![Images of 12 representative species of tribe Thlaspideae. A, Alliaria petiolata; B, Didymophysa aucheri; C, D. fedtschenkoana; D, D. fenestrata; E, Graellsia saxifragifolia; F, Lysakia rostrata; G, Pachyphragma macrophyllum; H, Parlatoria cakiloidea; I, Peltaria angustifolia; J, Peltariopsis planisiliqua; K, Pseudocamelina kleinii; L, Thlaspi arvense.-Photographs by Ihsan A. Al-Shehbaz (A, C, H, L), Shokouh Esmailbegi (D), Kourosh Kavoosi (K), Jan De Laet (G), Mansour Mirtadzadini (B, I, J), Jalil Noroozi (F), and Hamed Parizi (E)].](https://www.researchgate.net/profile/Martin-Lysak/publication/325049044/figure/fig3/AS:624997261385730@1526022367580/Images-of-12-representative-species-of-tribe-Thlaspideae-A-Alliaria-petiolata-B_Q320.jpg)
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Phylogeny and systematics of the tribe Thlaspideae (Brassicaceae) and the recognition of two new genera
Abstract and Figures
Thlaspideae is an Old World tribe of Brassicaceae centered in SW Asia. Thirty-seven of 42 species (ca. 88%) in 13 genera of the tribe were analyzed using nuclear ITS and chloroplast trnL-F markers in a family-wide context. Both single-marker and concatenated phylogenies corroborated Thlaspideae as a well-supported monophyletic clade. With the exception of polyphyletic Alliaria and Parlatoria and paraphyletic Thlaspi and Didymophysa, the remaining genera were monophyletic. Alliaria petiolata comprised diploid and hexaploid populations in two well-resolved clades. The non-weedy diploid and hexaploid populations are restricted to SW Asia, and together with diploid A. taurica (formerly P. taurica), formed a sister clade to well-resolved Sobolewskia (3 spp.) and P. rostrata (now treated as the new monospecific genus Lysakia) clades. By contrast, the European and North American weedy and invasive hexaploid A. petiolata populations clustered with the diploid P. caki-loidea. Polyphyletic Thlaspi formed two distinct clades easily distinguished morphologically, and two of its six species are segregated into the new genus Mummenhoffia. Elburzia is reduced to synonymy of Didymophysa, and the new combinations D. fenestrata, Lysakia rostrata, Mummenhoffia alliacea, and M. oliveri are proposed and a diagnostic key for determination of Thlaspideae genera is presented. Age estimations based only on calibration by the controversial fossil Thlaspi primeavum resulted in unrealistic old age estimates. Chromosome counts are reported for 16 species. © International Association for Plant Taxonomy (IAPT) 2018, all rights reserved
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Supplementary resources (2)
... The BPP program, which is a molecular species delimitation program based on a Bayesian framework, needs a divergence time prior to delimiting specimens; hence, the divergence time of the N. densiflora complex was estimated using Bayesian Evolutionary Analysis Sampling Trees (BEAST) version 2.5 software (Bouckaert et al. 2019). Esmailbegi et al. (2018) showed that divergence time estimation in Brassicaceae based on Thlaspi primaevum Becker as a fossil calibration point was unreliable at different nodes. Therefore, a secondary calibration approach was used to obtain the time of origin of the most recent common ancestor of the N. densiflora complex. ...
... Ma (at the split between Aethionema and core Brassicaceae), and the second at 15.56 (18.95-12.3) Ma (at the split point of Thlaspideae), were determined following the methods of Couvreur et al. (2010) and Esmailbegi et al. (2018), respectively. ...
