The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids.

Polyploidization is important to the evolution of plants. Subgenome dominance is a distinct phenomenon associated with most allopolyploids. A gene on the dominant subgenome tends to express to higher RNA levels in all organs as compared to the expression of its syntenic paralogue (homoeolog). The mechanism that underlies the formation of subgenome dominance remains unknown, but there is evidence for the involvement of transposon/DNA methylation density differences nearby the genes of parents as being causal. The subgenome with lower density of transposon and methylation near genes is positively associated with subgenome dominance. Here, we generated eight generations of allotetraploid progenies from the merging of parental genomes Brassica rapa and Brassica oleracea. We found that transposon/methylation density differ near genes between the parental (rapa:oleracea) existed in the wide hybrid, persisted in the neotetraploids (the synthetic Brassica napus), but these neotetraploids expressed no expected subgenome dominance. This absence of B. rapa vs. B. oleracea subgenome dominance is particularly significant because, while there is no negative relationship between transposon/methylation level and subgenome dominance in the neotetraploids, the more ancient parental subgenomes for all Brassica did show differences in transposon/methylation densities near genes and did express, in the same samples of cells, biased gene expression diagnostic of subgenome dominance. We conclude that subgenome differences in methylated transposon near genes are not sufficient to initiate the biased gene expressions defining subgenome dominance. Our result was unexpected, and we suggest a "nuclear chimera" model to explain our data.

Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus.

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.

BRAD V3.0: an upgraded Brassicaceae database.

The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.

Oxygen-Activated Boron Nitride for Selective Photocatalytic Coupling of Methanol to Ethylene Glycol.

The controllable photocatalytic C-C coupling of methanol to produce ethylene glycol (EG) is a highly desirable but challenging objective for replacing the current energy-intensive thermocatalytic process. Here, we develop a metal-free porous boron nitride catalyst that demonstrates exceptional selectivity in the photocatalytic production of EG from methanol under mild conditions. Comprehensive experiments and calculations are conducted to thoroughly investigate the reaction mechanism, revealing that the OB3 unit in the porous BN plays a critical role in the preferential activation of C-H bond in methanol to form ⋅CH2OH via a concerted proton-electron transfer mechanism. More prominent energy barriers are observed for the further dehydrogenation of the ⋅CH2OH intermediate on the OB3 unit, inhibiting the formation of some other by-products during the catalytic process. Additionally, a small downhill energy barrier for the coupling of ⋅CH2OH in the OB3 unit promotes the selective generation of EG. This study provides valuable insights into the underlying mechanisms and can serve as a guide for the design and optimization of photocatalysts for efficient and selective EG production under mild conditions.

A cluster of transcripts identifies a transition stage initiating leafy head growth in heading morphotypes of Brassica.

Leaf heading is an important and economically valuable horticultural trait in many vegetables. The formation of a leafy head is a specialized leaf morphogenesis characterized by the emergence of the enlarged incurving leaves. However, the transcriptional regulation mechanisms underlying the transition to leaf heading remain unclear. We carried out large-scale time-series transcriptome assays covering the major vegetative growth phases of two headingBrassica crops, Chinese cabbage and cabbage, with the non-heading morphotype Taicai as the control. A regulatory transition stage that initiated the heading process is identified, accompanied by a developmental switch from rosette leaf to heading leaf in Chinese cabbages. This transition did not exist in the non-heading control. Moreover, we reveal that the heading transition stage is also conserved in the cabbage clade. Chinese cabbage acquired through domestication a leafy head independently from the origins of heading in other cabbages; phylogenetics supports that the ancestor of all cabbages is non-heading. The launch of the transition stage is closely associated with the ambient temperature. In addition, examination of the biological activities in the transition stage identified the ethylene pathway as particularly active, and we hypothesize that this pathway was targeted for selection for domestication to form the heading trait specifically in Chinese cabbage. In conclusion, our findings on the transcriptome transition that initiated the leaf heading in Chinese cabbage and cabbage provide a new perspective for future studies of leafy head crops.

A near-complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres.

Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near-complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near-complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.

A complex locus regulates highly lobed-leaf formation in Brassica juncea.

