Complete Mitochondrial Genome of Eruca sativa Mill. (Garden Rocket)

Eruca sativa (Cruciferae family) is an ancient crop of great economic and agronomic importance. Here, the complete mitochondrial genome of Eruca sativa was sequenced and annotated. The circular molecule is 247 696 bp long, with a G+C content of 45.07%, containing 33 protein-coding genes, three rRNA genes, and 18 tRNA genes. The Eruca sativa mitochondrial genome may be divided into six master circles and four subgenomic molecules via three pairwise large repeats, resulting in a more dynamic structure of the Eruca sativa mtDNA compared with other cruciferous mitotypes. Comparison with the Brassica napus MtDNA revealed that most of the genes with known function are conserved between these two mitotypes except for the ccmFN2 and rrn18 genes, and 27 point mutations were scattered in the 14 protein-coding genes. Evolutionary relationships analysis suggested that Eruca sativa is more closely related to the Brassica species and to Raphanus sativus than to Arabidopsis thaliana.     

Factors affecting the use of chloramphenicol acetyltransferase as a marker for Brassica genetic transformation

The CAT gene which codes for the enzyme chloramphenicol acetyltransferase was found to be ineffective as a reporter gene in cells and tissues of Brassica species. High levels of endogenous CAT activity were found to be widespread among this genus and did not appear to be distributed in a tissue- or cell-specific manner. Moreover, the presence of an inhibitor of CAT activity was discovered in Brassica napus and Brassica juncea. This inhibitor appeared to act selectively on bacterial CAT in transgenic plants. These findings provided an explanation for difficulties experienced in the detection of transgenic CAT activity in B. napus.     

Flavonol glycosides in Brassica and Sinapis

The 7-glucosides and 3,7-diglucosides of kaempferol and isorhamnetin were identified in leaves and flowers of Sinapis arvensis. Additionally, the 3-sophoroside-7-glucosides of kaempferol, quercetin and isorhamnetin were found in leaves of S. arvensis and Brassica oleracea. Two dimensional surveys of leaf extracts of 27 species and cultivars of Brassica and Sinapis showed that the same pattern occurred in most species. B. tournefortii and S. flexuosa were exceptional in having flavonol 3-monosides and 3-diglycosides instead. The results suggest that it is the glycosidic patterns, rather than the distribution of the flavonol aglycones, which are likely to be of taxonomic value for distinguishing groups of species or genera within the Cruciferae.     

Codon Usage in Brassica Genes

We have examined codon bias in 20 Brassica gene sequences collected from the literature. A comparison with the codon usage profile derived from 207 plant genes showed that Brassica genes distinctly differ from the plant genes with respect to Gly, Asp, Arg, lie, Try, Thr, Leu and Gin. Codon preferences for various amino acids did not differ among the three Brassica species, B. napus, B. oleracea and B. campestris considered in the present analysis. G ending codons for Thr, Ala, Pro and Ser are avoided by Brassica genes as in plant genes, in general. However, the avoidance of CG and TA doublets in Brassica genes is less than that observed in plant genes.     

Sequence Organization of Simple, Highly Repetitive DNA Elements in Brassica species

The amphidiploid (AACC) nuclear genome of Brassica napus (oil-seedrape) contains c. 5 ? 10⁵ copies of a simple, highly repetitiveDNA element; each repeat is 176 or 177 base pairs long and isdefined by Hind III cutting sites. The diploid (AA) Brassicacampestris (turnip) possesses a very similar repetitive DNA,the consensus sequence of which does not differ from that inB. napus. The 176/177 bp unit consists of three 59 bp sub-units,defined by vestigial EcoRII sites. Analysis of the distributionof variants from consensus in adjacent and non-adjacent unitsprovides evidence for homogenization of sequences by the fixationof independent mutations and for tandem duplication of units.Within units, there is also evidence for inversion and tandemduplication of short (5–8 bp) motifs. Previously published data show that 176/177 base pair repetitiveDNA elements, defined by Hind III cutting sites, are also presentin Sinapis and Raphanus. There is a sequence homology betweenBrassica and Sinapis, and between Brassica and Raphanus, of75%. Sequence homology between Raphanus and Sinapis is 73%. Key words: Repetitive DNA, Brassica, Cruciferae     

The Mitochondrial Genome of Raphanus sativus and Gene Evolution of Cruciferous Mitochondrial Types