The accurate identification of an organism is the basis of all biological disciplines. Although there have been many different species concepts and methods proposed, researchers generally choose the most appropriate concept according to their interests. However, each species concept has both advantages and disadvantages. In such cases, an integrated concept based on evidence obtained from different species concepts and methods is suitable for the accurate delimitation of a species. The biggest dilemma of integrated species delimitation methods is the inconsistency between species concepts and methods. Herein, the congruency of the different concepts and methods was tested to reveal the relationship of the Noccaea densiflora species complex. nrITS, chloroplast trnL-F, and trnQ-5'rps16 regions were used for species delimitation using the multispecies coalescent model (MSC) as implemented in two developed Bayesian Methods. ITS and trnL-F regions were also used for TCS haplotype network analyses. In addition to morphological measurements from different populations and vouchers, specific bioclimatic data values were also used for the principal component analysis. Based on all of the analyses, it was determined that only one population of N. densiflora and and one of N. microstyla were clearly distinct, whereas the rest of the specimens remain taxonomically uncertain.
... A huge number of studies have been carried out on the family Brassicaceae and/or many genera, including their evolution, biodiversity, molecular systematics, fruit and seed coat sculpturing, seed germination, palynology, cytology, taxonomy, etc. (Appel and Al-Shehbaz 1997, Khalik et al. 2002, Murren et al. 2002, Koch et al. 2003, Lysak et al. 2005, Bailey et al. 2006, Koch and Kiefer 2006, Busch and Zachgo 2007, Beilstein et al. 2008, Denisow 2008, German et al. 2009, Chapman and Goring 2010, Couvreur et al. 2010, Franzke et al. 2011, Schmidt and Bancroft 2011, Mühlhausen et al. 2013, Huang et al. 2015, Özüdoğru et al. 2015, Esmailbegi et al. 2017, Mandáková et al. 2017. Especially for investigating morphological and palynological features, light microscopes (LM), stereo microscopes (SM) and scanning electron microscopes (SEM) have proven very useful instruments. ...
Fruit and seed morphology of 10 taxa of Iberis (Brassicaceae) from Turkey were investigated with stereo microscopy (SM) and scanning electron microscopy (SEM), in order to understand and check their diagnostic significance at generic and spesific level. Fruits and seeds of Iberis species were photographed and examined to evaluate different characteristics including fruit size, shape, color, indumentum, surface ornamentation, style length, sinus width, wing width, septum length, and also seed size, shape, color, surface ornamentation, cell types and anticlinal and periclinal cell wall features. SM photographs of both immature and mature fruits of the species are provided for the first time. Cluster analysis and principal coordinates analysis (PCoA) were performed to reveal similarities between related taxa in terms of seed and fruit morphology. According to fruit morphology, the Iberis taxa in Turkey are divided into three main groups, particularly characterized by fruit shape (ovate, ovate-obovate or ovate-orbicular). Style length, which is one of the most important diagnostic features of some Iberis taxa were also investigated. Three types of seed shapes were found: inequilateral obovate, broadly obovate and inequilateral elliptic. The fruit size limits of I. simplex were expanded. The cluster analysis based on a total of 20 fruit and seed characters represents the current taxonomic classification of the taxa in Turkey, which is updated in this study. A new identification key for Turkish Iberis is provided.
... Many molecular phylogenies have been inconsistent with a late Eocene age of T. primaevum, indicating a Miocene origin of 15 Ma for core Brassicaceae (Franzke et al., 2009(Franzke et al., , 2011Esmailbegi et al., 2018;etc.) or Oligocene (32.4 Ma: Hohmann et al., 2015). ...
The beetle Ceutorhynchus is used as a proxy for Eocene core Brassicaceae. The age of Brassicaceae has been strongly debated because their fossil record is scanty. There are four species of Ceutorhynchus inaffectatus species-group known in the Priabonian: Ceutorhynchus zerovae new species in Rovno amber and three in Baltic amber. There are numerous extant members of the group, all of which feed on core Brassicaceae. Together with differentiation of Brassicaceae-feeding Pierinae (Lepidoptera) in the Priabonian, the strong presence of Ceutorhynchus indicates at least an early Priabonian age of core Brassicaceae. The oldest fossil Brassicaceae is not known in the late Eocene of Europe, but was recorded in Montana, dated in some studies as late Oligocene, but recently as Priabonian (34 Ma). Ceutorhynchus zerovae n. sp. is very close to C . electrinus from Baltic amber.
