Most cited article - PubMed ID 37659415
Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
Progestogens and androgens are steroids found in a wide range of plants, but little is known about their physiological functions. In this study, we sowed seeds of angiosperms on progestogen- and androgen-containing medium and analysed their morphological effects. We further investigated the effects of progesterone and testosterone on brassinosteroid profiles and gene expression in A. thaliana. Additionally, we examined the effects of progesterone and testosterone on A. thaliana plants overexpressing the steroid 5α-reductase DET2. We found that progestogens and androgens have strong negative effects on root length, especially in Brassicaceae species. In addition, these steroids led to uncoordinated cell growth and increased lateral root formation. We failed to detect an effect on endogenous brassinosteroid levels and gene expression of brassinosteroid-regulated genes. The overexpression of DET2 led to increased root growth, but the effects of progesterone and testosterone were not reduced. We conclude that progestogens and androgens act in a brassinosteroid-independent manner. This suggests that progestogens and androgens could represent a potential new class of plant steroid signalling molecules.
- Keywords
- Arabidopsis thaliana, DET2, androgens, brassinosteroids, phytohormones, progestogens, root development, signalling molecules,
- MeSH
- Androgens * metabolism pharmacology MeSH
- Arabidopsis * genetics growth & development drug effects metabolism MeSH
- Brassinosteroids * metabolism MeSH
- Plants, Genetically Modified MeSH
- Plant Roots * growth & development drug effects anatomy & histology genetics metabolism MeSH
- Magnoliopsida * genetics growth & development drug effects metabolism MeSH
- Progesterone pharmacology metabolism MeSH
- Progestins * metabolism pharmacology MeSH
- Arabidopsis Proteins metabolism genetics MeSH
- Gene Expression Regulation, Plant drug effects MeSH
- Plant Growth Regulators * metabolism MeSH
- Seeds growth & development drug effects genetics MeSH
- Testosterone pharmacology metabolism MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Androgens * MeSH
- Brassinosteroids * MeSH
- Progesterone MeSH
- Progestins * MeSH
- Arabidopsis Proteins MeSH
- Plant Growth Regulators * MeSH
- Testosterone MeSH
Matthiola incana, commonly known as stock and gillyflower, is a widely grown ornamental plant whose genome is significantly larger than that of other species in the mustard family. However, the evolutionary history behind such a large genome (~2 Gb) is still unknown. Here, we have succeeded in obtaining a high-quality chromosome-scale genome assembly of M. incana by integrating PacBio HiFi reads, Illumina short reads and Hi-C data. The resulting genome consists of seven pseudochromosomes with a length of 1965 Mb and 38 245 gene models. Phylogenetic analysis indicates that M. incana and other taxa of the supertribe Hesperodae represent an early-diverging lineage in the evolutionary history of the Brassicaceae. Through a comparative analysis, we revisited the ancestral Hesperodae karyotype (AHK, n = 7) and found several differences from the well-established ancestral crucifer karyotype (ACK, n = 8) model, including extensive inter- and intra-chromosomal rearrangements. Our results suggest that the primary reason for genome obesity in M. incana is the massive expansion of long terminal repeat retrotransposons (LTR-RTs), particularly from the Angela, Athila and Retand families. CHG methylation modification is obviously reduced in the regions where the highest density of Copia-type LTR-RTs and the lowest density of Gypsy-type LTR-RTs overlap, corresponding to the putative centromeres. Based on insertion times and methylation profiling, recently inserted LTR-RTs were found to have a significantly different methylation pattern compared to older ones.
- Keywords
- Cruciferae, Hesperodae, Lineage III, genome assembly, genome obesity, retrotransposons,
- MeSH
- Brassicaceae * genetics MeSH
- Chromosomes, Plant genetics MeSH
- Phylogeny MeSH
- Genome, Plant * genetics MeSH
- Karyotype MeSH
- Evolution, Molecular * MeSH
- Retroelements * genetics MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Retroelements * MeSH
Boechera falcata (Turcz.) Al-Shehbaz, previously known as Arabis turczaninowii Ledeb., is a herbaceous perennial of the East Siberian, boreal-steppe ecotype. It is the sole species of the diverse genus Boechera found on the Eurasian continent, with all other species endemic to North America and Greenland. Likely migrating from North America to Eastern Siberia via the Bering Land Bridge during the Pleistocene glaciation, B. falcata presents a unique case for genomic study. The genus Boechera is notable for its many allodiploid and triploid apomicts, which have arisen through complex hybridization of sexual species and ecotypes. To date, only the genomes of 2 American Boechera species, B. stricta and B. retrofracta, have been sequenced and analyzed. In this study, we sequenced, assembled to the chromosome level, and analyzed the highly homozygous 189.36 Mb genome of B. falcata (2n = 14). Molecular phylogenetic analysis of nuclear and organelle genomes revealed a high degree of relatedness to North American relatives. Cytogenetic analysis identified all 22 genomic blocks of crucifers, showing that 5 of the 7 B. falcata chromosomes are collinear with their ancestral counterparts, while 2 have undergone inversions. Allelic analysis of the apomixis marker APOLLO gene revealed that B. falcata contains only sex alleles. The availability of the B. falcata genome will advance studies of the evolution and phylogeny of Brassicaceae species and the mechanisms of apomixis, providing a crucial resource for future research in plant genetics and breeding.
