Revised molecular phylogeny, global biogeography, and diversification of palms subfamily Coryphoideae (Arecaceae) based on low copy nuclear and plastid regions

Decoding the Chloroplast Genome of Korean endemic plant Acer okamotoanum: Comparative Genomics, Phylogenetic Insights, and Potential for Marker Development

Acer okamotoanum, a medicinally significant endemic plant of Korea, has seen limited genomic research. To address this gap, we conducted a comprehensive sequencing and analysis of its chloroplast genome. The assembled genome is 156,242 bp in length, with typical quadripartite structure, consisting of a large single-copy region, a small single-copy region, and two inverted repeat regions. It contains 130 genes, including 85 protein-coding, 37 tRNA, and 8 rRNA genes. Sixteen genes have a single intron, while clpP and ycf3 possess two introns each. Additionally, 17 genes are duplicated within the inverted repeat regions. The genome analysis revealed 92 Simple Sequence Repeats (SSRs), predominantly located in intergenic regions, with a bias toward A/T-rich codons. Comparative analysis with five closely related Acer species highlighted a highly conserved genomic structure, but also revealed differences in SSRs and repeat sequences. Hypervariable regions, such as rpl32-trnL and ycf1, were identified as potential molecular markers for phylogenetic and population studies. Phylogenetic analysis involving 37 chloroplast genomes confirmed the monophyly of the Acer genus and placed A. okamotoanum within the Platanoidea section, closely related to A. truncatum. This study improves the understanding of A. okamotoanum's genomic structure, offering insights for phylogenetic analysis, marker development, and conservation efforts.

Molecular phylogenetic and biogeographic evidence of Lepidagathis Willd. (Acanthaceae, Barlerieae) focusing on Indian endemics

Lepidagathis Willd., a genus belonging to the Acanthaceae family, is primarily distributed in tropical and subtropical regions worldwide, encompassing approximately 153 species. While considerable morphological research has been conducted on Lepidagathis, it has not completely dispelled taxonomic ambiguities and conflicting interpretations. Molecular analysis emerges as a valuable tool for resolving these taxonomic uncertainties, but the availability of nucleotide sequence data for Lepidagathis has been limited thus far. This study delivers a phylogenetic analysis of Lepidagathis species, utilizing both chloroplast and nuclear regions. The results of Bayesian Inference and Maximum Likelihood phylogenetic analyses consistently segregate the studied Lepidagathis species into two principal clades, denoted as Clade A and Clade B. Notably, this analysis firmly positions the Indian endemic Lepidagathis within Clade A, supported by robust statistical evidence. Furthermore, our biogeographical analysis strongly suggests that the origin of Lepidagathis might be traced back to Eurasia. This research establishes a foundational molecular phylogeny of Lepidagathis, offering valuable insights for future taxonomic investigations. Additionally, it sheds light on the evolutionary history and biogeographical origins of the Lepidagathis genus.

Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study

The Asteraceae family, particularly the Artemisia genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of Artemisia littoricola sourced from Dokdo Island, employing comparative analyses across six diverse Artemisia species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of A. littoricola spans 150,985 bp, consistent with other Artemisia species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while clpP and ycf3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position A. littoricola within subgenus Dracunculus, indicating a close relationship with A. scoparia and A. desertorum. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding Artemisia diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of Artemisia's intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

Cytogenetics, Typification, Molecular Phylogeny and Biogeography of Bentinckia (Arecoideae, Arecaceae), an Unplaced Indian Endemic Palm from Areceae

Bentinckia is a genus of flowering plants which is an unplaced member of the tribe Areceae (Arecaceae). Two species are recognized in the genus, viz. B. condapanna Berry ex Roxb. from the Western Ghats, India, and B. nicobarica (Kurz) Becc. from the Nicobar Islands. This work constitutes taxonomic revision, cytogenetics, molecular phylogeny, and biogeography of the Indian endemic palm genus Bentinckia. The present study discusses the ecology, morphology, taxonomic history, distribution, conservation status, and uses of Bentinckia. A neotype was designated for the name B. condapanna. Cytogenetical studies revealed a new cytotype of B. condapanna representing 2n = 30 chromosomes. Although many phylogenetic reports of the tribe Areceae are available, the relationship within the tribe is still ambiguous. To resolve this, we carried out Bayesian Inference (BI) and Maximum Likelihood (ML) analysis using an appropriate combination of chloroplast and nuclear DNA regions. The same phylogeny was used to study the evolutionary history of Areceae. Phylogenetic analysis revealed that Bentinckia forms a clade with other unplaced members, Clinostigma and Cyrostachys, and together they show a sister relationship with the subtribe Arecinae. Biogeographic analysis shows Bentinckia might have originated in Eurasia and India.