Molecular phylogenetic studies of Brassica, rorippa, arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA

Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus

SRS (SHI-related sequence) transcription factors play a crucial role in plant growth, development, and abiotic stress response. Although Brassica napus (B. napus) is one of the most important oil crops in the world, the role of SRS genes in B. napus (BnSRS) has not been well investigated. Therefore, we employed a bioinformatics approach to identify BnSRS genes from genomic data and investigated their characteristics, functions, and expression patterns, to gain a better understanding of how this gene family is involved in plant development and growth. The results revealed that there were 34 BnSRS gene family members in the genomic sequence of B. napus, unevenly distributed throughout the sequence. Based on the phylogenetic analysis, these BnSRS genes could be divided into four subgroups, with each group sharing comparable conserved motifs and gene structure. Analysis of the upstream promoter region showed that BnSRS genes may regulate hormone responses, biotic and abiotic stress response, growth, and development in B. napus. The protein-protein interaction analysis revealed the involvement of BnSRS genes in various biological processes and metabolic pathways. Our analysis of BnSRS gene expression showed that 23 BnSRS genes in the callus tissue exhibited a dominant expression pattern, suggesting their critical involvement in cell dedifferentiation, cell division, and tissue development. In addition, association analysis between genotype and agronomic traits revealed that BnSRS genes may be linked to some important agronomic traits in B. napus, suggesting that BnSRS genes were widely involved in the regulation of important agronomic traits (including C16.0, C18.0, C18.1, C18.2 C18.3, C20.1, C22.1, GLU, protein, TSW, and FFT). In this study, we predicted the evolutionary relationships and potential functions of BnSRS gene family members, providing a basis for the development of BnSRS gene functions which could facilitate targeted functional studies and genetic improvement for elite breeding in B. napus.

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species

The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein-protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.

Overexpression of LYK4, a lysin motif receptor with non-functional kinase domain, enhances tolerance to Alternaria brassicicola and increases trichome density in Brassica juncea

Lysin motif receptor-like kinases (LYKs) are involved in the recognition of chitin and activation of plant immune response. In this study, we found LYK4 to be strongly induced in resistant Sinapis alba compared with susceptible Brassica juncea on challenge with Alternaria brassicicola. In silico analysis and in vitro kinase assay revealed that despite the presence of canonical protein kinase fold, B.juncea LYK4 (BjLYK4) lacks several key residues of a prototype protein kinase which renders it catalytically inactive. Transient expression analysis confirmed that fluorescently tagged BjLYK4 localizes specifically to the plasma membrane. Overexpression (OE) of BjLYK4 in B. juncea enhanced tolerance against A. brassicicola. Interestingly, the OE lines also exhibited a novel trichome dense phenotype and increased jasmonic acid (JA) responsiveness. We further showed that many chitin responsive WRKY transcription factors and JA biosynthetic genes were strongly induced in the OE lines on challenge with the pathogen. Moreover, several JA inducible trichome developmental genes constituting the WD-repeat/bHLH/MYB activator complex were also upregulated in the OE lines compared with vector control and RNA interference line. These results suggest that BjLYK4 plays an essential role in chitin-dependent activation of defense response and chitin independent trichome development likely by influencing the JA signaling pathway.

Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus

AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.

The whole genome assembly and evolution analyze of carmine radish (Raphanus sativus L.) Mitochondrion

Carmine radish, which contained a high natural red pigment (red radish pigment), was peculiar produced in Fuling, Chongqing City. Here, the complete nucleotide sequences of the mitochondrial (mt) genome of carmine radish (Raphanus sativus L.) have been determined with a circular sequence with the lengths of 258,965 bp, comprised of 40 protein-coding genes, 23 tRNA genes, and three ribosomal RNA genes. To demonstrate the evolution of organelles genomes in plants, other plant mitochondrial genomes’ evolution were also selected for analyze. The results showed that carmine radish (Raphanus sativus L.) is related to MS_Gensuke (Raphanus sativus L.) and Black radish (Raphanus sativus L.), as well as related to Brassica nigra and Brassica carinata, comparing with other Brassicaceae species. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

Enhancement of ABA Sensitivity Through Conditional Expression of the ARF10 Gene in Brassica juncea Reveals Fertile Plants with Tolerance Against Alternaria brassicicola