KEY MESSAGE: Lineage-specific evolution of RCO was described in Brassicaceae. BjRCO.1 and BjRCO.2 within the complex locus regulated highly lobed-leaf formation in Brassica juncea. RCO regulates the formation of lobed leaves in Brassicaceae species. RCO originated from the duplication of LMI1-type sequences and evolved through gene duplication and loss within the Brassicaceae. However, the evolutionary process and diversification of RCO in different lineages of Brassicaceae remain unclear. Although the RCO locus in B. juncea has been associated with lobed-leaf formation, its complexity has remained largely unknown. This study involved the identification of 55 LMI1-like genes in 16 species of Brassicaceae through syntenic analysis. We classified these LMI1-like genes into two types, namely LMI1-type and RCO-type, based on their phylogenetic relationship. Additionally, we proposed two independent lineage-specific evolution routes for RCO following the divergence of Aethionema. Our findings revealed that the LMI1-like loci responsible for lobed-leaf formation in Brassica species are located on the LF subgenomes. For B. juncea (T84-66V2), we discovered that the complex locus underwent duplication through segments of nucleic acid sequence containing Exostosin-LMI1-RCO (E-R-L), resulting in the tandem presence of two RCO-type and two LMI1-type genes on chromosome A10. As additional evidence, we successfully mapped the complex locus responsible for highly lobed-leaf formation to chromosome A10 using a B. juncea F2 population, which corroborated the results of our evolutionary analysis. Furthermore, through transcriptome analysis, we clarified that BjRCO.1 and BjRCO.2 within the complex locus are functional genes involved in the regulation of highly lobed-leaf formation. The findings of this study offer valuable insights into the regulation of leaf morphology for the breeding of Brassica crops.

Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica.

Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions. To investigate the potential importance of distant contacts, we performed high-throughput chromatin conformation capture (Hi-C) experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea. We then combined our results with published Hi-C data from Arabidopsis thaliana. We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene. Genes with higher numbers of conserved noncoding sequences (CNSs) nearby were more likely to have contact with distant genes. With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity. In addition, for the genes we studied, distant contacting genes with CNSs were more likely to be transcriptionally coordinated. These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors, correlating with distant contacts to ensure coordinated expression. This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.

Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa.

Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.

Porous BN Nanofibers Enable Long-Cycling Life Sodium Metal Batteries.

Sodium metal anode, featuring high capacity, low voltage and earth abundance, is desirable for building advanced sodium-metal batteries. However, Na-ion deposition typically leads to morphological instability and notorious chemical reactivity between sodium and common electrolytes still limit its practical application. In this study, a porous BN nanofibers modified sodium metal (BN/Na) electrode is introduced for enhancing Na-ion deposition dynamics and stability. As a result, symmetrical BN/Na cells enable an impressive rate capability and markedly enhanced cycling durability over 600 h at 10 mA cm-2 . Density functional theory simulations demonstrate BN could effectively improve Na-ion adsorption and diffusion kinetics simultaneously. Finite element simulation clearly reveals the intrinsic smoothing effect of BN upon multiple Na-ion plating/stripping cycles. Coupled with a Na3 V2 O2 (PO4 )2 F/Ti3 C2 X cathode, sodium metal full cells offer an ultrastable capacity of 125/63 mA h g-1 (≈420/240 Wh kg-1 ) at 0.05/5 C rate over 500 cycles. These comprehensive analyses demonstrate the feasibility of BN/Na anode for the establishment of high-energy-density sodium-metal full batteries.

Improved Brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes.

Brassica oleracea is an important vegetable crop that has provided ancestor genomes of the two most important Brassica oil crops, Brassica napus and Brassica carinata. The current B. oleracea reference genome (JZS, also named 02-12) displays problems of large mis-assemblies, low sequence continuity, and low assembly integrity, thus limiting genomic analysis. We reported an updated assembly of the B. oleracea reference genome (JZS v2) obtained through single-molecule sequencing and chromosome conformation capture technologies. We assembled an additional 83.16 Mb of genomic sequences, and the updated genome features a contig N50 size of 2.37 Mb, representing an ~ 88-fold improvement. We detected a new round of long terminal repeat retrotransposon (LTR-RT) burst in the new assembly. Comparative analysis with the reported genome sequences of two other genomes of B. oleracea (TO1000 and HDEM) identified extensive gene order and gene structural variation. In addition, we found that the genome-specific amplification of Gypsy-like LTR-RTs occurred around 0-1 million years ago (MYA). In particular, the athila, tat, and Del families were extensively amplified in JZS around 0-1 MYA. Moreover, we identified that the syntenic genes were modified due to the insertion of genome-specific LTR-RTs. These results indicated that the genome-specific LTR-RT dynamics were associated with genome diversification in B. oleracea.

BrFLC5: a weak regulator of flowering time in Brassica rapa.

