Molecular phylogeny reveals the non-monophyly of tribe Yinshanieae (Brassicaceae) and description of a new tribe, Hillielleae

Characterization of the complete chloroplast genome of Eutrema deltoideum (Brassicaceae)

Eutrema deltoideum (Hook. f. et Thoms.) has been recognized as a potentially important vegetable and medicinal resource. In this study, we present the complete chloroplast genome of E. deltoideum and conduct a phylogenetic analysis. The chloroplast genome is 154,051 bp long and consists of a large single-copy (LSC) region of 84,149 bp, two inverted repeat (IR) regions of 26,065 bp each, and a small single-copy (SSC) region of 17,772 bp. It contains 132 complete genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. Additionally, we identified 78 simple sequence repeats (SSRs). The phylogenetic tree reveals that E. deltoideum is closely related to E. heterophyllum, and the Eutrema genus is monophyletic. This study provides valuable information about E. deltoideum and enhances our understanding of its taxonomic classification.

An updated classification of the Brassicaceae (Cruciferae)

Based on recent achievements in phylogenetic studies of the Brassicaceae, a novel infrafamilial classification is proposed that includes major improvements at the subfamilial and supertribal levels. Herein, the family is subdivided into two subfamilies, Aethionemoideae (subfam. nov.) and Brassicoideae. The Brassicoideae, with 57 of the 58 tribes of Brassicaceae, are further partitioned into five supertribes, including the previously recognized Brassicodae and the newly established Arabodae, Camelinodae, Heliophilodae, and Hesperodae. Additional tribus-level contributions include descriptions of the newly recognized Arabidopsideae, Asperuginoideae, Hemilophieae, Schrenkielleae, and resurrection of the Chamireae and Subularieae. Further detailed comments on 17 tribes in need of clarifications are provided.

Toward a better understanding of phylogenetic relationships within Conringieae (Brassicaceae)

One new tribe (Plagiolobeae), one new species (Plagioloba derakii) together with two new combinations (P. persica and P. clavata) are established within Brassicaceae based on a decisive consideration of molecular phylogenetic dataset, morphological characters, fruit septum nature, as well as seed microsculpturing features. Results distinctly justified Arabis ottonis-schulzii as a synonym of Conringia persica and further molecular analyses proved its placement as a member of genus Plagioloba. It is also placed in a new tribe Plagiolobeae as close relatives of Conringieae and Coluteocarpeae. Finally, the diagnostic morphological characters separating the new tribe from the previously assigned tribe (Conringieae) are also discussed.

Update on the Brassicaceae species checklist

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.

Phylogeny of Euclidieae (Brassicaceae) based on plastome and nuclear ribosomal DNA data

Euclidieae, a morphologically diverse tribe in the family Brassicaceae (Cruciferae), consists of 29 genera and more than 150 species distributed mainly in Asia. Prior phylogenetic analyses on Euclidieae are inadequate. In this study, sequence data from the plastid genome and nuclear ribosomal DNA of 72 species in 27 genera of Euclidieae were used to infer the inter- and intra-generic relationships within. The well-resolved and strongly supported plastome phylogenies revealed that Euclidieae could be divided into five clades. Both Cymatocarpus and Neotorularia are polyphyletic in nuclear and plastome phylogenies. Besides, the conflicts of systematic positions of three species of Braya and two species of Solms-laubachia s.l. indicated that hybridization and or introgression might have happened during the evolutionary history of the tribe. Results from divergence-time analyses suggested an early Miocene origin of Euclidieae, and it probably originated from the Central Asia, Pamir Plateau and West Himalaya. In addition, multiple ndh genes loss and pseudogenization were detected in eight species based on comparative genomic study.

Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research. Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family. Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome-wide expression signatures that distinguish simple from complex leaves in Brassicaceae. Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher-level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants.

New insights into the taxonomy of tribe Euclidieae (Brassicaceae), evidence from nrITS sequence data

As currently delimitated, the species-rich mustard tribe Euclidieae DC. (Brassicaceae) comprises 28 genera and 152 species distributed primarily in Asia. To date, no tribe-wide comprehensive phylogenetic analysis has been conducted. In this study, sequence data from the nuclear ribosomal internal transcribed spacer (nrITS) region of 82 species in all 28 genera of Euclidieae were used to test its monophyly and infer inter- and intra-generic relationships within. Phylogenetic analyses revealed that Rhammatophyllum and Sisymbriopsis are embedded within Solms-laubachia s.l., and Solms-laubachia lanuginosa (Eurycarpus lanuginosus) fell outside the tribe. Therefore, Solms-laubachia s.l. as currently recognized is not monophyletic and its generic delimitation needed further study. Besides, our results suggest that the genera Lepidostemon, Neotorularia, and Tetracme are polyphyletic.

Multispeed genome diploidization and diversification after an ancient allopolyploidization

Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of postpolyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an intertribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere. The reconstructed ancestral allopolyploid genome (n = 15) originated probably in northeastern Asia or western North America during the Late Miocene (c. 10.6-7 million years ago) and reached the Australian mainland via long-distance dispersal. In Australia, the allotetraploid genome diverged into at least three main subclades exhibiting different levels of PPD and diversity: 1.25-fold descending dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial Arabidella (3 species), 1.5-fold DD of n = 15 → n = 10 in the perennial Pachycladon (11 spp.) and 2.1-3.75-fold DD of n = 15 → n = 7-4 in the largely annual crown-group genera (42 spp. in 15 genera). These results are among the first to demonstrate multispeed genome evolution in taxa descending from a common allopolyploid ancestor. It is suggested that clade-specific PPD can operate at different rates and efficacies and can be tentatively linked to life histories and the extent of taxonomic diversity.