Combining molecular and geographical data to infer the phylogeny of Lamiales and its dispersal patterns in and out of the tropics

Plastome comparison and phylogenomics of Chinese endemic Schnabelia (Lamiaceae): insights into plastome evolution and species divergence

BACKGROUND

Schnabelia species, herbaceous perennial plants within the Lamiaceae family, possess medicinal value and are endemic to China. While previous studies have focused on morphological classification, molecular systematics, and medicinal components, there has been limited research on phylogenomics. To reveal their plastid genome characteristics and phylogenetic relationships, we sequenced and assembled the plastomes of all five Schnabelia species (S. oligophylla, S. tetrodonta, S. nepetifolia, S. terniflora, S. aureoglandulosa), conducted comparative genomic analyses, and constructed a phylogenetic tree incorporating closely related taxa in subfamily Ajugoideae, as well as conducting divergence time estimation.

RESULTS

Plastome size of the five species ranged from 155,733 bp to 156,944 bp, encompassing 115 unique genes, with a GC content of 37.8% same for all species. Five intergenic spacer regions (trnH-GUG-psbA, trnK-UUU-matK, petB-petD, ndhD-psaC, ndhA-ndhH) were identified as divergence hotspots. Gene selection pressure analysis demonstrated that all genes were under negative selection. Phylogenetic relationship of Ajugoideae species based on plastomes confirmed the monophyly of Schnabelia. Two clades within Schnabelia were supported, one containing two original species and the other comprising three species transferred from Caryopteris. The stem age of the Schnabelia is estimated to be approximately 30.24 Ma, with the split of two Sections occurring around 12.60 Ma.

CONCLUSIONS

We revealed plastid genome evolutionary features for five species within the genus Schnabelia. The identified highly variable regions can provide a tool for future identification of these medicinal plants. The diversification of Schnabelia during middle Miocene and the Quaternary suggests that historical geological and climatic shifts facilitated species differentiation. These findings enhance our understanding of Schnabelia's evolution and support future research on chloroplast diversity, aiding conservation and sustainable use.

Phylogenetic origin of dioecious Callicarpa (Lamiaceae) species endemic to the Ogasawara Islands revealed by chloroplast and nuclear whole genome analyses

Oceanic islands offer excellent opportunities to study the ecology, evolutionary biology, and biogeography of plants. To uncover the genetic basis of various evolutionary trends commonly observed on these islands, the origins and phylogenetic relationships of the species being studied should be understood. Callicarpa glabra, Callicarpa parvifolia, and Callicarpa subpubescens are evergreen woody plants endemic to the Ogasawara Islands, which are remote oceanic islands located off of the Japanese Archipelago. These species are ideal for studying evolutionary changes on oceanic islands because of their adaptive radiation and shift toward dioecious sex expression. We used a phylogenomic perspective to determine the evolutionary relationship of the three species within the genus and infer their colonization time. Based on the analysis of both chloroplast genomes and 86 nuclear single-copy genes, we found that these three species were monophyletic and embedded in a backbone clade that included multiple East Asian species. The phylogenetic tree based on over 10,000 nuclear genes placed the insular species in the East Asian clade, although the topology did not entirely correspond to the chloroplast tree, probably because of incomplete lineage sorting and interspecific hybridization. The three endemic species were estimated to have diverged from continental species approximately three million years ago (Mya). The results of this study suggested that the ancestor of the Ogasawara endemic species originated from long-distance dispersal from East Asia mainland in the late Pliocene, and then progressively speciated within the islands.