To explore the mitochondrial genes of the Cruciferae family, the mitochondrial genome of Raphanus sativus (sat) was sequenced and annotated. The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes, three rRNA genes and 17 tRNA genes. The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length, which may mediate genome reorga-nization into two sub-genomic circles, with predicted sizes of 124.8 kb and 115.0 kb, respectively. Furthermore, gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type (mitotype), together with six other re-ported mitotypes. The cruciferous mitochondrial genomes have maintained almost the same set of functional genes. Compared with Cycas taitungensis (a representative gymnosperm), the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes, but acquired six chloroplast-like tRNAs. Among the Cruciferae, to maintain the same set of genes that are necessary for mitochondrial function, the exons of the genes have changed at the lowest rates, as indicated by the numbers of single nucleotide polymorphisms. The open reading frames (ORFs) of unknown function in the cruciferous genomes are not conserved. Evolutionary events, such as mutations, genome reorganizations and sequence insertions or deletions (indels), have resulted in the non- conserved ORFs in the cruciferous mitochondrial genomes, which is becoming significantly different among mitotypes. This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family. It revealed significant variation in ORFs and the causes of such variation.     

Cloning of TTG1 gene and PCR identification of genomes A,B and C in Brassica species

Arabidopsis Transparent Testa Glabra 1 (TTG1) genes were cloned from three diploid Brassica species (B. rapa, B. nigra and B. oleracea) and two amphidiploids species (B. juncea and B. carinata) by homology cloning. TTG1 homologues identified in all the accessions of the investigated species had a coding sequence of 1,014 bp. One copy was obtained from each diploid species and two copies from each amphidiploid species. Combined analysis of the TTG1 sequences cloned in this study with those obtained from public databases demonstrated that three, forty-five and seven nucleotides were specific variations in TTG1 genes from genomes A, B and C, respectively. Primers designed with genome-specific nucleotide variations were able to distinguish among TTG1 genes originating from genomes A, B and C in Brassica. Therefore, the TTG1 gene could serve as a candidate marker gene to detect the pollen flow of Brassica and provide an alternative method for the detection of pollen drift and risk assessment of gene flow in Brassica species.     

Comparative Analysis between Homoeologous Genome Segments of Brassica napus and Its Progenitor Species Reveals Extensive Sequence-Level Divergence

Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent segments of the Brassica A genome as found in Brassica rapa and Brassica napus and the corresponding segments of the Brassica C genome as found in Brassica oleracea and B. napus. Analysis of synonymous base substitution rates within modeled genes revealed a relatively broad range of times (0.12 to 1.37 million years ago) since the divergence of orthologous genome segments as represented in B. napus and the diploid species. Similar, and consistent, ranges were also identified for single nucleotide polymorphism and insertion-deletion variation. Genes conserved across the Brassica genomes and the homoeologous segments of the genome of Arabidopsis thaliana showed almost perfect collinearity. Numerous examples of apparent transduplication of gene fragments, as previously reported in B. oleracea, were observed in B. rapa and B. napus, indicating that this phenomenon is widespread in Brassica species. In the majority of the regions studied, the C genome segments were expanded in size relative to their A genome counterparts. The considerable variation that we observed, even between the different versions of the same Brassica genome, for gene fragments and annotated putative genes suggest that the concept of the pan-genome might be particularly appropriate when considering Brassica genomes.     

Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.     

Chemical composition and ultrastructure of the epicuticular wax in three lines of Brassica napus (L)

The epicuticular wax in three lines of Brassica napus (rape) has been investigated and the detailed chemistry and ultrastructure of the waxes examined. A distinct chemical make-up has been found for all three waxes which is correlated with three distinct crystallite structures. A tentative scheme for classification of Brassica wax mutants is described in which the two newly analysed rape mutants can be placed. Mass spectral analysis of all wax components confirms and extends previous ideas about the chemistry of Brassica waxes.     

Molecular mechanism of manipulating seed coat coloration in oilseed Brassica species

Yellow seed is a desirable characteristic for the breeding of oilseed Brassica crops, but the manifestation of seed coat color is very intricate due to the involvement of various pigments, the main components of which are flavonols, proanthocyanidin (condensed tannin), and maybe some other phenolic relatives, like lignin and melanin. The focus of this review is to examine the genetics mechanism regarding the biosynthesis and regulation of these pigments in the seed coat of oilseed Brassica. This knowledge came largely from recent researches on the molecular mechanism of TRANSPARENT TESTA (tt) and similar mutations in the ancestry model plant of Brassica, Arabidopsis. Some key enzymes in the flavonoid (flavonols and proanthocyanidin) biosynthetic pathway have been characterized in tt mutants. Some orthologs to these TRANSPARENT TESTA genes have also been cloned in Brassica species. However, it is suggested that some alterative metabolism pathways, including lignin and melanin, might also be involved in seed color manifestation. Polyphenol oxidases, such as laccase, tyrosinase, or even peroxidase, participate in the oxidation step in proanthocyanidin, lignin, and melanin biosynthesis. Moreover, some researches also suggested that melanic pigment in black-seeded Brassica was several fold higher than in yellow-seeded Brassica. Although more experiments are required to evaluate the importance of lignin and melanin in seed coat browning, the current results suggest that the flavonols and proanthocyanidin are not the only roles affecting seed color.     

