Plastid Regions Research Articles

A Revised Taxonomy of the Bassia scoparia Complex (Camphorosmoideae, Amaranthaceae s.l.) with an Updated Distribution of B. indica in the Mediterranean Region

Bassia scoparia is a widespread weedy species in the temperate regions of the world and is valued as a medicinal and ornamental plant. To date, the taxonomic concept of B. scoparia remains insufficiently studied due to a limited number of samples used in the previous phylogenetic analyses. To solve the taxonomy of the B. scoparia complex, we constructed a new phylogeny based on the nuclear ribosomal internal transcribed spacer (ITS), plastid intergenic spacer atpB-rbcL, and plastid region rpL16 intron sequences for numerous samples with diverse morphology. Our analysis revealed a close proximity and intermixed positions of the samples of the B. scoparia group with various morphology. Because of this polyphyly, we prefer to broadly delimit the species. An updated nomenclature of B. scoparia is provided including four new synonyms: Bassia angustifolia, B. littorea, Kochia albovillosa, and K. scoparia subsp. hirsutissima. In its new circumscription, B. scoparia encompasses populations with glabrous or variously hairy leaves and perianths. The original material of Kochia sieversiana, previously considered a species with hairy leaves and inflorescences, has the same diagnostic characters as in B. scoparia s.str. The correct name for more hairy-leaved plants is B. scoparia var. subvillosa. Plants with hairy perianths known as Kochia albovillosa and K. scoparia subsp. hirsutissima have a restricted distribution in Central Asia and South Siberia and have never been recorded as alien in other regions; they can be classified as a separate variety, B. scoparia var. hirsutissima. The ornamental variant of oblong or pyramidal shape may be called B. scoparia var. trichophila. Bassia scoparia is often confused with a similarly looking relative, B. indica, especially in North Africa, a region where secondary ranges of both species overlap. Phylogenetically, these species are sister groups; they share some morphological characters but have different primary distribution ranges. We traced a recent expansion of B. indica in the Mediterranean with the first record reported from the European continent (Spain) and uncovered various introduction pathways of the species in this region.

Dictyanthus reflexiflorus (Apocynaceae: Asclepiadoideae) a new species from Mexico

A new species of Dictyanthus from the state of Michoacan, Mexico, is described and illustrated Dictyanthus reflexiflorus sp. nov. It grows in tropical deciduous forests located in the municipality of Tacámbaro. A phylogenetic analysis based on molecular data (plastid regions trnL-trnF and rps 16) was conducted to explore the relationship of the new species. Results place the new species in Dictyanthus. The morphological characters that support this relationship are the presence of uncinate hairs and a reticulate corolla. The species has unique characteristics within the genus, such as a reflexed corolla and the tube 10-lobed closely pressed to the side of the gynostegium. A key to distinguish Dictyanthus reflexiflorus from congeners in Mexico is included.

Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of Polygonatum.

The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, have garnered attention of scholars. This study sequenced and analyzed the chloroplast genomes of six species of Polygonatum medicinal plants (P. zanlanscianense, P. kingianum, P. sibiricum, P. cyrtonema, P. filipes, and P. odoratum, respectively) to explore their interspecific relationships. The sequence length (154, 578-155, 807 bp) and genome structure were conserved among the six Polygonatum species, with a typical tetrad structure. Among the 127-131 genes contained in the genomes, 84-85 are protein-coding genes, 37-38 are transfer RNA genes, and 6-8 are ribosomal RNA genes. The genomes contained 64-76 simple sequence repeats (SSRs) and 36-62 long repetitive sequences. Codon bias patterns tended to use codons ending in A/T. In 30 types of codons with RSCU > 1, 93.3% ended in A/T of the six species. Twenty-one highly variable plastid regions were identified in the chloroplast genomes of the six medicinal plants. Furthermore, a phylogenetic analysis encompassing these and 53 other chloroplast genomes of Polygonatum species revealed that P. cyrtonema, P. odoratum, and P. filipes clustered together on one clade, whereas P. kingianum and P. zanlanscianense formed separate clades. Notably, P. sibiricum emerged as a standalone clade, and our phylogenetic tree reinforces the classification of P. sibiricum as forming a monophyly. This study provides a novel basis for intragenus taxonomy and DNA barcoding molecular identification within the genus Polygonatum medicinal plants.