The Isodon serra genome sheds light on tanshinone biosynthesis and reveals the recursive karyotype evolutionary histories within Lamiales

Lamiales is one of the largest orders of angiosperms with a complex evolutionary history and plays a significant role in human life. However, the polyploidization and chromosome evolution histories within this group remain in mystery. Among Lamiales, Isodon serra (Maxim.) Kudô shines for its abundance of diterpenes, notably tanshinones, long used in East Asia to combat toxicity and inflammation. Yet, the genes driving its biosynthesis and the factors governing its regulation linger in obscurity. Here, we present the telomere-to-telomere genome assembly of I. serra and, through gene-to-metabolite network analyses, pinpoint the pivotal tanshinone biosynthesis genes and their co-expressed transcription factors. Particularly, through luciferase (LUC) assays, we speculate that IsMYB-13 and IsbHLH-8 may upregulate IsCYP76AH101, which is the key step in the biosynthesis of the tanshinone precursor. Among Lamiales, Oleaceae, Gesneriaceae and Plantaginaceae successively sister to a clade of seven Lamiales families, all sharing a recent whole-genome duplication (designated as α event). By reconstructing the ancestral Lamiales karyotypes (ALK) and post-α event (ALKα), we trace chromosomal evolution trajectories across Lamiales species. Notably, one chromosomal fusion is detected from ALK to ALKα, and three shared chromosomal fusion events are detected sequentially from ALKα to I. serra, which fully supports the phylogeny constructed using single-copy genes. This comprehensive study illuminates the genome evolution and chromosomal dynamics of Lamiales, further enhancing our understanding of the biosynthetic mechanisms underlying the medicinal properties of I. serra.

Cell Wall Microdomains in the External Glands of Utricularia dichotoma Traps

The genus Utricularia (bladderworts) species are carnivorous plants that prey on invertebrates using traps with a high-speed suction mechanism. The outer trap surface is lined by dome-shaped glands responsible for secreting water in active traps. In terminal cells of these glands, the outer wall is differentiated into several layers, and even cell wall ingrowths are covered by new cell wall layers. Due to changes in the cell wall, these glands are excellent models for studying the specialization of cell walls (microdomains). The main aim of this study was to check if different cell wall layers have a different composition. Antibodies against arabinogalactan proteins (AGPs) were used, including JIM8, JIM13, JIM14, MAC207, and JIM4. The localization of the examined compounds was determined using immunohistochemistry techniques and immunogold labeling. Differences in composition were found between the primary cell wall and the cell secondary wall in terminal gland cells. The outermost layer of the cell wall of the terminal cell, which was cuticularized, was devoid of AGPs (JIM8, JIM14). In contrast, the secondary cell wall in terminal cells was rich in AGPs. AGPs localized with the JIM13, JIM8, and JIM14 epitopes occurred in wall ingrowths of pedestal cells. Our research supports the hypothesis of water secretion by the external glands.

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

Introduction

The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae.

Methods

In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses.

Results

The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic.

Discussion

Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.

A new species of Schlegelia (Schlegeliaceae) from wet montane forest of Colombia and a key for the species of the genus

In this paper we describe and illustrate Schlegelialongirachis a new species from montane forest remnants (1200--1900 m) in the Western slope of the Eastern Cordillera of Colombia ("Serranía de Las Quinchas" and Virolín county) in the Departments of Boyacá and Santander. A root-climbing liana, the new species is contrasted to S.fuscata, S.monachinoi and S.parviflora, the three most morphologically similar species of Schlegelia. This new species is differentiated from its putative close relatives by vegetative (texture, colour, pubescence and shape in leaves, bracts, bracteoles pedicel, calyx and corolla), inflorescences as well as floral characters (staminode absent). We provide an updated key to 24 known species of Schlegelia. For the identification key, S.fuscata and S.roseiflora are regarded here as different from S.parviflora. S.urbaniana is considered a synonym of S.axillaris, whereas S.fastigiata is separated from S.sulphurea as a recognizable species. Schlegelia has its center of distribution in Colombia, where 17 of the species are known to occur.

The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae)

Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine

The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are responsible for the uncommon length of the genome. At least four events of IR expansion were observed among the seven Bignoniaceae species compared, suggesting multiple expansions of the IRs over the SC regions in the family. A comparison with 6,231 other complete plastomes of flowering plants available on GenBank revealed that the plastome of B. magnifica is the longest Lamiid plastome described to date. The newly generated plastid genome was used as a source of selected genes. These genes were combined with orthologous regions sampled from other species of Bignoniaceae and all gene alignments concatenated to infer a phylogeny of the family. The tree recovered is consistent with known relationships within the Bignoniaceae.