- Keywords
- Boechera falcata, Brassicaceae, chloroplast genome, chromosome rearrangements, chromosome-level genome assembly and annotation, comparative chromosome painting, genome structure, molecular phylogeny,
- MeSH
- Brassicaceae * genetics classification MeSH
- Chromosomes, Plant genetics MeSH
- Phylogeny * MeSH
- Genome, Plant * MeSH
- Genomics * methods MeSH
- Publication type
- Journal Article MeSH
The ancestral crucifer karyotype and 22 conserved genomic blocks (CGBs) facilitate phylogenomic analyses in the Brassicaceae. Chromosomal rearrangements reshuffled CGBs of ancestral chromosomes during karyotype evolution. Here, we identify eight protochromosomes representing the common ancestral karyotype (ACBK) of the two Brassicoideae supertribes: Camelinodae (Lineage I) and Brassicodae (Lineage II). The characterization of multiple cascading fusion events allows us to infer evolutionary relationships based on these events. In the Camelinodae, the ACBK first evolved into the AKI genome, which remained conserved in the Cardamineae, whereas it was altered to tAKI by a reciprocal translocation that preceded the diversification of most Camelinodae tribes. The identified fusion breakpoints largely overlap with CGB boundaries, suggesting that CGBs are mainly disrupted by chromosome fusions. Our results demonstrate the stable inheritance of chromosome fusions and their importance for reconstructing evolutionary relationships. The chromosomal breakpoint approach provides a basis for ancestral state reconstruction based on chromosome-level genome assemblies.
Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control both plant development and adaptive responses. Type-A RESPONSE REGULATOR (RRA) genes, the downstream members of the MSP cascade and cytokinin primary response genes, are thought to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, transcriptional data also suggest the involvement of RRA genes in stress-related responses. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRA genes, we identified five and 38 novel putative RRA genes in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassicaceae. We categorized RRA genes based on the kinetics of their cytokinin-mediated up-regulation and observed both similarities and specificities in this type of response across Brassicaceae species. Using bioinformatic analysis and experimental data demonstrating the cytokinin and abiotic stress responsiveness of the A. thaliana-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin- and stress-mediated up-regulation of RRA genes in B. rapa and B. napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus further demonstrating the role of cytokinin signaling in crop adaptive responses.
- Keywords
- Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, cytokinins, multistep phosphorelay, osmotic stress, salinity, two-component signaling, type-A response regulator,
- MeSH
- Arabidopsis genetics physiology metabolism MeSH
- Brassica napus genetics physiology metabolism MeSH
- Brassica * genetics physiology metabolism MeSH
- Cytokinins * metabolism MeSH
- Phylogeny MeSH
- Stress, Physiological * MeSH
- Gene Expression Regulation, Plant MeSH
- Plant Growth Regulators metabolism MeSH
- Plant Proteins * genetics metabolism MeSH
- Signal Transduction MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Cytokinins * MeSH
- Plant Growth Regulators MeSH
- Plant Proteins * MeSH
The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles.
- Keywords
- conditionally expressed genes, dosage balance, environmental stress, subgenome dominance, transposable elements, whole-genome duplication,
- MeSH
- Brassicaceae genetics MeSH
- Gene Duplication MeSH
- Stress, Physiological MeSH
- Genome, Plant * MeSH
- Evolution, Molecular MeSH
- Gene Expression Regulation, Plant MeSH
- DNA Transposable Elements MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- DNA Transposable Elements MeSH
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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.
- Keywords
- classification, subfamily, supertribe, taxonomy, tribe,
- Publication type
- Journal Article MeSH