To Lump or to Split? Revision of Cuscuta section Indecorae Using a Combined Morphometric, Phylogenetic, and Host Range Approach

Abstract— Cuscuta section Indecorae is an infrageneric clade of Cuscuta subgenus Grammica that originated in North America which includes three species: C. indecora, C. coryli, and C. warneri. Some forms of C. indecora are agricultural weeds, while C. warneri and C. coryli face conservation problems regionally or globally. Cuscuta indecora is a morphologically diverse species with three recognized varieties: C. indecora var. indecora, C. indecora var. longisepala, and C. indecora var. attenuata. Two recent broad-scale molecular phylogenetic studies raised questions about the circumscription of C. indecora and the validity of its infraspecific taxa. Therefore, we conducted an extensive morphometric study, and used DNA sequences from plastid and nuclear ribosomal non-coding regions to reconstruct evolutionary relationships among taxa. In addition, we studied the host range of all taxa using herbarium specimens, bipartite networks, and Venn diagrams. Results from all types of evidence confirmed the circumscription of the three species, but differed on the infraspecific structure of C. indecora. The molecular phylogeny inferred C. indecora as paraphyletic, consisting of two distinct clades, with C. coryli nested within one of them. The morphometric and host range studies uncovered extensive overlaps both among the traditional varieties of C. indecora as well as between the two molecular lineages of C. indecora. Previously, Iva annua had been considered the sole host of C. indecora var. attenuata (C. attenuata) and this presumed host specificity was the main criterion for accepting this taxon. We found that the type of C. indecora var. longisepala was also growing on Iva annua, which together with the morphological and genetical similarity, indicates that C. indecora var. attenuata is identical to C. indecora var. longisepala. Overall, considering the lack of morphological, host range, and geographical patterns distinguishing either the current three varieties of C. indecora or the two cryptic lineages, the most appropriate solution is to tentatively recognize C. indecora as variable species without recognizing any infraspecific taxa.

Generation of genomic resources and phylogenetic contributions in Oxalis from desert fog oases in Peru

AbstractSeveral species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitat‐adapted and endemic diversity. Acknowledging this aspect, the genus Oxalis is a conceivable group for evolutionary and biogeographic hypothesis testing; however, molecular resources for the genus still need improvement. We conducted a genome skimming approach to assemble new plastomes from 18 accessions (six species) of Oxalis collected in Lomas locations in Peru. These complete plastomes of Oxalis species (several reported for the first time) present a highly conserved composition. Our phylogenetic results were congruent with previous section‐based backbone phylogenies of Oxalis; however, a closer look at the phylogeny of sect. Carnosae revealed nonmonophyletic arrangements involving Oxalis megalorrhiza and Oxalis bulbocastanum individuals. We also propose a set of three hypervariable plastid regions as potential molecular markers. Likewise, an array of primers for nuclear simple sequence repeat markers based on the most widely distributed species, O. megalorrhiza, were listed and evaluated for their transferability to the other species under examination. These new genomic resources represent a significant development for future population, phylogenetic, and biogeographic studies in Oxalis.

Impatiens fujianensis (Balsaminaceae), a new species from China: evidence from morphological and molecular analyses

We here describe and illustrate a new species, Impatiens fujianensis (Balsaminaceae), from Fujian Province in southern China. Morphological comparisons indicated that I. fujianensis is similar to I. noli-tangere and I. yilingiana but showed distinct differences in leaves, inflorescences, pedicels and flowers. The molecular phylogenetic analysis based on nuclear ribosomal internal transcribed spacer (ITS) and two plastid regions (atpB-rbcL and trnL-F) indicated that I. fujianensis is a distinct species, which forms an independent lineage. Both morphological and molecular evidence supported the status of I. fujianensis as a new species.