Concomitant increase of auxin-responsive factors ARF16 and ARF17, along with enhanced expression of ARF10 in resistant Sinapis alba compared with that in susceptible Brassica juncea upon challenge with Alternaria brassicicola, revealed that abscisic acid (ABA)-auxin crosstalk is a critical factor for resistance response. Here, we induced the ABA response through conditional expression of ARF10 in B. juncea using the A. brassicicola-inducible GH3.3 promoter. Induced ABA sensitivity caused by conditional expression of ARF10 in transgenic B. juncea resulted in tolerance against A. brassicicola and led to enhanced expression of several ABA-responsive genes without affecting the auxin biosynthetic gene expression. Compared with ABI3 and ABI4, ABI5 showed maximum upregulation in the most tolerant transgenic lines upon pathogen challenge. Moreover, elevated expression of ARF10 by different means revealed a direct correlation between ARF10 expression and the induction of ABI5 protein in B. juncea. Through in vitro DNA-protein experiments and chromosome immunoprecipitation using the ARF10 antibody, we demonstrated that ARF10 interacts with the auxin-responsive elements of the ABI5 promoter. This suggests that ARF10 may function as a modulator of ABI5 to induce ABA sensitivity and mediate the resistance response against A. brassicicola.

New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones

DNA metabarcoding is a rapidly growing technique for obtaining detailed dietary information. Current metabarcoding methods for herbivory, using a single locus, can lack taxonomic resolution for some applications. We present novel primers for the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) designed for dietary studies in Mauritius and the UK, which have the potential to give unrivalled taxonomic coverage and resolution from a short-amplicon barcode. In silico testing used three databases of plant ITS2 sequences from UK and Mauritian floras (native and introduced) totalling 6561 sequences from 1790 species across 174 families. Our primers were well-matched in silico to 88% of species, providing taxonomic resolution of 86.1%, 99.4% and 99.9% at the species, genus and family levels, respectively. In vitro, the primers amplified 99% of Mauritian (n = 169) and 100% of UK (n = 33) species, and co-amplified multiple plant species from degraded faecal DNA from reptiles and birds in two case studies. For the ITS2 region, we advocate taxonomic assignment based on best sequence match instead of a clustering approach. With short amplicons of 187-387 bp, these primers are suitable for metabarcoding plant DNA from faecal samples, across a broad geographic range, whilst delivering unparalleled taxonomic resolution.

Glucosinolate diversity within a phylogenetic framework of the tribe Cardamineae (Brassicaceae) unraveled with HPLC-MS/MS and NMR-based analytical distinction of 70 desulfoglucosinolates

As a basis for future investigations of evolutionary trajectories and biosynthetic mechanisms underlying variations in glucosinolate structures, we screened members of the crucifer tribe Cardamineae by HPLC-MS/MS, isolated and identified glucosinolates by NMR, searched the literature for previous data for the tribe, and collected HPLC-MS/MS data for nearly all glucosinolates known from the tribe as well as some related structures (70 in total). This is a considerable proportion of the approximately 142 currently documented natural glucosinolates. Calibration with authentic references allowed distinction (or elucidation) of isomers in many cases, such as distinction of β-hydroxyls, methylthios, methylsulfinyls and methylsulfonyls. A mechanism for fragmentation of secondary β-hydroxyls in MS was elucidated, and two novel glucosinolates were discovered: 2-hydroxy-3-methylpentylglucosinolate in roots of Cardamine pratensis and 2-hydroxy-8-(methylsulfinyl)octylglucosinolate in seeds of Rorippa amphibia. A large number of glucosinolates (ca. 54 with high structural certainty and a further 28 or more suggested from tandem MS), representing a wide structural variation, is documented from the tribe. This included glucosinolates apparently derived from Met, Phe, Trp, Val/Leu, Ile and higher homologues. Normal side chain elongation and side chain decoration by oxidation or methylation was observed, as well as rare abnormal side chain decoration (hydroxylation of aliphatics at the δ rather than β-position). Some species had diverse profiles, e.g. R. amphibia and C. pratensis (19 and 16 individual glucosinolates, respectively), comparable to total diversity in literature reports of Armoracia rusticana (17?), Barbarea vulgaris (20-24), and Rorippa indica (>20?). The ancestor or the tribe would appear to have used Trp, Met, and homoPhe as glucosinolate precursor amino acids, and to exhibit oxidation of thio to sulfinyl, formation of alkenyls, β-hydroxylation of aliphatic chains and hydroxylation and methylation of indole glucosinolates. Two hotspots of apparent biochemical innovation and loss were identified: C. pratensis and the genus Barbarea. Diversity in other species mainly included structures also known from other crucifers. In addition to a role of gene duplication, two contrasting genetic/biochemical mechanisms for evolution of such combined diversity and redundancy are discussed: (i) involvement of widespread genes with expression varying during evolution, and (ii) mutational changes in substrate specificities of CYP79F and GS-OH enzymes.