UUID: http://zoobank.org/7f10761f-463d-44c5-9eef-bb4697bfb116 .
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
Following the publication of the seventh edition of the Nouvelle Flore, in 2023, this contribution provides an overview of nomenclatural and taxonomic changes compared to the previous edition of the Flora, which was published in 2012.
This study investigates the seed and fruit anatomy and micromorphology of five pennycress taxa (Thlaspi L. sensu lato) from Turkey, some of which have not been previously investigated. Systematic work in this group suffers from a lack of comprehensive anatomical and micromorphological data, especially for narrowly endemic species. We find that seed surface structure is taxonomically more useful than seed coat anatomy in Thlaspi s. lat., but despite this, it remains understudied. Our results indicate that the most useful anatomical characters are seed-epidermis cell shape and the presence of mucilage cells. As for micromorphology, seed periclinal walls and cell shape were most significant. Thlaspi ceratocarpon Murray, the only taxa remaining in Thlaspi sensu stricto, was unique among these taxa both anatomically and micromorphologically. It notably differs from Thlaspi alliaceum L., according to our results, corroborating recent studies that placed the latter into Mummenhoffia Esmailbegi & Al-Shehbaz. Our PCoA analysis resulted in a close grouping of T. jaubertii Hedge, T. crassum P.H. Davis and T. cilicicum (Boiss) Hayek, three species that have been moved to Noccaea Moench, based on molecular evidence. We discuss the fragmentation of Thlaspi s. lat. into smaller genera in the context of broader trends in plant systematics.
Brassicaceae family is an important one since it includes many economic and significant industrial oilseeds, spices, vegetables and some forage plants. In this study, sequences analysis among Chrysochamela (Brassicaceae) species distributed in Turkey were conducted nrDNA ITS and cpDNA trnL intron sequences. Chrysochamela species were collected and brought to the laboratory. ITS and trnL intron sequences were corrected with BioEdit and FinchTV programs. As a result of the study, ITS nucleotide compound compositions were determined as 22.7% T, 29.1 C, 21.5% A and 26.7% G. The lowest distance was 0.000 and the highest distance was 0.037. The phylogenetic tree obtained using the MEGA 6.0 program consists of two large groups. According to trnL intron sequences 37.9% T, 18.4 C, 28.3% A and 15.5% G. Nucleotide compound compositions were determined. The genetic distance between species was determined between 0.000 and 0.022. Maximum likelihood phylogenetic tree consists of two large groups. As a result, phylogenetic analyzes using ITS and trnL intron sequences were compatible with each other. It was also in past studies found to be supported by morphological, anatomical and RAPD data.
Whole genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large‐scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus‐ and species‐specific CRs, mostly pericentric inversions, as the main genome‐diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes vs. chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes and identified repetitive elements applicable as unique species‐ and genus‐specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow‐up whole genome sequencing efforts.
The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.
Background:
Here we present a revised species checklist for the Brassicaceae, updated from Warwick SI, Francis, A, Al-Shehbaz IA (2006), Brassicaceae: Species checklist and database on CD-ROM, Plant Systematics and Evolution 259: 249─25. This update of the checklist was initiated, based on recent taxonomic and molecular studies on the Brassicaceae that have resulted in new species names, combinations and associated synonyms.
New information:
New data have been added indicating tribal affiliations within the family and where type specimens have been designated. In addition, information from many early publications has been checked and added to the database. The database now includes information on 14983 taxa, 4636 of which are currently accepted and divided into 340 genera and 52 tribes. A selected bibliography of recent publications on the Brassicaceae is included.
