The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Identification and expression analysis of the Xyloglucan transglycosylase/hydrolase (XTH) gene family under abiotic stress in oilseed (Brassica napus L.)

XTH genes are key genes that regulate the hydrolysis and recombination of XG components and plays role in the structure and composition of plant cell walls. Therefore, clarifying the changes that occur in XTHs during plant defense against abiotic stresses is informative for the study of the plant stress regulatory mechanism mediated by plant cell wall signals. XTH proteins in Arabidopsis thaliana was selected as the seed sequences in combination with its protein structural domains, 80 members of the BnXTH gene family were jointly identified from the whole genome of the Brassica napus ZS11, and analyzed for their encoded protein physicochemical properties, phylogenetic relationships, covariance relationships, and interoperating miRNAs. Based on the transcriptome data, the expression patterns of BnXTHs were analyzed in response to different abiotic stress treatments. The relative expression levels of some BnXTH genes under Al, alkali, salt, and drought treatments after 0, 6, 12 and 24 h were analyzed by using qRT-PCR to explore their roles in abiotic stress tolerance in B. napus. BnXTHs showed different expression patterns in response to different abiotic stress signals, indicating that the response mechanisms of oilseed rape against different abiotic stresses are also different. This paper provides a theoretical basis for clarifying the function and molecular genetic mechanism of the BnXTH gene family in abiotic stress tolerance in rapeseed.

Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa

BACKGROUND AND AIMS

The grass genus Urochloa (Brachiaria) sensu lato includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis and Megathyrsus maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems and frequent polyploidy are widely shared within the genus. The combination of these traits probably favoured the selection for forage domestication and weediness, but trait emergence across Urochloa cannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted. We aim to produce a phylogeny for Urochloa that includes all important forage species, and identify their closest wild relatives (crop wild relatives). Finally, we will use our phylogeny and available trait data to infer the ancestral states of important forage traits across Urochloa s.l. and model the evolution of forage syndromes across the genus.

METHODS

Using a target enrichment sequencing approach (Angiosperm 353), we inferred a species-level phylogeny for Urochloa s.l., encompassing 54 species (~40 % of the genus) and outgroups. Phylogenies were inferred using a multispecies coalescent model and maximum likelihood method. We determined the phylogenetic placement of agriculturally important species and identified their closest wild relatives, or crop wild relatives, based on well-supported monophyly. Further, we mapped key traits associated with Urochloa forage crops to the species tree and estimated ancestral states for forage traits along branch lengths for continuous traits and at ancestral nodes in discrete traits.

KEY RESULTS

Agricultural species belong to five independent clades, including U. brizantha and U. decumbens lying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings in Urochloa based on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis and large seeds) independently evolved in forage clades.

CONCLUSIONS

Urochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. All forage species and their crop wild relatives naturally occur on the African continent and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives need to be better assessed both to develop conservation strategies and to exploit the diversity in the genus for improved sustainability in Urochloa cultivar production.

Genome-wide identification and stress response analysis of BcaCPK gene family in amphidiploid Brassica carinata

BACKGROUND

Calcium-dependent protein kinases (CPKs) are crucial for recognizing and transmitting Ca2+ signals in plant cells, playing a vital role in growth, development, and stress response. This study aimed to identify and detect the potential roles of the CPK gene family in the amphidiploid Brassica carinata (BBCC, 2n = 34) using bioinformatics methods.

RESULTS

Based on the published genomic information of B. carinata, a total of 123 CPK genes were identified, comprising 70 CPK genes on the B subgenome and 53 on the C subgenome. To further investigate the homologous evolutionary relationship between B. carinata and other plants, the phylogenetic tree was constructed using CPKs in B. carinata and Arabidopsis thaliana. The phylogenetic analysis classified 123 family members into four subfamilies, where gene members within the same subfamily exhibited similar conserved motifs. Each BcaCPK member possesses a core protein kinase domain and four EF-hand domains. Most of the BcaCPK genes contain 5 to 8 introns, and these 123 BcaCPK genes are unevenly distributed across 17 chromosomes. Among these BcaCPK genes, 120 replicated gene pairs were found, whereas only 8 genes were tandem duplication, suggesting that dispersed duplication mainly drove the family amplification. The results of the Ka/Ks analysis indicated that the CPK gene family of B. carinata was primarily underwent purification selection in evolutionary selection. The promoter region of most BcaCPK genes contained various stress-related cis-acting elements. qRT-PCR analysis of 12 selected CPK genes conducted under cadmium and salt stress at various points revealed distinct expression patterns among different family members in response to different stresses. Specifically, the expression levels of BcaCPK2.B01a, BcaCPK16.B02b, and BcaCPK26.B02 were down-regulated under both stresses, whereas the expression levels of other members were significantly up-regulated under at least one stress.