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes

This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

SHORT HYPOCOTYL UNDER BLUE1 or HAIKU2 mixepression alters canola and Arabidopsis seed development

Canola (Brassica napus) is a widely cultivated species and provides important resources of edible vegetable oil, biodiesel production and animal feed. Seed development in Arabidopsis and canola shares a similar path: an early proliferation of endosperm to form a large seed cavity, followed by a second phase in which the embryo grows to replace the endosperm. In Arabidopsis, the seed reaches almost its final volume before the enlargement of the embryo. SHORT HYPOCOTYL UNDER BLUE1 (SHB1) is a key regulatory gene of seed development with a broad expression beyond endosperm development. By contrast, its two target genes, MINISEED3 (MINI3) and HAIKU2 (IKU2), are narrowly expressed in early developing endosperm and early embryo. We overexpressed SHB1 in canola to explore the possibility of altering seed development. As an alternative strategy, we expressed the canola IKU2 ortholog in Arabidopsis endosperm under the control of a stronger MINI3 promoter. SHB1 targeted canola orthologs of Arabidopsis MINI3 and IKU2 and caused a significantly increased seed mass. Overaccumulation of IKU2 in the early stage of Arabidopsis seed development also significantly increased the final seed mass. Our studies provide a strong case for increasing the final seed mass by manipulating endosperm proliferation at a rather early developmental stage in crops.

Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica

This manuscript provides a Brassica conserved ortholog set (COS) that can be used as diagnostic cross-species markers as well as tools for genetic mapping and genome comparison of the Brassicaceae. A conserved ortholog set (COS) is a collection of genes that are conserved in both sequence and copy number between closely related genomes. COS is a useful resource for developing gene-based markers and is suitable for comparative genome mapping. We developed a COS for Brassica based on proteome comparisons of Arabidopsis thaliana, B. rapa, and B. oleracea to establish a basis for comparative genome analysis of crop species in the Brassicaceae. A total of 1,194 conserved orthologous single-copy genes were identified from the genomes based on whole-genome BLASTP analysis. Gene ontology analysis showed that most of them encoded proteins with unknown function and chloroplast-related genes were enriched. In addition, 152 Brassica COS primer sets were applied to 16 crop and wild species of the Brassicaceae and 57.9-92.8 % of them were successfully amplified across the species representing that a Brassica COS can be used as diagnostic cross-species markers of diverse Brassica species. We constructed a genetic map of Raphanus sativus by analyzing the segregation of 322 COS genes in an F2 population (93 individuals) of Korean cultivars (WK10039 × WK10024). Comparative genome analysis based on the COS genes showed conserved genome structures between R. sativus and B. rapa with lineage-specific rearrangement and fractionation of triplicated subgenome blocks indicating close evolutionary relationship and differentiation of the genomes. The Brassica COS developed in this study will play an important role in genetic, genomic, and breeding studies of crop Brassicaceae species.

De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.)

Radish (Raphanus sativus L.) is an edible root vegetable crop that is cultivated worldwide and whose genome has been sequenced. Here we report the complete nucleotide sequence of the radish cultivar WK10039 chloroplast (cp) genome, along with a de novo assembly strategy using whole genome shotgun sequence reads obtained by next generation sequencing. The radish cp genome is 153,368 bp in length and has a typical quadripartite structure, composed of a pair of inverted repeat regions (26,217 bp each), a large single copy region (83,170 bp), and a small single copy region (17,764 bp). The radish cp genome contains 87 predicted protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence analysis revealed the presence of 91 simple sequence repeats (SSRs) in the radish cp genome. Phylogenetic analysis of 62 protein-coding gene sequences from the 17 cp genomes of the Brassicaceae family suggested that the radish cp genome is most closely related to the cp genomes of Brassica rapa and Brassicanapus. Comparisons with the B. rapa and B. napus cp genomes revealed highly divergent intergenic sequences and introns that can potentially be developed as diagnostic cp markers. Synonymous and nonsynonymous substitutions of cp genes suggested that nucleotide substitutions have occurred at similar rates in most genes. The complete sequence of the radish cp genome would serve as a valuable resource for the development of new molecular markers and the study of the phylogenetic relationships of Raphanus species in the Brassicaceae family.

Construction of a high-resolution linkage map of Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility conferred by DCGMS cytoplasm in radish (Raphanus sativus L.) using synteny between radish and Arabidopsis genomes