The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family. Moreover, we selected the genus Cochlearia to test the transferability and polymorphism of these markers among species. Additionally, we annotated Cochlearia pyrenaica transcriptome in order to identify the position of each of the mined SSRs. While we introduce a new set of tools that will further enable evolutionary studies across the Brassicaceae, we also discuss some broader aspects of SSR evolution. Overall, we developed 2012 ready-to-use SSR markers with their respective primers in 19 Brassicaceae species and a high quality annotated transcriptome for C. pyrenaica. As indicated by our transferability test with the genus Cochlearia these SSRs are transferable to species within the genus increasing exponentially the number of targeted species. Also, our polymorphism results showed substantial levels of variability for these markers. Finally, despite its complex evolutionary history, SSR evolution across the Brassicaceae family is highly conserved and we found no deviation from patterns reported in other Angiosperms.
Premise of the study:
The Irano-Turanian region harbors three biodiversity hotspots and ∼25% of Brassicaceae species are endemic to the region. Aethionema (∼61 species) is the sister lineage to the core Brassicaceae and occurs mainly in the Irano-Turanian region. The evolutionary important position of Aethionema makes it an ideal reference for broader comparative genetics and genomics. To understand the evolution of Aethionema, and for a broader understanding of crucifer evolution, a time-calibrated phylogenetic tree and biogeographical history of the genus is needed.
Methods:
Seventy-six plastome coding regions and nuclear rDNA genes, mainly from herbarium material, covering 75% of all Aethionema species, were used to resolve a time-calibrated Aethionema phylogeny. The different clades were characterized based on four morphological characters. The ancestral area of Aethionema was estimated with historical biogeographical analyses.
Key results:
Three well-supported major clades within Aethionema were resolved. The ancestral area reconstruction and divergence-time estimates are consistent with major dispersal events during the Pliocene from the Anatolian Diagonal.
Conclusions:
We find that most Aethionema lineages originated along the Anatolian Diagonal, a floristic bridge connecting the east to the west, during the Pliocene. The dispersal of Aethionema correlates with the local geological events, such as the uplift of the Anatolian and Iranian plateaus and the formation of the major mountain ranges of the Irano-Turanian region. Knowing the paleo-ecological context for the evolution of Aethionema, in addition to the other lineages of Brassicaceae, facilitates our broader understanding for trait evolution and species diversification across the Brassicaceae.
Graellsia includes nine species, of which five (three endemic) are native to Iran. The new species G. isfahan is described and illustrated, and its relationship to the Turkish endemic G. davisiana is discussed. The new combination G. longistyla is proposed, and the lectotypes of G. graellsiifolia, G. integrifolia, and G. stylosa are designated.
Pseudocamelina comprises nine species, of which seven are endemic to Iran and one each to Pakistan and Kurdistan Iraq. The new species P. bakhtiarica and P. kermanica are described, illustrated, and their relationships to nearest relatives are discussed. The new combination P. kurdica is proposed, and the genus Camelinopsis is reduced to synonymy of Pseudocamelina. Second-step lectotypifications are designated for P. camelinae and P. violacea.
Background
The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. ResultsBayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Conclusions
Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.
Heldreichia Boiss. is a monospecific genus mainly distributed in Anatolia and the Lebanon. Although morphological variation and infrageneric phylogenetic relationships were recently studied in detail, Heldreichia remained as one of the few orphan genera that have not yet been assigned to any tribe. In the current study, we used sequence data from the nuclear ITS and chloroplast ndhF regions of Heldreichia and representatives of main Brassicaceae lineages and tribes to determine its tribal affiliation. Bayesian-based phylogenetic analyses clearly show with high support that Heldreichia is a member of the recently expanded tribe Biscutelleae. Furthermore, we characterize the tribe Biscutelleae morphologically and provide a determination key for all its genera.
Despite its small nuclear genome and minute chromosomes, the model plant Arabidopsis thaliana has become a well established model in the field of plant cytogenetics. Since 2000, most cytogenetic and epigenetic approaches have been developed for this species and its congeners. In this chapter, we describe two step-by-step protocols for preparing chromosome preparations from root tip meristems and generative organ tissues of A. thaliana. Although both protocols have been optimized for A. thaliana, the detailed procedures are equally applicable to other members of the genus Arabidopsis as well as other crucifer species (Brassicaceae).