CONCLUSION

This study systematically identified the BcaCPK gene family in B. carinata, which contributes to a better understanding the CPK genes in this species. The findings also serve as a reference for analyzing stress responses, particularly in relation to cadmium and salt stress in B. carinata.

Identification, Evolutionary Dynamics, and Gene Expression Patterns of the ACP Gene Family in Responding to Salt Stress in Brassica Genus

Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this study, we conducted a comprehensive analysis and identified a total of 120 ACP genes across six species in the Brassica genus. Among these, there were 27, 26, and 30 ACP genes in the allotetraploid B. napus, B. juncea, and B. carinata, respectively, and 14, 13, and 10 ACP genes in the diploid B. rapa, B. oleracea, and B. nigra, respectively. These ACP genes were further classified into six subclades, each containing conserved motifs and domains. Interestingly, the majority of ACP genes exhibited high conservation among the six species, suggesting that the genome evolution and polyploidization processes had relatively minor effects on the ACP gene family. The duplication modes of the six Brassica species were diverse, and the expansion of most ACPs in Brassica occurred primarily through dispersed duplication (DSD) events. Furthermore, most of the ACP genes were under purifying selection during the process of evolution. Subcellular localization experiments demonstrated that ACP genes in Brassica species are localized in chloroplasts and mitochondria. Cis-acting element analysis revealed that most of the ACP genes were associated with various abiotic stresses. Additionally, RNA-seq data revealed differential expression levels of BnaACP genes across various tissues in B. napus, with particularly high expression in seeds and buds. qRT-PCR analysis further indicated that BnaACP genes play a significant role in salt stress tolerance. These findings provide a comprehensive understanding of ACP genes in Brassica plants and will facilitate further functional analysis of these genes.

Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U

The interaction and coevolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, 2 billion yr later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance versus cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features 3 diploid species that together have formed 3 separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in Brassica carinata (BBCC) and 2 varieties of Brassica juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these 2 separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the Brassica nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.

Phylogenomic curation of Ovate Family Proteins (OFPs) in the U's Triangle of Brassica L. indicates stress-induced growth modulation

The Ovate Family Proteins (OFPs) gene family houses a class of proteins that are involved in regulating plant growth and development. To date, there is no report of the simultaneous functional characterization of this gene family in all members of U's Triangle of Brassica. Here, we retrieved a combined total of 256 OFP protein sequences and analyzed their chromosomal localization, gene structure, conserved protein motif domains, and the pattern of cis-acting regulatory elements. The abundance of light-responsive elements like G-box, MRE, and GT1 motif suggests that OFPs are sensitive to the stimuli of light. The protein-protein interaction network analysis revealed that OFP05 and its orthologous genes were involved in regulating the process of transcriptional repression through their interaction with homeodomain transcription factors like KNAT and BLH. The presence of domains like DNA binding 2 and its superfamily speculated the involvement of OFPs in regulating gene expression. The biotic and abiotic stress, and the tissue-specific expression analysis of the RNA-seq datasets revealed that some of the genes such as BjuOFP30, and BnaOFP27, BolOFP11, and BolOFP10 were highly upregulated in seed coat at the mature stage and roots under various chemical stress conditions respectively which suggests their crucial role in plant growth and development processes. Experimental validation of prominent BnaOFPs such as BnaOFP27 confirmed their involvement in regulating gene expression under salinity, heavy metal, drought, heat, and cold stress. The GO and KEGG pathway enrichment analysis also sheds light on the involvement of OFPs in regulating plant growth and development. These findings have the potential to serve as a forerunner for future studies in terms of functionally diverse analysis of the OFP gene family in Brassica and other plant species.

Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations

Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.

Identification of the High-Affinity Potassium Transporter Gene Family (HKT) in Brassica U-Triangle Species and Its Potential Roles in Abiotic Stress in Brassica napus L

Members of the high-affinity potassium transporter (HKT) protein family regulate the uptake and homeostasis of sodium and potassium ions, but little research describes their roles in response to abiotic stresses in rapeseed (Brassica napus L.). In this study, we identified and characterized a total of 36 HKT genes from the species comprising the triangle of U model (U-triangle species): B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinata. We analyzed the phylogenetic relationships, gene structures, motif compositions, and chromosomal distributions of the HKT family members of rapeseed. Based on their phylogenetic relationships and assemblage of functional domains, we classified the HKT members into four subgroups, HKT1;1 to HKT1;4. Analysis of the nonsynonymous substitutions (Ka), synonymous substitutions (Ks), and the Ka/Ks ratios of HKT gene pairs suggested that these genes have experienced strong purifying selective pressure after duplication, with their evolutionary relationships supporting the U-triangle theory. Furthermore, the expression profiles of BnaHKT genes varies among potassium, phytohormone and heavy-metal treatment. Their repression provides resistance to heavy-metal stress, possibly by limiting uptake. Our results systematically reveal the characteristics of HKT family proteins and their encoding genes in six Brassica species and lay a foundation for further exploration of the role of HKT family genes in heavy-metal tolerance.

The high-quality sequencing of the Brassica rapa 'XiangQingCai' genome and exploration of genome evolution and genes related to volatile aroma

'Vanilla' (XQC, brassica variety chinensis) is an important vegetable crop in the Brassica family, named for its strong volatile fragrance. In this study, we report the high-quality chromosome-level genome sequence of XQC. The assembled genome length was determined as 466.11 Mb, with an N50 scaffold of 46.20 Mb. A total of 59.50% repetitive sequences were detected in the XQC genome, including 47 570 genes. Among all examined Brassicaceae species, XQC had the closest relationship with B. rapa QGC ('QingGengCai') and B. rapa Pakchoi. Two whole-genome duplication (WGD) events and one recent whole-genome triplication (WGT) event occurred in the XQC genome in addition to an ancient WGT event. The recent WGT was observed to occur during 21.59-24.40 Mya (after evolution rate corrections). Our findings indicate that XQC experienced gene losses and chromosome rearrangements during the genome evolution of XQC. The results of the integrated genomic and transcriptomic analyses revealed critical genes involved in the terpenoid biosynthesis pathway and terpene synthase (TPS) family genes. In summary, we determined a chromosome-level genome of B. rapa XQC and identified the key candidate genes involved in volatile fragrance synthesis. This work can act as a basis for the comparative and functional genomic analysis and molecular breeding of B. rapa in the future.

Sequencing and Analysis of Complete Chloroplast Genomes Provide Insight into the Evolution and Phylogeny of Chinese Kale (Brassica oleracea var. alboglabra)

Chinese kale is a widely cultivated plant in the genus Brassica in the family Brassicaceae. The origin of Brassica has been studied extensively, but the origin of Chinese kale remains unclear. In contrast to Brassica oleracea, which originated in the Mediterranean region, Chinese kale originated in southern China. The chloroplast genome is often used for phylogenetic analysis because of its high conservatism. Fifteen pairs of universal primers were used to amplify the chloroplast genomes of white-flower Chinese kale (Brassica oleracea var. alboglabra cv. Sijicutiao (SJCT)) and yellow-flower Chinese kale (Brassica oleracea var. alboglabra cv. Fuzhouhuanghua (FZHH)) via PCR. The lengths of the chloroplast genomes were 153,365 bp (SJCT) and 153,420 bp (FZHH) and both contained 87 protein-coding genes and eight rRNA genes. There were 36 tRNA genes in SJCT and 35 tRNA genes in FZHH. The chloroplast genomes of both Chinese kale varieties, along with eight other Brassicaceae, were analyzed. Simple sequence repeats, long repeats, and variable regions of DNA barcodes were identified. An analysis of inverted repeat boundaries, relative synonymous codon usage, and synteny revealed high similarity among the ten species, albeit the slight differences that were observed. The Ka/Ks ratios and phylogenetic analysis suggest that Chinese kale is a variant of B. oleracea. The phylogenetic tree shows that both Chinese kale varieties and B. oleracea var. oleracea were clustered in a single group. The results of this study suggest that white and yellow flower Chinese kale comprise a monophyletic group and that their differences in flower color arose late in the process of artificial cultivation. Our results also provide data that will aid future research on genetics, evolution, and germplasm resources of Brassicaceae.