Characterization and expression patterns of small RNAs in synthesized Brassica hexaploids

Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. We used high-throughput sequencing to compare miRNA expression profiles between Brassica hexaploid and its parents. A total of 613, 784 and 742 known miRNAs were identified in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. We detected 618 miRNAs were differentially expressed (log₂Ratio ≥ 1, P ≤ 0.05) between Brassica hexaploid and its parents, and 425 miRNAs were non-additively expressed in Brassica hexaploid, which suggest a trend of non-additive miRNA regulation following hybridization and polyploidization. Remarkably, majority of the non-additively expressed miRNAs in the Brassica hexaploid are repressed, and there was a bias toward repression of B. rapa miRNAs, which is consistent with the progenitor-biased gene repression in the synthetic allopolyploids. In addition, we identified 653 novel mature miRNAs in Brassica hexaploid and its parents. Finally, we found that almost all the non-additive accumulation of siRNA clusters exhibited a low-parent pattern in Brassica hexaploid. Non-additive small RNA regulation is involved in a range of biological pathways, probably providing a driving force for variation and adaptation in allopolyploids.     

Beneficial endophytic microorganisms of Brassica – A review

Brassica species display enormous diversity and subsequently provide the widest assortment of products used by man from a single plant genus. Many species are important for agriculture, horticulture, in bioremediation, as medicines, soil conditioners, composting crops, and in the production of edible and industrial oils such as liquid fuels and lubricants. Many wild Brassica relatives possess a number of useful agronomic traits, including beneficial microbial endophytes that could be incorporated into breeding programs. Endophytes of Brassica, and/or their metabolites, have been demonstrated to improve and promote plant growth; increase yield; reduce disease symptoms caused by plant pathogens; reduce herbivory from insect pests; remove contaminants from soil; improve plant performance under extreme conditions of temperature and water availability; solubilise phosphate and contribute assimilable nitrogen to their hosts. Brassica napus (oilseed rape) and Brassica oleracea var. botrytis (broccoli and cauliflower) are the most economically important species of Brassica worldwide. These commercial crops are attacked by a wide range of pathogens and insect pests that are responsible for millions of dollars in lost revenue, with current control options offering little mitigation. No alternative control products are available for the Brassica industry, although it has been well documented in the literature that the use of endophytic microorganisms can offer beneficial traits to their host plants, including pest and disease resistance. The aim of this review is to describe the literature concerning beneficial microbial endophytes and their prospects to enhance or provide additional traits to their Brassica host species.     

The response of transgenic <Emphasis Type="Italic">Brassica</Emphasis> species to salt stress: a review

Salt stress is considered one of the main abiotic factors to limit crop growth and productivity by affecting morpho-physiological and biochemical processes. Genetically, a number of salt tolerant Brassica varieties have been developed and introduced, but breeding of such varieties is time consuming. Therefore, current focus is on transgenic technology, which plays an important role in the development of salt tolerant varieties. Various salt tolerant genes have been characterized and incorporated into Brassica. Therefore, such genetic transformation of Brassica species is a significant step for improvement of crops, as well as conferring salt stress resistance qualities to Brassica species. Complete genome sequencing has made the task of genetically transforming Brassica species easier, by identifying desired candidate genes. The present review discusses relevant information about the principles which should be employed to develop transgenic Brassica species, and also will recommend tools for improved tolerance to salinity.     

Salinity-induced expression of pyrrolline-5-carboxylate synthetase determine salinity tolerance in Brassica spp

The objective of the present study was to assess the role of salinity-induced expression of pyrrolline 5-carboxylate synthetase (P5CS), P5CS activity, and proline accumulation on salinity tolerance in Brassica genotypes. A pot culture experiment was conducted with four Brassica genotypes viz. CS 52, CS 54, Varuna, (B. juncea) and T 9 (B. campestris) under control and two salinity levels, i.e., 1.65, 4.50 and 6.76?dS?m^?1. Proline contents increased with increasing levels of salinity, and the highest content were recorded at post-flowering stage in CS 52 and CS 54. Activity of P5CS recorded at flowering stage was highest at higher level of salinity, with CS 52 and CS 54 recording highest activity. Gene expression of P5CS, which regulates the synthesis of proline, was higher in CS 52 and CS 54 under salt stress than Varuna and T 9. Comparison of partial nucleotide as well as amino acid sequence showed conserved domains, and inter and intra generic relatedness of these genes. The study suggests that salinity-induced expression of P5CS, pyrrolline-phosphate synthetase activity and proline accumulation may serve as one of the mechanism of salinity stress tolerance in Brassica genotypes.     