Molecular and morphological support for transferring the tropical African species of Gnidia to Lasiosiphon (Thymelaeaceae: Thymelaeoideae) and a worldwide synopsis of the species

Lasiosiphon Fresen. (Thymelaeaceae: Thymelaeoideae) is now understood to be a morphologically diverse genus distributed across southern and tropical Africa, Madagascar, and India. It is diagnosed morphologically by ± involucrate, mostly pedunculate heads of pentamerous or tetramerous flowers, with or without petaloid scales, and a bright yellow, orange, or red corolla. The taxonomic history of Lasiosiphon has been marked by several revisions in its circumscription and status, particularly regarding its relationship with Gnidia L. Our phylogenetic analysis of nuclear (ITS) and plastid (matK, rbcL, rps16 and trnL-F) regions of an expanded sampling of the tropical African species of Gnidia provides compelling supporting evidence for existing morphological evidence to include all the tropical African species of Gnidia in Lasiosiphon. We accordingly provide 31 new combinations in Lasiosiphon for species of Gnidia that currently lack combinations in that genus. We also provide a comprehensive nomenclator of all currently recognized Lasiosiphon species at the regional level encompassing their distribution across different geographic regions globally. This will serve as the framework for future taxonomic revisions in the genus.

Molecular phylogenetic reconstruction improves the taxonomic understanding of Indian Dipcadi (Asparagaceae) and reveals a new species from the bank of Hiranyakeshi River, Maharashtra, India.

Dipcadi (Scilloideae: Asparagaceae) is a genus of bulbous monocots with approximately 40 species, of which 13 occur in India. Species delimitation within the genus has been troublesome hindering a comprehensive phylogenetic analysis. The most recent phylogeny of the subfamily Ornithogaloideae included six species of Dipcadi only from Africa. Here, we reconstructed the phylogeny of Ornithogaloideae including 23 accessions comprising 13 recognized taxa (11 species and two varieties) of Indian Dipcadi. The phylogenetic analyses were based on nucleotide sequences of three plastid regions (rbcL, matK and trnL-F spacer) and one nuclear region (ITS). Pseudogaltonia clavata exhibited sister relationship to Dipcadi. Our combined nuclear + plastid dataset analyses revealed a monophyletic Dipcadi with five clades, Clade I-V. Clade I, II and III included mainly Indian species whereas Clade V included mostly African species. Clade IV comprised D. serotinum. Clade I included nine taxa including our newly described species, D. mukaianum. The new species was phylogenetically placed with D. erythraeum, D. saxorum and D. ursulae. Morphologically, the species resembled D. montanum and D. ursulae but differed in characters such as tepal cohesion, number of ovules per locule and foul-smelling flowers. Clade II and III included 11 and six taxa, respectively. D. erythraeum which has a native range from Egypt to western India was found in Clades I and V. The widespread Dipcadi species, viz. D. erythraeum and D. serotinum showed polyphyly however, the monophyly of Dipcadi is established. Our studies suggest that additional molecular markers (plastid as well asnuclear) should be tested for their taxonomy utility. Further work on the historical biogeography of Dipcadi on the subfamily Ornithogaloideae with more genetic data will yield insights how aridification of the landscape would have shaped the evolution of the geographical clades.

Phylogenetic and phylogeographic evidence for the colonization success of the diplochorous Astydamia latifolia across the Canary Islands.

Astydamia latifolia is the only species of the genus Astydamia, which forms an early-diverging lineage of Apiaceae, subfamily Apioideae. This species is subendemic to the Canary Islands and one of the most representative species of the coastal environments of this archipelago. Astydamia displays diplochory, that is, diaspores with two long-distance dispersal (LDD) syndromes. In particular, A. latifolia has both anemochorous and thalassochorous fruit traits (corky and winged mericarps). Although we expect this species to have a high dispersal capacity, there is no genetic study addressing it. The divergence time of this species from its sister taxon is also unknown. In this study, we aimed (i) to unveil the phylogenetic relationships and divergence times of A. latifolia; (ii) to reconstruct its phylogeographic structure across the Canary Islands; and (iii) to estimate the number of inter-island colonization events. To these ends, we first sequenced the internal transcribed spacer (ITS) region for A. latifolia, reconstructed the phylogenetic relationships of Astydamia and Apiaceae relatives and estimated divergence times. Then, two plastid DNA regions (psaI-aacD and psbK-trnS) were sequenced for 158 individuals (from 36 Canarian population and one NW African population) to reconstruct a haplotype network. The recently developed method Phylogeographic Analysis of Island Colonization Events (PAICE) was used to estimate the number of inter-island colonization events. Results show that A. latifolia is a phylogenetically isolated lineage that diverged from the most closely related genus (Molopospermum) in the Eocene-Miocene. It displays a low plastid DNA diversity (only four haplotypes detected), which is accompanied by a high degree of haplotype sharing between islands and highly linear rarefaction curves of colonization obtained in PAICE. These findings suggest a high colonization ability for this species, most likely related to the availability of two LDD syndromes.