Genome-wide characterization of the VQ genes in Triticeae and their functionalization driven by polyploidization and gene duplication events in wheat

Valine-glutamine motif-containing (VQ) proteins are transcriptional cofactors widely involved in plant growth, development, and response to various stresses. Although the VQ family has been genome-wide identified in some species, but the knowledge regarding duplication-driven functionalization of VQ genes among evolutionarily related species is still lacking. Here, 952 VQ genes have been identified from 16 species, emphasizing seven Triticeae species including the bread wheat. Comprehensive phylogenetic and syntenic analyses allow us to establish the orthologous relationship of VQ genes from rice (Oryza sativa) to bread wheat (Triticum aestivum). The evolutionary analysis revealed that whole-genome duplication (WGD) drives the expansion of OsVQs, while TaVQs expansion is associated with a recent burst of gene duplication (RBGD). We also analyzed the motif composition and molecular properties of TaVQ proteins, enriched biological functions, and expression patterns of TaVQs. We demonstrate that WGD-derived TaVQs have become divergent in both protein motif composition and expression pattern, while RBGD-derived TaVQs tend to adopt specific expression patterns, suggesting their functionalization in certain biological processes or in response to specific stresses. Furthermore, some RBGD-derived TaVQs are found to be associated with salt tolerance. Several of the identified salt-related TaVQ proteins were located in the cytoplasm and nucleus and their salt-responsive expression patterns were validated by qPCR analysis. Yeast-based functional experiments confirmed that TaVQ27 may be a new regulator to salt response and regulation. Overall, this study lays the foundation for further functional validation of VQ family members within the Triticeae species.

Transcriptional Interactions of Single B-Subgenome Chromosome with C-Subgenome in B. oleracea-nigra Additional Lines

Serial monosomic alien addition lines (MAALs) provide an ideal system to elucidate the transcriptomic interactions between the alien chromosomes and recipient genome under aneuploidy. Herein, five available Brassica oleracea-nigra MAALs (CCB1, CCB4, CCB5, CCB6, CCB8), their derived B. oleracea plants (non-MAALs), and two parents were analyzed for their gene expressions by using high-throughput technology. Compared to parental B. oleracea, all MAALs showed various numbers of DEGs, but CCB8 gave much higher DEGs; the number of downregulated DEGs was slightly higher than the number of upregulated ones, except for in relation to CCB8. All derived B. oleracea plants also gave certain numbers of DEGs, despite these being much lower than in the respective MAALs. Compared to B. nigra, in all five MAALs more DEGs were downregulated than upregulated. Trans-effects were likely more prevailing than cis-effects, and these DEGs were predominantly associated with material transport by dysregulating the cellular component. Meanwhile, the orthologous genes on alien chromosomes could only play a feeble compensatory role for those gene pairs in C-subgenome, and different levels of the expressed genes had a greater tendency towards downregulation. These results revealed transcriptional aneuploidy response patterns between two genomes and suggested that cis- and trans-mechanisms synergistically regulated alien gene transcriptions after distant hybridization.

