Nejvíce citovaný článek - PubMed ID 37659415
Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
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.
- Klíčová slova
- Boechera falcata, Brassicaceae, chloroplast genome, chromosome rearrangements, chromosome-level genome assembly and annotation, comparative chromosome painting, genome structure, molecular phylogeny,
- MeSH
- Brassicaceae * genetika klasifikace MeSH
- chromozomy rostlin genetika MeSH
- fylogeneze * MeSH
- genom rostlinný * MeSH
- genomika * metody MeSH
- Publikační typ
- časopisecké články 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.
- Klíčová slova
- Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, cytokinins, multistep phosphorelay, osmotic stress, salinity, two-component signaling, type-A response regulator,
- MeSH
- Arabidopsis genetika fyziologie metabolismus MeSH
- Brassica napus genetika fyziologie metabolismus MeSH
- Brassica * genetika fyziologie metabolismus MeSH
- cytokininy * metabolismus MeSH
- fylogeneze MeSH
- fyziologický stres * MeSH
- regulace genové exprese u rostlin MeSH
- regulátory růstu rostlin metabolismus MeSH
- rostlinné proteiny * genetika metabolismus MeSH
- signální transdukce MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- cytokininy * MeSH
- regulátory růstu rostlin MeSH
- rostlinné proteiny * 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.
- Klíčová slova
- conditionally expressed genes, dosage balance, environmental stress, subgenome dominance, transposable elements, whole-genome duplication,
- MeSH
- Brassicaceae genetika MeSH
- duplikace genu MeSH
- fyziologický stres MeSH
- genom rostlinný * MeSH
- molekulární evoluce MeSH
- regulace genové exprese u rostlin MeSH
- transpozibilní elementy DNA MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- transpozibilní elementy DNA 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.
- Klíčová slova
- classification, subfamily, supertribe, taxonomy, tribe,
- Publikační typ
- časopisecké články MeSH