Cytoplasmic male sterility caused by Dongbu cytoplasmic and genic male-sterility (DCGMS) cytoplasm and its nuclear restorer-of-fertility locus (Rfd1) with a linked molecular marker (A137) have been reported in radish (Raphanus sativus L.). To construct a linkage map of the Rfd1 locus, linked amplified fragment length polymorphism (AFLP) markers were screened using bulked segregant analysis. A 220-bp linked AFLP fragment sequence from radish showed homology with an Arabidopsis coding sequence. Using this Arabidopsis gene sequence, a simple PCR marker (A220) was developed. The A137 and A220 markers flanked the Rfd1 locus. Two homologous Arabidopsis genes with both marker sequences were positioned on Arabidopsis chromosome-3 with an interval of 2.4 Mb. To integrate the Rfd1 locus into a previously reported expressed sequence tag (EST)-simple sequence repeat (SSR) linkage map, the radish EST sequences located in three syntenic blocks within the 2.4-Mb interval were used to develop single nucleotide polymorphism (SNP) markers for tagging each block. The SNP marker in linkage group-2 co-segregated with male fertility in an F(2) population. Using radish ESTs positioned in linkage group-2, five intron length polymorphism (ILP) markers and one cleaved amplified polymorphic sequence (CAPS) marker were developed and used to construct a linkage map of the Rfd1 locus. Two closely linked markers delimited the Rfd1 locus within a 985-kb interval of Arabidopsis chromosome-3. Synteny between the radish and Arabidopsis genomes in the 985-kb interval were used to develop three ILP and three CAPS markers. Two ILP markers further delimited the Rfd1 locus to a 220-kb interval of Arabidopsis chromosome-3.

Convergent evolution of a complex fruit structure in the tribe Brassiceae (Brassicaceae)

PREMISE OF STUDY

Many angiosperms have fruit morphologies that result in seeds from the same plant having different dispersal capabilities. A prime example is found in the Brassiceae (Brassicaceae), which has many members with segmented or heteroarthrocarpic fruits. Since only 40% of the genera are heteroarthrocarpic, this tribe provides an opportunity to study the evolution of an ecologically significant novelty and its variants.

METHODS

We analyzed nuclear (PHYA) and plastid (matK) sequences from 66 accessions using maximum parsimony, maximum likelihood, and Bayesian inference approaches. The evolution of heteroarthrocarpy and its variants was evaluated using maximum parsimony and maximum likelihood ancestral state reconstructions.

KEY RESULTS

Although nuclear and plastid phylogenies are incongruent with each other, the following findings are consistent: (1) Cakile, Crambe, Vella, and Zilla lineages are monophyletic; (2) the Nigra lineage is not monophyletic; and (3) within the Cakile clade, Cakile, Didesmus, and Erucaria are paraphyletic. Despite differences in the matK and PHYA topologies at both deep and shallow nodes, similar patterns of morphological evolution emerge. Heteroarthrocarpy, a complex morphological trait, has evolved multiple times across the tribe. Moreover, there are convergent transitions in dehiscence capabilities and fruit disarticulation across the tribe.

CONCLUSIONS

We present the first explicit analysis of fruit evolution within the Brassiceae, which exemplifies evolutionary lability. The repeated loss and gain of segment dehiscence and disarticulation suggests conservation in the genetic pathway controlling abscission with differential expression across taxa. This study provides a strong foundation for future studies of mechanisms underlying variation in dispersal capabilities of Brassiceae.

Identification of functional BrFAD2-1 gene encoding microsomal delta-12 fatty acid desaturase from Brassica rapa and development of Brassica napus containing high oleic acid contents

Microsomal delta-12 fatty acid desaturase (FAD2) functions in the first committed step of the biosynthesis of polyunsaturated fatty acids via the desaturation of oleic acid to linoleic acid. In this study, two FAD2 genes were identified through genome-wide analysis of Brassica rapa. One BrFAD2-1 gene harbors functional sequence information, but another BrFAD2-2 gene has mutations that generated a premature stop codon, rendering it nonfunctional. From a database of 120,000 B. rapa expressed sequence tags, we determined that all sequences coding for FAD2 corresponded to the BrFAD2-1 gene. The BrFAD2-1 protein was shown to share high sequence homology (71-99%) with FAD2 proteins from other plant species. An intron in the 5'-untranslated region and three histidine boxes in the protein, which are characteristic of plant FAD2 genes, have been well-conserved. BrFAD2-1 transcripts were detected in various organs of B. rapa. When a pBrFAD2-1:mRFP construct was introduced into tobacco epidermal cells, the fluorescent signal was noted in the endoplasmic reticulum. Ectopic expression of BrFAD2-1:mRFP complemented the Arabidopsis fad2-2 mutant. Finally, transgenic Korean rapeseed Tammi containing high oleic acid contents (78 mol%) was developed via the expression of the BrFAD2-1 gene in an antisense orientation. The data demonstrate that B. rapa harbors only one functional FAD2 that can be utilized for the development of the high-oleic acid Korean rapeseed cultivar Tammi, which might be useful for both human consumption and industrial applications.

Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae)

Brassicaceae is an important family at both the agronomic and scientific level. The family not only includes several model species, but it is also becoming an evolutionary model at the family level. However, resolving the phylogenetic relationships within the family has been problematic, and a large-scale molecular phylogeny in terms of generic sampling and number of genes is still lacking. In particular, the deeper relationships within the family, for example between the three major recognized lineages, prove particularly hard to resolve. Using a slow-evolving mitochondrial marker (nad4 intron 1), we reconstructed a comprehensive phylogeny in generic representation for the family. In addition, and because resolution was very low in previous single marker phylogenies, we adopted a supermatrix approach by concatenating all checked and reliable sequences available on GenBank as well as new sequences for a total 207 currently recognized genera and eight molecular markers representing a comprehensive coverage of all three genomes. The supermatrix was dated under an uncorrelated relaxed molecular clock using a direct fossil calibration approach. Finally, a lineage-through-time-plot and rates of diversification for the family were generated. The resulting tree, the largest in number of genera and markers sampled to date and covering the whole family in a representative way, provides important insights into the evolution of the family on a broad scale. The backbone of the tree remained largely unresolved and is interpreted as the consequence of early rapid radiation within the family. The age of the family was inferred to be 37.6 (24.2-49.4) Ma, which largely agrees with previous studies. The ages of all major lineages and tribes are also reported. Analysis of diversification suggests that Brassicaceae underwent a rapid period of diversification, after the split with the early diverging tribe Aethionemeae. Given the dates found here, the family appears to have originated under a warm and humid climate approximately 37 Ma. We suggest that the rapid radiation detected was caused by a global cooling during the Oligocene coupled with a genome duplication event. This duplication could have allowed the family to rapidly adapt to the changing climate.

Sequence-level comparative analysis of the Brassica napus genome around two stearoyl-ACP desaturase loci

We conducted a sequence-level comparative analyses, at the scale of complete bacterial artificial chromosome (BAC) clones, between the genome of the most economically important Brassica species, Brassica napus (oilseed rape), and those of Brassica rapa, the genome of which is currently being sequenced, and Arabidopsis thaliana. We constructed a new B. napus BAC library and identified and sequenced clones that contain homoeologous regions of the genome including stearoyl-ACP desaturase-encoding genes. We sequenced the orthologous region of the genome of B. rapa and conducted comparative analyses between the Brassica sequences and those of the orthologous region of the genome of A. thaliana. The proportion of genes conserved (approximately 56%) is lower than has been reported previously between A. thaliana and Brassica (approximately 66%). The gene models for sets of conserved genes were used to determine the extent of nucleotide conservation of coding regions. This was found to be 84.2 +/- 3.9% and 85.8 +/- 3.7% between the B. napus A and C genomes, respectively, and that of A. thaliana, which is consistent with previous results for other Brassica species, and 97.5 +/- 3.1% between the B. napus A genome and B. rapa, and 93.1 +/- 4.9% between the B. napus C genome and B. rapa. The divergence of the B. napus genes from the A genome and the B. rapa genes was greater than anticipated and indicates that the A genome ancestor of the B. napus cultivar studied was relatively distantly related to the cultivar of B. rapa selected for genome sequencing.

Tests of adaptation: functional studies of pollen removal and estimates of natural selection on anther position in wild radish

BACKGROUND

There are a number of difficulties associated with the study of adaptation. One is a lack of variation in the trait, which is common in adaptations because past selection has removed unfit variants. This lack of variation makes it difficult to determine the relationship between trait variation and fitness. Another difficulty is proving causation in this trait-fitness relationship, because a correlated trait might be the actual adaptation. These difficulties can be ameliorated at least partially by combining studies of natural variation with studies of experimentally manipulated traits and traits whose variance has been augmented by artificial selection.

SCOPE

We review here a number of our studies on the adaptive value of two aspects of anther position in wild radish (Raphanus raphanistrum, Brassicaceae): anther exsertion, i.e. the degree to which anthers protrude from the mouth of the corolla tube, and anther height dimorphism, i.e. the difference in lengths of the filaments between the two short and four long stamens. We have used both functional analyses, in which the response variable is pollen removal, and measurements of selection, in which the response variable is lifetime male fitness estimated by molecular genetic paternity analyses. In these studies we use both the natural variation in populations as well as manipulated variation, the latter through both stamen removal and artificial selection, to re-create the ancestral trait conditions.

CONCLUSIONS

Our work provides convincing evidence that intermediate anther exsertion values are adaptive, and that this is probably an adaptation to a subset of the pollinator fauna, small bees. The picture for anther height dimorphism is much less clear, as the weight of current evidence suggests that current values of this trait might actually be maladaptive; however, if this is true it is difficult to understand how the dimorphism is maintained across the family Brassicaceae.

Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.)