The polyphyletic Caucasus-centred Campanula subg. Scapiflorae (Campanulaceae) revisited with a newly circumscribed C. sect. Tridentatae for its core clade.

Campanula L. is among the genera with the highest number of endemics in the Caucasus ecoregion. A group of attractive alpine and subalpine perennial rosette plants with short single-flowered stems centred in the Caucasus has been treated as Campanulasubg.Scapiflorae or at other ranks, with considerably varying circumscription and classification. Molecular phylogenetic analysis of three plastid DNA regions (trnK/matK, petD, rpl16) of a strongly extended sampling, comprising 23 of the 27 commonly accepted taxa (85%) with 330 accessions built on and guided by the results of our previous study of the group, confirmed the polyphyly of C.subg.Scapiflorae in any of its circumscriptions. The core clade of the group comprises exclusively endemics and near-endemics of the Caucasus and is treated here as C.sect.Tridentatae in a revised circumscription. The phylogenetic relationships of the disparate other elements of the Scapiflorae group are outlined.

Phylogenetic position and plastid genome structure of Vietorchis, a mycoheterotrophic genus of Orchidaceae (subtribe Orchidinae) endemic to Vietnam

The orchid genus Vietorchis comprises three species, all discovered in the 21 century. Each of these species is achlorophyllous, mycoheterotrophic and is known to be endemic to Vietnam. The type species of the genus, V. aurea, occurs in a single location in northern Vietnam within a lowland limestone karstic area. Vietorchis furcata and V. proboscidea, in contrast, are confined to mountains of southern Vietnam, far away from any limestone formations. Taxonomic placement of Vietorchis remained uncertain for the reason of inconclusive morphological affinities. At the same time, the genus has never been included into molecular phylogenetic studies. We investigate the phylogenetic relationships of two species of Vietorchis (V. aurea and V. furcata) based on three DNA datasets: (1) a dataset comprising two nuclear regions, (2) a dataset comprising two plastid regions, and (3) a dataset employing data on the entire plastid genomes. Our phylogenetic reconstructions support the placement of Vietorchis into the subtribe Orchidinae (tribe Orchideae, subfamily Orchidoideae). This leads to a conclusion that the previously highlighted similarities in the rhizome morphology between Vietorchis and certain mycoheterotrophic genera of the subfamilies Epidendroideae and Vanilloideae are examples of a convergence. Vietorchis is deeply nested within Orchidinae, and therefore the subtribe Vietorchidinae is to be treated as a synonym of Orchidinae. In the obtained phylogenetic reconstructions, Vietorchis is sister to the photosynthetic genus Sirindhornia. Sirindhornia is restricted to limestone mountains, which allows to speculate that association with limestone karst is plesiomorphic for Vietorchis. Flower morphology is concordant with the molecular data in placing Vietorchis into Orchidinae and strongly supports the assignment of the genus to one of the two major clades within this subtribe. Within this clade, however, Vietorchis shows no close structural similarity with any of its genera; in particular, the proximity between Vietorchis and Sirindhornia has never been proposed. Finally, we assembled the plastid genome of V. furcata, which is 65969 bp long and contains 45 unique genes, being one of the most reduced plastomes in the subfamily Orchidoideae. The plastome of Vietorchis lacks any rearrangements in comparison with the closest studied autotrophic species, and possesses substantially contracted inverted repeats. No signs of positive selection acting on the protein-coding plastid sequences were detected.

Molecular phylogenetic studies on Asparagus (Asparagaceae) revealed the position of the highly endangered Irano-Turkish halophytic species A. lycaonicus P.H.Davis related to A. officinalis L.