KEY MESSAGE: A splicing site mutation in BrFLC5, a non-syntenic paralogue of FLOWERING LOCUS C, was demonstrated to be related to flowering time variation in Brassica rapa. Flowering time regulation in Brassica rapa is more complex than in Arabidopsis, as there are multiple paralogues of flowering time genes in B. rapa. Brassica rapa contains four FLOWERING LOCUS C (FLC) genes, three of which are syntenic orthologues of AtFLC, while BrFLC5 is not. BrFLC1, BrFLC2, and BrFLC3 have been reported to be involved in flowering time regulation. However, BrFLC5 has thus far been deemed a pseudogene. We detected two alternative splicing patterns of BrFLC5 resulting from a nucleotide mutation (G/A) at the first nucleotide of intron 3 (named as Pi3+1(G/A)). Genotyping of BrFLC5Pi3 + 1(G/A) for 301 B. rapa accessions showed that this single nucleotide polymorphism was significantly related to flowering time variation (p < 0.001). In the collection, the frequency of the functional G allele (35.2%) was much lower than that of the nonfunctional A allele (59.1%); however, the frequency of the G allele was very high among the turnips (83.6%). An F2 population segregating at this locus was developed to analyze the genetic effect of BrFLC5. The result showed that the G allele individuals began to bolt two days later than the A allele individuals, indicating that BrFLC5 is a weak regulator of flowering time. BrFLC5 was expressed at the lowest level among the three analyzed BrFLCs. The late allele (G allele) was dominant to the early allele (A allele) at the BrFLC5 locus, which was in contrast to that of BrFLC1 and BrFLC2. This characteristic suggests that BrFLC5 would be more efficient for breeding premature bolting resistance in B. rapa.

Map-based cloning of the dominant genic male sterile Ms-cd1 gene in cabbage (Brassica oleracea).

KEY MESSAGE: Using map-based cloning, we delimited the Ms - cd1 gene responsible for the male sterile phenotype in B. oleracea to an approximately 39-kb fragment. Expression analysis suggests that a new predicted gene, a homolog of the Arabidopsis SIED1 gene, is a potential candidate gene. A dominant genic male sterile (DGMS) mutant 79-399-3 in Brassica oleracea (B. oleracea) is controlled by a single gene named Ms-cd1, which was genetically mapped on chromosome C09. The derived DGMS lines of 79-399-3 have been successfully applied in hybrid cabbage breeding and commercial hybrid seed production of several B. oleracea cultivars in China. However, the Ms-cd1 gene responsible for the DGMS has not been identified, and the molecular basis of the DGMS is unclear, which then limits its widespread application in hybrid cabbage seed production. In the present study, a large BC9 population with 12,269 individuals was developed for map-based cloning of the Ms-cd1 gene, and Ms-cd1 was mapped to a 39.4-kb DNA fragment between two InDel markers, InDel14 and InDel24. Four genes were identified in this region, including two annotated genes based on the available B. oleracea annotation database and two new predicted open reading frames (ORFs). Finally, a newly predicted ORF designated Bol357N3 was identified as the candidate of the Ms-cd1 gene. These results will be useful to reveal the molecular mechanism of the DGMS and develop more practical DGMS lines with stable male sterility for hybrid seed production in cabbage.

Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.

Subgenome dominance is an important phenomenon observed in allopolyploids after whole genome duplication, in which one subgenome retains more genes as well as contributes more to the higher expressing gene copy of paralogous genes. To dissect the mechanism of subgenome dominance, we systematically investigated the relationships of gene expression, transposable element (TE) distribution and small RNA targeting, relating to the multicopy paralogous genes generated from whole genome triplication in Brassica rapa. The subgenome dominance was found to be regulated by a relatively stable factor established previously, then inherited by and shared among B. rapa varieties. In addition, we found a biased distribution of TEs between flanking regions of paralogous genes. Furthermore, the 24-nt small RNAs target TEs and are negatively correlated to the dominant expression of individual paralogous gene pairs. The biased distribution of TEs among subgenomes and the targeting of 24-nt small RNAs together produce the dominant expression phenomenon at a subgenome scale. Based on these findings, we propose a bucket hypothesis to illustrate subgenome dominance and hybrid vigor. Our findings and hypothesis are valuable for the evolutionary study of polyploids, and may shed light on studies of hybrid vigor, which is common to most species.

Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa.