Four types of cytoplasms (Ogura, DCGMS, DBRMF1, and DBRMF2) were identified in the previous studies using molecular markers based on mitochondrial genome variations in radish (Raphanus sativus L.). However, mtDNA markers have limitations in obtaining clear results due to complexity of radish mitochondrial genomes. To improve fidelity, molecular markers based on variation of chloroplast genome sequences were developed in this study. We searched for the sequence variations of chloroplast genome among the four cytoplasm types in 11 noncoding intergenic regions of ~8.7 kb. Highly variable intergenic regions between trnK and rps16 were identified, and a couple of 4-34 bp indels were used to develop a simple PCR-based marker that distinguished the four cytoplasm types based on the PCR product length polymorphism. Two additional cpDNA markers were developed by using a single nucleotide polymorphism and 17-bp insertion. Analysis of 90 accessions using both mtDNA and cpDNA markers showed the perfect match of results of both the markers, suggesting strict co-transmission of mitochondria and chloroplast in radish. Phylogenetic trees showed that two male-sterility inducing cytoplasms, Ogura and DCGMS, were closely related to DBRMF1 and DBRMF2, respectively. Analysis of 120 radish germplasms introduced from diverse countries showed that the frequency of male-sterility inducing mitotypes of Ogura and DCGMS was very low, and DCGMS was predominately detected in eastern European countries. Majority of accessions from Europe and Asia were shown to contain DBRMF2 and DBRMF1 mitotypes, respectively.

Microarray analysis of gene expression in seeds of Brassica napus planted in Nanjing (altitude: 8.9 m), Xining (altitude: 2261.2 m) and Lhasa (altitude: 3658 m) with different oil content

The regulation of seed oil synthesis in rapeseed is largely unknown. In this study, Arabidopsis microarray was used to analyze the gene differential expression of the immature seeds 30 days after flowering of a high oil Brassica napus, H105, whose oil content was 46.04 +/- 1.42, 53.94 +/- 1.35 and 53.09 +/- 1.35% when planted in Nanjing (altitude: 8.9 m), Xining (altitude: 2261.2 m) and Lhasa (altitude: 3658 m), respectively. Transcript levels of 363 genes and 421 genes were altered twofold or more for H105 planted in Xining and Lhasa compared to that in Nanjing, respectively. Together, there were 53 common up-regulated and 42 common down-regulated expression transcripts shared by H105 planted in Xining and Lhasa compared to that in Nanjing. Some important genes, such as sucrose synthase, pyruvate kinase and 6-phosphogluconate dehydrogenase which related to sugar metabolism were identified common up-regulated in higher oil content H105. These results revealed the expressional disciplinarian of correlative genes, and provided important information of the molecular genetic mechanism of oil content difference of rapeseed. In addition, these differential expression genes could be suitable as targets for genetic improvement of seed oil content.

The evolution and diversification of S-locus haplotypes in the Brassicaceae family

Self-incompatibility (SI) in the Brassicaceae plant family is controlled by the SRK and SCR genes situated at the S locus. A large number of S haplotypes have been identified, mainly in cultivated species of the Brassica and Raphanus genera, but recently also in wild Arabidopsis species. Here, we used DNA sequences from the SRK and SCR genes of the wild Brassica species Brassica cretica, together with publicly available sequence data from other Brassicaceae species, to investigate the evolutionary relationships among S haplotypes in the Brassicaceae family. The results reveal that wild and cultivated Brassica species have similar levels of SRK diversity, indicating that domestication has had but a minor effect on S-locus diversity in Brassica. Our results also show that a common set of S haplotypes was present in the ancestor of the Brassica and Arabidopsis genera, that only a small number of haplotypes survived in the Brassica lineage after its separation from Arabidopsis, and that diversification within the two Brassica dominance classes occurred after the split between the two lineages. We also found indications that recombination may have occurred between the kinase domain of SRK and the SCR gene in Brassica.

A and C genome distinction and chromosome identification in brassica napus by sequential fluorescence in situ hybridization and genomic in situ hybridization

The two genomes (A and C) of the allopolyploid Brassica napus have been clearly distinguished using genomic in situ hybridization (GISH) despite the fact that the two extant diploids, B. rapa (A, n = 10) and B. oleracea (C, n = 9), representing the progenitor genomes, are closely related. Using DNA from B. oleracea as the probe, with B. rapa DNA and the intergenic spacer of the B. oleracea 45S rDNA as the block, hybridization occurred on 9 of the 19 chromosome pairs along the majority of their length. The pattern of hybridization confirms that the two genomes have remained distinct in B. napus line DH12075, with no significant genome homogenization and no large-scale translocations between the genomes. Fluorescence in situ hybridization (FISH)-with 45S rDNA and a BAC that hybridizes to the pericentromeric heterochromatin of several chromosomes-followed by GISH allowed identification of six chromosomes and also three chromosome groups. Our procedure was used on the B. napus cultivar Westar, which has an interstitial reciprocal translocation. Two translocated segments were detected in pollen mother cells at the pachytene stage of meiosis. Using B. oleracea chromosome-specific BACs as FISH probes followed by GISH, the chromosomes involved were confirmed to be A7 and C6.