Asparagus lycaonicus P.H.Davis (Asparagaceae), a highly interesting halophytic species was found in two disjunct populations of ca. 1550 km aerial distance, one in Central Anatolia (Bolluk Salt Lake) and the other in Central Iran (Meyghan Salt Lake). Using one nuclear phytochrome C (PHYC) and two plastid regions (trnH-psbA and trnD-T) the phylogenetic position of this Irano-Turkish endemic species was studied. In contrast to low resolution of plastid sequences, the PHYC provides good resolution for understanding species level phylogeny in SW Asian Asparagus. Molecular data confirms a conspecific position of the two disjunct localities in Turkey and Iran and their position in a clade containing cultivated Asparagus and many other Irano-Turkish species. Asparagus lycaonicus is extremely rare in Iran and since its discovery in 1986, it has never been rediscovered in Iran, even in its initial collection site. Intensive land use activities, water level changes and the passage of Arak wastewater into the Meyghan Salt Lake area has drastically changed the habitat of A. lycaonicus and might have caused its extinction. Since its discovery in 1960 in Turkey, the species is only found in a small area around and inside a sodic extraction factory around Bolluk Lake. Considering the critical condition of its populations in Iran and Turkey, we evaluate the conservation status of Asparagus lycaonicus as Critically Endangered (CR). In conclusion we urge the authorities to implement in situ measures for conservation and restoration of the habitats of A. lycaonicus, a halophytic species related to cultivated Asparagus. The taxonomic status of some newly described Asparagus from Iran is discussed with reducing A. touranensis Hamdi & Assadi to synonym of A. griffithii Baker., A. khorasanensis Hamdi & Assadi to synonym of A. breslerianus Schult. & Schult.f, and Asparagus bojnurdensis Hamdi & Assadi to synonym of A. verticillatus L.

Evolutionary history of an Irano-Turanian cushion-forming legume (Onobrychis cornuta).

The Irano-Turanian region is one of the largest floristic regions in the world and harbors a high percentage of endemics, including cushion-like and dwarf-shrubby taxa. Onobrychis cornuta is an important cushion-forming element of the subalpine/alpine flora of the Irano-Turanian floristic region. To specify the genetic diversity among the populations of this species (including individuals of O. elymaitica), we employed nrDNA ITS and two noncoding regions of plastid DNA (rpl32-trnL(UAG) and trnT(UGU)-trnL(UAA)). The most striking feature of O. cornuta assemblages was the unexpectedly high nucleotide diversity in both the nDNA and cpDNA dataset. In the analyses of nuclear and plastid regions, 25 ribotypes and 42 haplotypes were found among 77 and 59 accessions, respectively, from Iran, Turkey, and Afghanistan. Network analysis of the datasets demonstrated geographic differentiation within the species. Phylogenetic analyses of all dataset retrieved O. cornuta as a non-monophyletic species due to the inclusion of O. elymaitica, comprising four distinct lineages. In addition, our analyses showed cytonuclear discordance between both nuclear and plastid topologies regarding the position of some O. cornuta individuals. The underlying causes of this inconsistency remain unclear. However, we speculate that chloroplast capture, incomplete lineage sorting, and introgression were the main reasons for this event. Furthermore, molecular dating analysis indicated that O. cornuta originated in the early Pliocene (around 4.8 Mya) and started to diversify throughout the Pliocene and in particular the Pleistocene. Moreover, O. elymaitica was reduced to a subspecific rank within the species.

A complex biosystematic approach to reveal evolutionary and diversity patterns in West Asian brambles (Rubus subgen. Rubus, Rosaceae)