Systematic analysis of MADS-box gene family in the U's triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus

MADS-box transcription factors play an important role in regulating floral organ development and participate in environmental responses. To date, the MADS-box gene family has been widely identified in Brassica rapa (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus); however, there are no analogous reports in Brassica nigra (B. nigra), Brassica juncea (B. juncea), and Brassica carinata (B. carinata). In this study, a whole-genome survey of the MADS-box gene family was performed for the first time in the triangle of U species, and a total of 1430 MADS-box genes were identified. Based on the phylogenetic relationship and classification of MADS-box genes in Arabidopsis thaliana (A. thaliana), 1430 MADS-box genes were categorized as M-type subfamily (627 genes), further divided into Mα, Mβ, Mγ, and Mδ subclades, and MIKC-type subfamily (803 genes), further classified into 35 subclades. Gene structure and conserved protein motifs of MIKC-type MADS-box exhibit diversity and specificity among different subclades. Comparative analysis of gene duplication events and syngenic gene pairs among different species indicated that polyploidy is beneficial for MIKC-type gene expansion. Analysis of transcriptome data within diverse tissues and stresses in B. napus showed tissue-specific expression of MIKC-type genes and a broad response to various abiotic stresses, particularly dehydration stress. In addition, four representative floral organ mutants (wtl, feml, aglf-2, and aglf-1) in the T0 generation were generated by editing four AGAMOUS (BnaAG) homoeologs in B. napus that enriched the floral organ variant phenotype. In brief, this study provides useful information for investigating the function of MADS-box genes and contributes to revealing the regulatory mechanisms of floral organ development in the genetic improvement of new varieties.

Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication

The genus Brassica contains a diverse group of important vegetables and oilseed crops. Genome sequencing has been completed for the six species (B. rapa, B. oleracea, B. nigra, B. carinata, B. napus, and B. juncea) in U's triangle model. The purpose of the study is to investigate whether positively and negatively selected genes (PSGs and NSGs) affect gene feature and function differentiation of Brassica tetraploids in their evolution and domestication. A total of 9,701 PSGs were found in the A, B and C subgenomes of the three tetraploids, of which, a higher number of PSGs were identified in the C subgenome as comparing to the A and B subgenomes. The PSGs of the three tetraploids had more tandem duplicated genes, higher single copy, lower multi-copy, shorter exon length and fewer exon number than the NSGs, suggesting that the selective modes affected the gene feature of Brassica tetraploids. The PSGs of all the three tetraploids enriched in a few common KEGG pathways relating to environmental adaption (such as Phenylpropanoid biosynthesis, Riboflavin metabolism, Isoflavonoid biosynthesis, Plant-pathogen interaction and Tropane, piperidine and pyridine alkaloid biosynthesis) and reproduction (Homologous recombination). Whereas, the NSGs of the three tetraploids significantly enriched in dozens of biologic processes and pathways without clear relationships with evolution. Moreover, the PSGs of B. carinata were found specifically enriched in lipid biosynthesis and metabolism which possibly contributed to the domestication of B. carinata as an oil crop. Our data suggest that selective modes affected the gene feature of Brassica tetraploids, and PSGs contributed in not only the evolution but also the domestication of Brassica tetraploids.

Sinapis genomes provide insights into whole-genome triplication and divergence patterns within tribe Brassiceae

Sinapis alba and Sinapis arvensis are mustard crops within the Brassiceae tribe of the Brassicaceae family, and represent an important genetic resource for crop improvement. We performed the de novo assembly of Brassica nigra, S. alba, and S. arvensis, and conducted comparative genomics to investigate the pattern of genomic evolution since an ancient whole-genome triplication event. Both Sinapis species retained evidence of the Brassiceae whole-genome triplication approximately 20.5 million years ago (Mya), with subgenome dominance observed in gene density, gene expression, and selective constraint. While S. alba diverged from the ancestor of Brassica and Raphanus at approximately 12.5 Mya, the divergence time of S. arvensis and B. nigra was approximately 6.5 Mya. S. arvensis and B. nigra had greater collinearity compared with their relationship to either Brassica rapa or Brassica oleracea. Two chromosomes of S. alba (Sal03 and Sal08) were completely collinear with two ancestral chromosomes proposed in the Ancestral Crucifer Karyotype (ACK) genomic block model, the first time this has been observed in the Brassiceae. These results are consistent with S. alba representing a relatively ancient lineage of the species evolved from the common ancestor of tribe Brassiceae, and suggest that the phylogeny of the Brassica and Sinapis genera requires some revision. Our study provides new insights into the genome evolution and phylogenetic relationships of Brassiceae and provides genomic information for genetic improvement of these plants.

Investigation of Brassica and its relative genomes in the post-genomics era

The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.