Gene polymorphisms for elucidating the genetic structure of the heavy-metal hyperaccumulating trait in Thlaspi caerulescens and their cross-genera amplification in Brassicaceae

Genetic polymorphism was investigated in Thlaspi caerulescens J. & C. Presl at 15 gene regions, of which seven have been identified to putatively play a role in heavy-metal tolerance or hyperaccumulation. Single nucleotide and length polymorphisms were assessed at four cleaved amplified polymorphic sequences (CAPS) and 11 simple sequence repeat (microsatellite) loci, respectively. The utility of these loci for genetic studies in T. caerulescens was measured among seven natural populations (135 individuals). Fourteen loci rendered polymorphism, and the number of alleles per locus varied from 2 to 5 and 1 to 27 for CAPS and microsatellites, respectively. Up to 12 alleles per locus were detected in a population. The global observed heterozygosity per population varied between 0.01 and 0.31. Additionally, cross-species/genera amplification of loci was investigated on eight other Brassicaceae (five individuals per population). Overall, 70% of the cross-species/genera amplifications were successful, and among them, more than 40% provided intraspecific polymorphisms within a single population. This indicates that such markers may, as well, allow comparative population genetic or mapping studies between and within several Brassicaceae, particularly for genes involved in traits such as heavy-metal tolerance and/or hyperaccumulation.

New evidence from Sinapis alba L. for ancestral triplication in a crucifer genome

We present clear evidence of ancestral genome triplication in Sinapis alba, a close relative of the cultivated Brassica species. Exceptionally high levels of heterozygosity in the parents of an F1 intercross permitted the mapping of an estimated 87% of all detected restriction fragment length polymorphism (RFLP) loci, with each RFLP probe typically detecting 2 or 3 loci. These duplicated loci were arranged in 8 triplicated homologous linkage blocks and 2 small, duplicated, homologous linkage blocks covering the majority of the S. alba genome. Several large-scale inversions and translocations appear to have rearranged the order of loci within homologous blocks. The role of successive polyploidization events on the evolution of crucifer species is discussed.

Toward a Global Phylogeny of the Brassicaceae

The Brassicaceae is a large plant family (338 genera and 3,700 species) of major scientific and economic importance. The taxonomy of this group has been plagued by convergent evolution in nearly every morphological feature used to define tribes and genera. Phylogenetic analysis of 746 nrDNA internal transcribed spacer (ITS) sequences, representing 24 of the 25 currently recognized tribes, 146 genera, and 461 species of Brassicaceae, produced the most comprehensive, single-locus-based phylogenetic analysis of the family published to date. Novel approaches to nrDNA ITS analysis and extensive taxonomic sampling offered a test of monophyly for a large complement of the currently recognized tribes and genera of Brassicaceae. In the most comprehensive analysis, tribes Alysseae, Anchonieae plus Hesperideae, Boechereae, Cardamineae, Eutremeae, Halimolobeae, Iberideae, Noccaeeae, Physarieae, Schizopetaleae, Smelowskieae, and Thlaspideae were all monophyletic. Several broadly defined genera (e.g., Draba and Smelowskia) were supported as monophyletic, whereas others (e.g., Sisymbrium and Alyssum) were clearly polyphyletic. Analyses of ITS data identified several problematic sequences attributable to errors in sample identification or database submission. Results from parsimony ratchet and Bayesian analyses recovered little support for the backbone of the phylogeny, suggesting that many lineages of Brassicaceae have undergone rapid radiations that may ultimately be difficult to resolve with any single locus. However, the development of a preliminary supermatrix including the combination of 10 loci for 65 species provides an initial estimate of intertribal relations and suggests that broad application of such a method will provide greater understanding of relationships in the family.

A multiplex real-time PCR assay for detection of Xanthomonas campestris from brassicas

AIMS

To develop a sensitive real-time PCR-based protocol for the detection of Xanthomonas campestris pathovars from Brassica seed.

METHODS AND RESULTS

A 5' nuclease real-time PCR assay was developed to screen Brassica spp. seed for the presence of X. campestris pathovars that cause black rot. The assay amplifies a 78-bp segment of the X. campestris hrpF gene and a 100-bp segment of the Brassica spp. 18S-25S internal transcribed spacer region. The Brassica spp. target provides an internal control for the amplification process to prevent false negatives that may arise from inhibitors that are often present in extracts from plant material. Whilst the primers were compatible with SYBR Green I assays, the use of fluorescently labelled probes in a 5' nuclease assay afforded greatest sensitivity and specificity. Seed batches carrying one artificially infected seed among 10,000 were readily detected using the assay. The multiplex real-time PCR assay permitted the rapid detection of pathogenic strains of X. campestris from bacterial colonies, Brassica seed and plants.

CONCLUSIONS

Strains of X. campestris pathogenic to brassicas were readily detected from seed via a multiplex 5' nuclease real-time PCR assay. The real-time assay offers an improvement in sensitivity and a reduced turn-around time over the conventional multiplex PCR.