A cDNA clone encoding Brassica calmodulin

A 834 bp cDNA encoding calmodulin (CaM) has been isolated from Brassica juncea. On Northern analysis this cDNA hybridises this cDNA to mRNAs of about 0.9 kb in leaf, silique and peduncle. Genomic Southern analysis indicates the presence of a CaM multigene family in Brassica juncea. Comparison of the predicted amino acid sequence of Brassica CaM with that of Arabidopsis CaM ACaM-2 and ACaM-3 showed 100% homology, which is not unusual, since both plants belong to the family Cruciferae. In situ hybridisation studies on Brassica seedlings using a digoxigenin-labelled RNA probe showed that high levels of CaM mRNA were detected in the leaf primordia and the shoot apical meristem, and to a lesser degree, in the zone of root elongation of the root tip. The occurrence of a higher rate of cell division and growth in these regions than its surrounding tissue may possibly be related to higher levels of CaM mRNA.     

Polymorphism of the S -locus glycoprotein gene (SLG ) and the S -locus related gene (SLR1 ) in Raphanus sativus L. and self-incompatible ornamental plants in the Brassicaceae

The S-locus glycoprotein gene, SLG, which participates in the pollen-stigma interaction of self-incompatibility, and its unlinked homologue, SLR1, were analyzed in Raphanus sativus and three self-incompatible ornamental plants in the Brassicaceae. Among twenty-nine inbred lines of R. sativus, eighteen S haplotypes were identified on the basis of DNA polymorphisms detected by genomic Southern analysis using Brassica SLG probes. DNA fragments of SLG alleles specifically amplified from eight S haplotypes by PCR with class I SLG-specific primers showed different profiles following polyacrylamide gel electrophoresis, after digestion with a restriction endonuclease. The nucleotide sequences of the DNA fragments of these eight R. sativus SLG alleles were determined. Degrees of similarity of the nucleotide sequences to a Brassica SLG (S? ⁶ SLG) ranged from 85.6% to 91.9%. Amino acid sequences deduced from these had the twelve conserved cysteine residues and the three hypervariable regions characteristic of Brassica SLGs. Phylogenetic analysis of the SLG sequences from Raphanus and Brassica revealed that the Raphanus SLGs did not form an independent cluster, but were dispersed in the tree, clustering together with Brassica SLGs. These results suggest that diversification of the SLG alleles of Raphanus and Brassica occurred before differentiation of these genera. Although SLR1 sequences from Orychophragmus violaceus were shown to be relatively closely related to Brassica and Raphanus SLR1 sequences, DNA fragments that are highly homologous to the Brassica SLG were not detected in this species. Two other ornamental plants in the Brassicaceae, which are related more distantly to Brassica than Orychophragmus, also lacked sequences highly homologous to Brassica SLG genes. The evolution of self-incompatibility in the Brassicaceae is discussed.     

In Vitro Activity of Glucosinolates and Their Degradation Products against Brassica-Pathogenic Bacteria and Fungi

Glucosinolates (GSLs) are secondary metabolites found in Brassica vegetables that confer on them resistance against pests and diseases. Both GSLs and glucosinolate hydrolysis products (GHPs) have shown positive effects in reducing soil pathogens. Information about their in vitro biocide effects is scarce, but previous studies have shown sinigrin GSLs and their associated allyl isothiocyanate (AITC) to be soil biocides. The objective of this work was to evaluate the biocide effects of 17 GSLs and GHPs and of leaf methanolic extracts of different GSL-enriched Brassica crops on suppressing in vitro growth of two bacterial (Xanthomonas campestris pv. campestris and Pseudomonas syringae pv. maculicola) and two fungal (Alternaria brassicae and Sclerotinia scletoriorum) Brassica pathogens. GSLs, GHPs, and methanolic leaf extracts inhibited the development of the pathogens tested compared to the control, and the effect was dose dependent. Furthermore, the biocide effects of the different compounds studied were dependent on the species and race of the pathogen. These results indicate that GSLs and their GHPs, as well as extracts of different Brassica species, have potential to inhibit pathogen growth and offer new opportunities to study the use of Brassica crops in biofumigation for the control of multiple diseases.     

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.