Allium Sect Research Articles

Allium goumenissanum (Allium sect. Codonoprasum), a new species for Bulgaria and new localities in Greece: testing an integrated approach to species identification

Allium sect. Codonoprasum represents an evolutionarily young and rapidly radiating group of bulbous geophytes, with a significant proportion of polyploids and minor morphological differences between species. In the last 20 years, dozens of new species of this section have been described from the Mediterranean. Still, very little new information has been obtained on most of them since their description, especially concerning cytogenetic, molecular, and distribution data. Allium goumenissanum is a recently described species of this section, known only from three nearby localities in northern Greece. During the last 10 years, the senior authors' team collected population samples of an unknown species of this section from the southern Balkans, which appeared to be representative of A. goumenissanum. Using an integrated approach employing a range of methods (cytogenic, molecular, morpho- and micromorphological methods), the populations of an unknown species were compared with morphologically similar species A. goumenissanum and A. stamatiadae. AFLP, ITS sequencing and genome size analyses revealed that all the populations of the unknown species represent A. goumenissanum, and that this species is differentiated genetically and in genome size from A. stamatiadae. ITS sequencing indicates an allotriploid origin of A. goumenissanum from unknown ancestors. The characterization of the morphology and reproduction of A. goumenissanum is completed and micromorphological and anatomical characteristics of the leaves of both species are newly published. The distribution of A. goumenissanum, based on new data, now includes a more extensive area of north central Greece and the species has been found as a new one for Bulgaria.

Taxonomic evidences supporting the establishment of ‘sibujing', a traditional condiment crop from the Philippines, as Allium chinense G.Don

‘Sibujing' is an emerging crop species in the Philippines with recorded traditional use as condiment in localized areas in Mindanao. However, its taxonomic identity is confused as it has been attributed to various taxa of Allium. We characterized the morphological, phytochemical and molecular characteristics of a ‘sibujing' accession to establish the taxonomic belonging and correct species name of the crop and elucidate its baseline characteristics for its continued utilization. Through next‐generation sequencing, we assembled the quadripartite genome of a ‘sibujing' accession from Zamboanga del Norte. The generated chloroplast genome revealed 100% similarity to the earlier established 152 525‐bp‐long A. chinense G.Don. plastome from China. Morphological characteristics also support this identification as both bears leaves with hollow 3–5‐angled cross‐sections, scapes that are terete and solid, and distinctly toothed filament base. Saponins were also detected from its methanolic extract. Phylogenetic reconstruction based on the sequenced ITS region, a nuclear barcode, suggested that the species was closest to taxa belonging to Allium sect. Sacculiferum subg. Cepa, further supporting its potential identity with A. chinense. Using a separate accession from a different locality in the Philippines, these findings were validated as the chloroplast genome assembled, phytochemical and morphological characteristics recorded were similarly established as close to A. chinense. This is the first definitive record of an Allium species from sect. Sacculiferum in the Philippines.

Allium murat-sonayii (Amaryllidaceae), a new species from Türkiye

Allium murat-sonayii Balos, Sonay & C. Çeçen is described as a new species from Elazığ Province, Eastern Türkiye. Diagnostic characteristics, a comprehensive description, photographs and a distribution map are provided. Based on morphological features, it belongs in Allium subgen. Allium sect. Allium. It is similar to A. stearnianum, A. stearnianum subsp. vanense, A. aybukeae, A. gemiciana, A. yamadagensis and A. dictyoprasum, but differs from them by several morphological characters, such as bulblets color, stem length, leaf, umbel shape, perigon colour, outer and inner tepal, anther colour, filaments and ovary.

Disentangling the taxonomic structure of the Allium paniculatum species complex in central and eastern Europe using molecular, cytogenetic and morphological tools

Allium section Codonoprasum includes a group of evolutionarily young taxa with unclear taxonomic boundaries, evolutionary relationships and complex synonymy. The most complicated taxon in this section is A. paniculatum, which until recently was considered to be the most widespread and morphologically most variable species, with a distribution extending from the Mediterranean area to central Europe and the Pontic region. A recent taxonomic study has shown that true A. paniculatum is a morphologically and genetically distinct species occurring in southern Ukraine and southern Russia. The clarification of its taxonomic identity questioned the taxonomic identity of populations referred to as A. paniculatum in other parts of Europe, including populations in central (Slovakia, Hungary, northeast Serbia) and the western part of eastern Europe (Romania, Ukraine), from where four other species of this complex (i.e. A. fuscum, A. fussii, A. marginatum and A. podolicum) were described and later frequently merged as synonyms with A. paniculatum. Here, the diversification within this complex in the abovementioned region is explored, using various biosystematic methods (morphometry, leaf anatomy and epidermal micromorphometry, karyology, estimation of genome size and GC content using flow cytometry, and molecular fingerprinting using Amplified Fragment Length Polymorphisms). By this means the existence of three well-separated population groups were revealed in the material studied, taxonomically corresponding to A. fuscum, A. marginatum and the group A. paniculatum + A. podolicum. The genetic patterns indicate that populations of at least some of these taxa might have survived in their current ranges or in neighbouring areas during the last glacial and the early Holocene. Allium fuscum is a species that inhabits shaded rocky outcrops in the wide neighbourhood of the Iron Gate area (south-western Romania, north-western Bulgaria and northeast Serbia). Allium marginatum is a species closely related to A. fuscum, inhabiting dry grasslands and dry oak forests in the Pannonian and Transylvanian Basins. Two eastern-European taxa, A. podolicum and A. paniculatum,which are very similar inmorphology, genome size and genetic markers, are considered to be conspecific and named A. paniculatum. This species inhabits zonal steppe and forest steppe regions in eastern Europe from western Ukraine to southern Russia. In addition, a taxonomic and nomenclatural treatment, as well as a key for identifying the recognized species of the A. paniculatum complex in the region studied, are presented.

