in these two countries remain unclear. Our previous study suggested that the tea plant includes three distinct lineages (China type tea, Chinese Assam type tea and Indian Assam type tea), which were independently domesticated in China and India, respectively. To determine the origin and historical timeline of tea domestication in these two countries we used a combination of 23 nSSRs (402 samples) and three cpDNA regions (101 samples) to genotype domesticated tea plants and its wild relative. Based on a combination of demographic modeling, NewHybrids and Neighbour joining tree analyses, three independent domestication centers were found. In addition, two origins of Chinese Assam type tea were detected: Southern and Western Yunnan of China. Results from demographic modeling suggested that China type tea and Assam type tea first diverged 22,000 year ago during the last glacial maximum and subsequently split into the Chinese Assam type tea and Indian Assam type tea lineages 2770 year ago, corresponding well with the early record of tea usage in Yunnan, China. Furthermore, we found that the three tea types underwent different breeding histories where hybridization appears to have been the most important approach for tea cultivar breeding and improvements: a high proportion of the hybrid lineages were found to be F and BCs. Collectively, our results underscore the necessity for the conservation of Chinese Assam type tea germplasm and landraces as a valuable resource for future tea breeding.

The genus Premna , one of the largest woody genera of Lamiaceae, comprises approximately 130 species distributed across the tropics and subtropics of the Old World. Previous classification and identification of the genus has mainly relied on morphological studies, resulting in significant taxonomic ambiguity and misidentification. In Thailand, over 20 Premna species have been recorded but their phylogenetic relationships have never been well investigated, particularly within the P . serratifolia complex which is the most taxonomically complicated species with the most extensive synonymy within the genus, leading to uncertainty regarding species recognition. This study presents the first comprehensive molecular phylogeny of Premna in Thailand by utilizing four chloroplast regions ( ndhF , rbcL , rps16 , and trnL-F ), and focuses on resolving the intricate relationships within the P. serratifolia complex while providing taxonomic notes for Thai species. The results confirm the monophyly of Premna and reveal two primary clades which are discussed in the context of both morphological and molecular evidence. We successfully disentangled the taxonomic confusion surrounding the P . serratifolia complex with reinstatement of P . paniculata , and P . punctulata while P . cordifolia was confirmed as a distinct species and occurs in Thailand. We also treated P. octonervia under P . serratifolia . Additionally, P. interrupta  var.  smitinandii  was reduced to a synonym of P. interrupta , P . coriacea was excluded from the Thai flora, and P . coriacea var. villosa was lectotypified. As a result, 21 species are now recognized in Thailand. To facilitate future identification efforts, we provide an updated diagnostic key for all species, detailed morphological descriptions, a comprehensive list of examined specimens within the P . serratifolia complex, and field photographs of several species. These findings enhance our understanding of the taxonomy and phylogeny of Premna in Thailand, offering a robust framework for further research on this taxonomically challenging genus.