West Asia, with its high mountain ranges and glacial refugia, stands out as a biodiversity hotspot for various plant taxa, including the taxonomically complex Rubus subgen. Rubus. Despite this significance, our understanding of the evolutionary processes shaping this group in the region has been limited. We employed an integrative approach combining flow cytometry, Sanger sequencing of two plastid regions, microsatellite genotyping, and double digest restriction-site associated DNA sequencing to characterize evolutionary and diversity patterns in West Asian brambles. We identified four diploid and two sexual tetraploid species, with the remaining diversity comprising apomictic tetra- and triploids, mostly belonging to R. ser. Discolores, and sexual pentaploid hybrids/hybridogens derived from R. caesius. Rubus dolichocarpus, newly reported here as diploid, emerged as a significant ancestor for many polyploids. Most apomictic genotypes are locally distributed and only three genotypes exhibit extremely large ranges from Armenia to Kyrgyzstan and from Georgia to Iran. These genotypes are probably of an ancient (Pleistocene) European origin and likely laid the foundations for the evolution of apomicts in West Asia, whose diversification was subsequently boosted by the genetic contribution of sexual taxa. DNA markers confirmed the West Asian origin of Rubus armeniacus, a globally significant invasive species, yet rare in its native range. We report on the first indigenous occurrence of this species based on microsatellite genotyping. Our findings contribute to filling existing gaps in understanding the evolution and diversity of Rubus subgen. Rubus in West Asia.

A New Record of Pogonatum tahitense (Polytrichaceae) from Tibet, China: Taxonomic Description, Range Expansion, and Biogeographic History

The genus Pogonatum stands out as the most diverse within the family Polytrichaceae, encompassing over 50 species. Pogonatum tahitense has been recorded across various Pacific regions, including Hawaii in the United States and Tahiti in French Polynesia, as well as in Asia, such as in Taiwan in China, Java in Indonesia, and Sabah in Malaysia. In the current study, a specimen collected in Tibet, China, is described, confirming its taxonomic classification as P. tahitense through a comprehensive analysis integrating morphological evidence and molecular study based on sequences from the plastid (rbcL, rps4, trnL-F), mitochondrial (nad5), and nuclear (ITS2) regions. This documentation represents the first record of the species within mainland China. A time-calibrated, molecular-based phylogenetic analysis was conducted, employing various approaches for ancestral range inference. The findings suggest that P. tahitense originated during the Pleistocene epoch, approximately 1.8 mya, in Tibet, China.

Phylogenetics of Cruckshanksia and Oreopolus (Rubiaceae) based on nuclear and plastid DNA sequences

Cruckshanksia Hook. & Arn. and Oreopolus Schltdl. Rubiaceae (Rubioideae – Coussareeae), endemic genera of Chile and Andean Argentina, have historically been highly taxonomically unstable. Molecular analyses have confirmed Oreopolus as the sister group of Cruckshanksia; however, the relationships among its species are still not resolved because previous studies have not considered all species of the genus and the published topologies have many unsupported nodes. For this reason, we carried out a phylogenetic study with all the species currently recognized by recent revisions, using two nuclear DNA regions and five plastid regions, to elucidate the relationships between species. In addition, the evolutionary history of the group was estimated based on divergence times, and a character reconstruction was performed. The results corroborate that Oreopolus is the sister group of Cruckshanksia. Cruckshanksia is monophyletic and composed of two principal clades. Clade I is composed of Subclade I (C. pumila and C. verticillata) associated with C. montiana; Clade II is composed of Subclade II (C. palmae and C. macrantha) and Subclade III (C. lithiophila and C. hymenodon). With 81% probability the common ancestor of the genus Cruckshanksia had petaloid appendices associated with two independent lines of evolution. The probability that the common ancestor of the Oreopolus‒Cruckshanksia clade had equal calyx lobes is 50%.

DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value.

Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness.

Phylogeny of Prosthechea (Laeliinae, Orchidaceae) based on nrITS and plastid DNA sequences: Reassessing the lumper‐splitter debate and shedding light on the evolution of this Neotropical genus