Allium ayhan-toprakii (Amaryllidaceae), a New Species from Turkey

Allium ayhan-toprakii Yıldırım (Amaryllidaceae) is described as a new species from Mt. Sandras, Muğla Province, western Anatolia, Turkey. Based on morphological features, it belongs in Allium subgen. Allium sect. Codonoprasum. It is similar to A. carium and A. flavum subsp. tauricum var. Pilosum, but differs from them in several morphological characters, such as its flexous stem, stem length, indumentum, pedicel length, perigone length and colour, and ovary shape.

Allium saricanense (Amaryllidaceae), a New Species from Eastern Turkey

Allium saricanense Balos, Sonay & Koçyiğit (Amaryllidaceae), a new species of Allium sect. Codonoprasum, is described from Elazığ Province, eastern Turkey. It resembles A. turcicum and A. nerimaniae but differs from them by several morphological characters, such as its filament length, inner tepal shape, ovary shape and style colour. Diagnostic characters, a comprehensive description, photographs, and a distribution map of A. saricanense are provided.

Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution.

With the development of molecular sequencing approaches, many taxonomic and phylogenetic problems of the genus Allium L. have been solved; however, the phylogenetic relationships of some subgenera or sections, such as section Bromatorrhiza, remain unresolved, which has greatly impeded our full understanding of the species relationships among the major clades of Allium. In this study, the complete chloroplast (cp) genomes of nine species in the Allium sect. Bromatorrhiza were determined using the Illumina paired-end sequencing, the NOVOPlasty de novo assembly strategy, and the PGA annotation method. The results showed that the cp genome exhibited high conservation and revealed a typical circular tetrad structure. Among the sect. Bromatorrhiza species, the gene content, SSRs, codon usage, and RNA editing site were similar. The genome structure and IR regions’ fluctuation were investigated while genes, CDSs, and non-coding regions were extracted for phylogeny reconstruction. Evolutionary rates (Ka/Ks values) were calculated, and positive selection analysis was further performed using the branch-site model. Five hypervariable regions were identified as candidate molecular markers for species authentication. A clear relationship among the sect. Bromatorrhiza species were detected based on concatenated genes and CDSs, respectively, which suggested that sect. Bromatorrhiza is monophyly. In addition, there were three genes with higher Ka/Ks values (rps2, ycf1, and ycf2), and four genes (rpoC2, atpF, atpI, and rpl14) were further revealed to own positive selected sites. These results provide new insights into the plastome component, phylogeny, and evolution of Allium species.

Allium goumenissanum a new autumnal species of Allium sect. Codonoprasum (Amaryllidaceae) from north Greece

Allium goumenisannum from the north continental Greece (NC) is described and illustrated as a species new to science. It is an autumn-flowering species classified to Allium sect. Codonoprasum and is characterized by a triploid chromosome number (2n = 3x = 24), unusual for this late-flowering species group. This paper focuses on the presentation of the main morphological and karyological characters of the new species and its possible relationships with other Greek and East Mediterranean autumnal species.

Allium sultanae-ferhanii (Amaryllidaceae), a New Species from Southeastern Turkey

Allium sultanae-ferhanii Balos (Amaryllidaceae), a new species of Allium sect. Codonoprasum, is described from Şanlıurfa Province, SE Turkey. It resembles A. albotunicatum and A. stamineum but differs from them by several morphological characters, such as its filament length, perigone colour, stipitate ovary, and capsule and seed size. Diagnostic characters, a comprehensive description, photographs and a distribution map of A. sultanae-ferhanii are provided.