The glucosinolate biosynthetic gene AOP2 encodes an enzyme that plays a crucial role in catalysing the conversion of beneficial glucosinolates into anti-nutritional ones. In Brassica rapa, three copies of BrAOP2 have been identified, but their function in establishing the glucosinolate content of B. rapa is poorly understood. Here, we used phylogenetic and gene structure analyses to show that BrAOP2 proteins have evolved via a duplication process retaining two highly conserved domains at the N-terminal and C-terminal regions, while the middle part has experienced structural divergence. Heterologous expression and in vitro enzyme assays and Arabidopsis mutant complementation studies showed that all three BrAOP2 genes encode functional BrAOP2 proteins that convert the precursor methylsulfinyl alkyl glucosinolate to the alkenyl form. Site-directed mutagenesis showed that His356, Asp310, and Arg376 residues are required for the catalytic activity of one of the BrAOP2 proteins (BrAOP2.1). Promoter-ß-glucuronidase lines revealed that the BrAOP2.3 gene displayed an overlapping but distinct tissue- and cell-specific expression profile compared with that of the BrAOP2.1 and BrAOP2.2 genes. Quantitative real-time reverse transcription-PCR assays demonstrated that BrAOP2.1 showed a slightly different pattern of expression in below-ground tissue at the seedling stage and in the silique at the reproductive stage compared with BrAOP2.2 and BrAOP2.3 genes in B. rapa. Taken together, our results revealed that all three BrAOP2 paralogues are active in B. rapa but have functionally diverged.

Anthocyanin biosynthetic genes in Brassica rapa.

BACKGROUND: Anthocyanins are a group of flavonoid compounds. As a group of important secondary metabolites, they perform several key biological functions in plants. Anthocyanins also play beneficial health roles as potentially protective factors against cancer and heart disease. To elucidate the anthocyanin biosynthetic pathway in Brassica rapa, we conducted comparative genomic analyses between Arabidopsis thaliana and B. rapa on a genome-wide level. RESULTS: In total, we identified 73 genes in B. rapa as orthologs of 41 anthocyanin biosynthetic genes in A. thaliana. In B. rapa, the anthocyanin biosynthetic genes (ABGs) have expanded and most genes exist in more than one copy. The anthocyanin biosynthetic structural genes have expanded through whole genome and tandem duplication in B. rapa. More structural genes located upstream of the anthocyanin biosynthetic pathway have been retained than downstream. More negative regulatory genes are retained in the anthocyanin biosynthesis regulatory system of B. rapa. CONCLUSIONS: These results will promote an understanding of the genetic mechanism of anthocyanin biosynthesis, as well as help the improvement of the nutritional quality of B. rapa through the breeding of high anthocyanin content varieties.

Synchronization of non-smooth chaotic systems via an improved reservoir computing.

The reservoir computing (RC) is increasingly used to learn the synchronization behavior of chaotic systems as well as the dynamical behavior of complex systems, but it is scarcely applied in studying synchronization of non-smooth chaotic systems likely due to its complexity leading to the unimpressive effect. Here proposes a simulated annealing-based differential evolution (SADE) algorithm for the optimal parameter selection in the reservoir, and constructs an improved RC model for synchronization, which can work well not only for non-smooth chaotic systems but for smooth ones. Extensive simulations show that the trained RC model with optimal parameters has far longer prediction time than those with empirical and random parameters. More importantly, the well-trained RC system can be well synchronized to its original chaotic system as well as its replicate RC system via one shared signal, whereas the traditional RC system with empirical or random parameters fails for some chaotic systems, particularly for some non-smooth chaotic systems.

Development of self-compatible Chinese cabbage lines of Chiifu through marker-assisted selection.

The continuously refined genome assembly of the Chinese cabbage accession Chiifu is widely recognized as the reference for Brassica rapa. However, the high self-incompatibility of Chiifu limits its broader utilization. In this study, we report the development of self-compatible Chiifu lines through a meticulous marker-assisted selection (MAS) strategy, involving the substitution of the Chiifu allele of MLPK (M-locus protein kinase) with that from the self-compatible Yellow Sarson (YS). A YS-based marker (SC-MLPK) was employed to screen 841 B. rapa accessions, confirming that all eight accessions with the mlpk/mlpk (mm) genotype exhibited self-compatibility. Additionally, we designed 131 High-Resolution Melting (HRM) markers evenly distributed across the B. rapa genome as genomic background selection (GBS) markers to facilitate the introgression of self-compatibility from YS into Chiifu along with SC-MLPK. Genome background screening revealed that the BC3S1 population had a proportion of the recurrent parent genome (PR) ranging from 93.9% to 98.5%. From this population, we identified self-compatible individuals exhibiting a high number of pollen tubes penetrating stigmas (NPT) (>25) and a maximum compatibility index (CI) value of 7.5. Furthermore, we selected two individuals demonstrating significant similarity to Chiifu in both genetic background and morphological appearance, alongside self-compatibility. These selected individuals were self-pollinated to generate two novel lines designated as SC-Chiifu Lines. The development of these self-compatible Chiifu lines, together with the SC-MLPK marker and the set of HRM markers, represents valuable tools for B. rapa genetics and breeding.