AbstractAfter a confused taxonomic history, Prosthechea (Laeliinae, Orchidaceae) has been circumscribed in a broad sense to include species previously placed in Encyclia subg. Osmophytum. However, recent alternative classifications resurrecting old names such as Anacheilium and Hormidium, and proposing new genera such as Euchile, Panarica, Pollardia, and Pseudencyclia were presented, splitting Prosthechea into narrower genera. In this study, we provide a molecular phylogeny of Prosthechea to reassess alternative generic classifications and shed light on evolutionary aspects of this highly diverse Neotropical lineage. Eighty species of Prosthechea s.l. and 12 species of related genera were sampled. Bayesian and maximum parsimony analyses of sequences from three plastid regions (rpl32‐trnL, trnD‐trnT, ycf1) and nrITS were included. Possible conflicts between nuclear and plastid data were assessed with partitioned Bremer support. Ancestral state reconstructions of morphological characters relevant to the genus taxonomy are provided. Our results reinforce the monophyly of the lineage corresponding to a broad circumscription of Prosthechea. The small lineages corresponding to Euchile, Panarica, and Hormidium are monophyletic, whereas the larger Anacheilium, Pollardia, and Pseudencyclia are not monophyletic. Splitting Prosthechea into smaller genera is not supported by our phylogeny, and nonmonophyly also hinders the proposal of a comprehensive infrageneric classification. The phylogenetic relationships recovered reflect better the biogeographic patterns than the previously proposed morphological affinities, pointing to the existence of homoplastic floral traits within the genus. Conflicts between nuclear and plastid partitions were detected, suggesting a possible scenario of reticulate evolution.

Taxonomic and phylogenetic study of the subgenus Tricercandra in the genus Chloranthus</o> (Chloranthaceae)

The genus Chloranthus consists of 17 taxa with the two subgenera Chloranthus and Tricercandra. These two subgenera can be distinguished by the morphology of the androecium. In South Korea, C. japonicus and C. fortunei of the subgenus Tricercandra are distributed. Although C. fortunei is typically not branched, a variant that branches from the stem has recently been discovered. Here, we conducted morphological and molecular phylogenetic analyses to elucidate the interspecific relationships within the subgenus Tricercandra and to evaluate the taxonomic position of the variant of C. fortunei. Morphological analyses revealed distinct differences among C. angustifolius, C. japonicus, C. fortunei, and the variant of C. fortunei. However, distinguishing between C. holostegius and C. nervosus was challenging. A principal component analysis also showed that while C. angustifolius, C. japonicus, C. fortunei, and the corresponding variant clustered independently, C. holostegius and C. nervosus overlapped, rendering them indistinguishable. Molecular phylogenetic studies using nuclear ribosomal internal transcribed spacer (nrITS) regions and three plastid regions, rbcL, rpl20-rps12, and trnL-F, revealed that the subgenus Tricercandra was monophyletic. Within the subgenus Tricercandra, C. angustifolius formed a sister clade with C. fortunei in the combined three plastid gene tree, while C. japonicus displayed different phylogenetic relationships between the nrITS and plastid gene trees. In addition, neither C. holostegius nor C. nervosus was monophyletic, consistent with the morphological analyses. The variant of C. fortunei formed an independent subclade on the nrITS tree but was not distinguished from other C. fortunei on the plastid gene tree. Our study elucidated clear species delimitation among C. angustifolius, C. japonicus, and C. fortunei and suggested key morphological characters useful for distinguishing them. Furthermore, our findings highlighted the ambiguous species delimitation and phylogenetic uncertainty between C. holostegius and C. nervosus. While we demonstrated morphological differences between the typical C. fortunei and its variant, the limited molecular phylogenetic evidence implies a need for further study.

Intraspecific discrimination power of plastid coding region rbcL as DNA barcoding marker in Dalbergia sissoo population of Pakistan

The conservation of diseases resistant sources of Dalbergia sissoo germplasm has attained the key status among the Agricultural prospects and solution against their possible threats. For this purpose, the best strategy is DNA barcoding based on nuclear, mitochondrial and plastid genomic regions. This approach is frequently used for species discrimination but its potential to discriminate the individuals at intraspecific level could also be worth exploring considerably. Hence, in the present study the potential of rbcL DNA barcode was evaluated for demonstrating intraspecific variation among the shisham genotypes collected across Pakistan. DNA barcoding analysis was performed on 20 selected shisham genotypes. Nucleotide sequences were analyzed to confirm genetic diversity among studied genotypes (θw = 1.000, π = 0.00172). The allelic profile of data yielded 11 unique sequence types (STs) numbers. The phylogenetic tree based on SYM+G model revealed the discriminatory power of rbcL DNA barcode to resolve and differentiate the individuals at intraspecific level. Keywords: Allelic profile, Sequence types, Akaike Information Criterion, Typing efficiency, DNA substitution.