Allium tsinlingense (Amaryllidaceae, Allioideae), a new species from Shaanxi, China

A new species, Allium tsinlingense, from southern Shaanxi Province, China, is described and illustrated here. This species is similar to A. maowenense in Allium sect. Daghestanica, but it can be distinguished by its leaves solid, its spathe persistent after flowering, its flowers changing color from green, greenish to white in different stage, but never purplish, with the midvein of tepal greenish and never pale red, and its pedicels with bracteoles at base. Molecular phylogenetic analyses also suggested that this new species is a member of Allium sect. Daghestanica and a sister taxon to A. maowenense.

Seed macro- and micromorphology in Allium (Amaryllidaceae) and its phylogenetic significance.

Macro- and micromorphology of seeds are diagnostic characteristics of importance in delimiting taxa in Allium (Amaryllidaceae). However, there is no consensus on the phylogenetic significance of testa cell characteristics and whether they reflect the different evolutionary levels recognized in Allium. Seeds of 95 species (98 samples) representing 14 subgenera and 58 sections of Allium were examined using scanning electron microscopy (SEM) for such traits as periclinal wall surface area of ten testa cells, distance between testa cells (macromorphology), testa cell shapes, and arrangement and structure of anticlinal and periclinal walls (micromorphology). The data matrix was subjected to cladistic analysis. The produced phylogenetic tree was examined against the molecular tree obtained from publically available ITS sequences. The periclinal wall surface area of ten testa cells and the distance between them, examined for the first time, were found useful for delimitation of species in Allium. Based on seed macro- and micromorphology, we present a taxonomic key and a hypothetical reconstruction of the migration routes during the early stages of evolution of Allium. The ancestors of Allium originated in an area bounded by the Caucasus, Central Asia and Iran. The seed testa morphology-based evolutionary state of a species is determined by two parameters: the shape of the periclinal walls and curvature of the anticlinal walls.

Alliumheterophyllum (Amaryllidaceae), a new species from Henan, China.

Alliumheterophyllum D.F.Xie & X.J.He, sp. nov. (Amaryllidaceae), is a new species from Henan, China and is described based on morphological and molecular evidence. It is morphologically most similar to A.dumebuchum in the rhomboid scape in cross-section. However, distinctive differences were detected in perianth color, leaf shape and cross-section, flowers’ density as well as flowering season. Similarly, the karyotype of A.heterophyllum is 2n = 2x = 16 and in A.dumebuchum is 2n = 4x = 32. Phylogenetic analysis based on nuclear ribosomal Internal Transcribed Spacers (ITS) and three cpDNA regions strongly supports that A.heterophyllum is a member of Allium section Rhizirideum and sister to the other species of this section (e.g. A.senescens, A.spirale, and A.prostratum). Currently, only one population and approximately 120 individuals were discovered; the development of scenic spots in this region may affect its growth and threaten this population. Therefore, this new species is preliminarily considered as Near Threatened (NT) according to criteria of the IUCN Red List.

Allium shinasii (Amaryllidaceae), a new species from Turkey

Allium shinasii (Amaryllidaceae) is described here as a new species. Diagnostic morphological characters, a full description, and detailed illustrations are given herein. Allium shinasii is known from Tunceli province in eastern Anatolia, Turkey. According to its morphological features, it belongs to Allium sect. Codonoprasum. It is related to A. kurtzianum that belongs to the same section, A. sieheanum and A. sivasicum that belong to A. sect. Scorodon. However, it is easily distinguished from these species mainly by tepals, leaves and spathe characters.

Allium mardinense (Amaryllidaceae), a New Species from Southeastern Turkey

Allium mardinense Balos, H. Akan & Yıldırım, a new species of Allium sect. Allium, is described from Mardin Province, southeastern Turkey. It resembles A. aybukeae and A. enginii but differs from them by several morphological characters, such as its filament length, inner tepal shape and surface, and anther colour. Diagnostic characters, a comprehensive description, photographs, and a distribution map of A. mardinense are provided.

Notes on Allium section Rhizirideum (Amaryllidaceae) in South Korea and northeastern China: with a new species from Ulleungdo Island.

Allium section Rhizirideum is reviewed for South Korea and neighboring northeastern China based on critical observation of wild populations and herbarium materials. Species delimitations are re-evaluated on the basis of morphological and somatic chromosome numbers, resulting in the recognition of five species. Allium dumebuchum from Ulleungdo Island, South Korea, is described as a new species. This species is most similar to A. senescens due to its habits, but is clearly distinguished particularly by its rhomboid scapes in cross-secion, light purple perianth color, entire and narrowly triangular inner filaments, and flowering season from late September. One previously recognized species is placed into synonymy: A. pseudosenescens (under A. senescens). Photographs and a key to species of Allium section Rhizirideum in South Korea and northeastern China are provided in addition to information on nomenclatural types, synonymies, chromosome numbers, distribution, and specimens examined.

Out of the Qinghai-Tibetan Plateau and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae).

The disjunctive distribution (Europe–Caucasus–Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL–trnF and rpl32–trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidated the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian–European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the Qinghai–Tibetan Plateau (QTP) and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 million years ago (Mya). Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

Taxonomy and phylogenetics ofAlliumsectionDecipientia(Amaryllidaceae): morphological characters do not reflect the evolutionary history revealed by molecular markers

AbstractPhylogenetic and phylogeographic patterns in Allium section Decipientia (subgenus Melanocrommyum) were analysed, including most species of this section and representative species of most other sections of the monophyletic Allium subgenus Melanocrommyum. We constructed a molecular phylogenetic tree based on predominantly non-coding sequences from nuclear ribosomal RNA and four plastid regions. In Allium section Decipientia, 2n = 16 and 2n = 20 chromosomes were confirmed and, in part, newly reported. All plants with 2n = 20 form a clade that is sister to the European A. decipiens and A. quercetorum with 2n = 16 in the ITS analysis and are genetically distant from the Eurasian steppe species with 16 chromosomes, A. tulipifolium and A. robustum. The plastid analysis does not reveal a clear relationship between these three monophyletic groups. The karyotype of A. tulipifolium is similar to those of other members of subgenus Melanocrommyum, but only preliminary chromosomal dimensions could be presented for the species with 2n = 20 chromosomes. The latter group comprises A. grande, A. subscabrum, A. viridulum and the newly described taxa A. koksuense and A. lepsicum. Allium tulipifolium and A. robustum have been placed in a new section Tulipifolia, and all species with 2n = 20 have been placed in a new subsection, Viceniprason, of section Decipientia. A nomenclatorial conspectus and a key for determination of the members of Allium sections Decipientia and Tulipifolia are also provided. According to the time divergence estimation, subgenus Melanocrommyum diversified c. 25 Mya in the late Oligocene. The split between most species of the section Decipientia and other taxa in this subgenus was estimated as early Miocene, which furthermore diversified into two sister clades in mid Miocene. Allium decipiens split off from the ancestors of the 2n = 20 species also in the mid Miocene. Further branching in this species group is of rather young age, and occurred within the last 6 Myr (late Miocene to late Pliocene and Pleistocene).

<p><strong><em>Allium gilanense</em>, a new species of <em>Allium</em> sect. <em>Codonoprasum</em> (Amaryllidaceae) from Iran: evidence from morphological and molecular data</strong></p>

As a result of recent botanical expeditions to the north of Iran, we describe here a new endemic Allium species from Gilan province named Allium gilanense. Molecular and morphological data indicate that it belongs to Allium sect. Codonoprasum. We provide a morphological description, comparing Allium gilanense with the closest relative taxa A. lenkoranicum and A. paniculatum, the preliminary karyotype of the new species, and molecular phylogenetic data derived from the nuclear ribosomal DNA internal transcribed spacers (ITS) and the chloroplast intergenic spacer trnH-psbA. The chromosome number of the new species is 2n = 16 with 0-3 B chromosomes.

<p><strong><em>Allium shahinii</em></strong><strong>: a new species of <em>A.</em> sect. <em>Scorodon</em> (Amaryllidaceae) from Turkey</strong></p>

Allium shahinii, a new species of Allium sect. Scorodon, is described and illustrated from Erzincan Province, Eastern Turkey. It is a narrowly distributed geophyte growing on siliceous screes of warm exposure in mountain ranges of the nemoral and thermophilous deciduous woodland zone, showing close morphological relationships mainly with A. moschatum, A. stocksianum, A. spirophyllum, A. circumflexum but it is clearly differentiated due to perigon, outer tunic, indumentum, leaf and scape characteristics. In this study, diagnostic characters, description, taxonomic comments, photographs, distribution map, detailed illustration, the conservation status of A. shahinii and identification key are provided for A. shahinii and related taxa. According to IUCN Red List Categories and Criteria, A. shahinii is assessed here as a Critically Endangered (CR) species.

Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion

Allium sect. Cepa (Amaryllidaceae) comprises economically important plants, yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent. Until now, phylogenetic studies of the section have been based on a few genes. In this study, we sequenced the complete chloroplast genome (plastomes) of four central Asian species of sect. Cepa: Allium oschaninii, A. praemixtum, A. pskemense and A. galanthum. Their chloroplast (cp) genomes included 114 unique genes of which 80 coded proteins. Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies. Our plastome-based phylogenetic tree of Allium sect. Cepa revealed two separate clades: one comprising the central Asian species A. oschaninii, A. praemixtum, and A. pskemense, and another comprising A. galanthum, A. altaicum, and two cultivated species, A. cepa and A. fistulosum. These findings contradict previously reported phylogenies that relied on ITS and morphology. Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A. galanthum and A. cepa followed by chloroplast capture; however, this is impossible to prove without additional data. Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion. Among the chloroplast genes, rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.