SIGNIFICANCE AND IMPACT OF THE STUDY

Real-time PCR can be used to rapidly screen Brassica spp. seed batches for the presence of X. campestris pathovars. This assay provides a means for growers and the seed industry to be aware of the black rot status of their planting material, so that they may more effectively employ disease control measures or seed disinfection.

Molecular identification of Astragalus membranaceus at the species and locality levels

Astragalus membranaceus (Fisch.) Bunge, a commonly used Chinese medicinal material, from certain localities contains more favourable trace elements and fewer harmful trace elements than those from other localities. Therefore, there is a need to distinguish Astragalus membranaceus from different localities. Internal transcribed spacer 1 (ITS1) of the nuclear ribosomal RNA gene of 23 Astragalus membranaceus samples were sequenced to confirm the species of the samples. Arbitrarily primed polymerase chain reaction (APPCR) was then used to obtain unique fingerprints for each sample using several primers. The presence and absence of bands were used for calculating mean similarity indexes among the samples. It was found that the Heilongjiang samples were markedly distinguishable from samples of other localities. In addition, bands common for samples from the same locality were also identified and used to distinguish samples from Neimengu and Shanxi. Therefore, Astragalus membranaceus from these provinces, the major cultivation places in China, can be differentiated.

Mode of reproduction in Arabidopsis suecica

The breeding system of Arabidopsis suecica was investigated through genetic analysis of microsatellite segregation patterns in five controlled crosses as well as in 16 single-mother families collected in the wild. Analysis of single and two-locus segregations in the F2 generation following a cross clearly shows that A. suecica is reproduces sexually. The single-mother families show a high level of homozygosity corroborating earlier results indicating a high level of inbreeding. The high level of individual homozygosity is due both to a high level of selfing and to the underlying population structure.

Genetic diversity within the Albugo candida complex (Peronosporales, Oomycota) inferred from phylogenetic analysis of ITS rDNA and COX2 mtDNA sequences

Albugo candida is a destructive fungus infecting brassicaceous hosts. The genetic diversity within the A. candida complex from various host plants was investigated by sequence analysis of the internal transcribed spacer (ITS) region of rDNA and the cytochrome c oxidase subunit II (COX2) region of mtDNA. The aligned nucleotide sequences of A. candida shared significantly high distances, up to 20.4 and 8.9%, in two genes. The phylogenetic trees, obtained using the Bayesian method and maximum parsimony analysis, showed two separate groups that corresponded to the host genera. Group I included A. candida isolates infecting Arabis, Autrieta, Berteroa, Biscutella, Brassica, Cardaminopsis, Diplotaxis, Eruca, Erysimum, Heliophila, Iberis, Lunaria, Raphanus, Sinapis, Sisymbrium, and Thlaspi. Group II contained all isolates from Capsella, Descurainia, Diptychocarpus, Draba, and Lepidium. The genetic similarities between the two genes among isolates within Group I were 99.0-100% and 99.6-100%, while those within Group II were 90.4-100% and 91.1-100%, respectively, showing considerably lower values than for Group I. The A. candida isolates from Capsella bursa-pastoris in Korea are clearly separated by sequence analysis for the two genes compared to those from Wales, England, and the USA. Based on the molecular data from the two genes, we suggest the high degree of genetic diversity exhibited within A. candida complexes warrants their division into several distinct species.

Partial shotgun sequencing of the Boechera stricta genome reveals extensive microsynteny and promoter conservation with Arabidopsis

Comparative genomics provides insight into the evolutionary dynamics that shape discrete sequences as well as whole genomes. To advance comparative genomics within the Brassicaceae, we have end sequenced 23,136 medium-sized insert clones from Boechera stricta, a wild relative of Arabidopsis (Arabidopsis thaliana). A significant proportion of these sequences, 18,797, are nonredundant and display highly significant similarity (BLASTn e-value < or = 10(-30)) to low copy number Arabidopsis genomic regions, including more than 9,000 annotated coding sequences. We have used this dataset to identify orthologous gene pairs in the two species and to perform a global comparison of DNA regions 5' to annotated coding regions. On average, the 500 nucleotides upstream to coding sequences display 71.4% identity between the two species. In a similar analysis, 61.4% identity was observed between 5' noncoding sequences of Brassica oleracea and Arabidopsis, indicating that regulatory regions are not as diverged among these lineages as previously anticipated. By mapping the B. stricta end sequences onto the Arabidopsis genome, we have identified nearly 2,000 conserved blocks of microsynteny (bracketing 26% of the Arabidopsis genome). A comparison of fully sequenced B. stricta inserts to their homologous Arabidopsis genomic regions indicates that indel polymorphisms >5 kb contribute substantially to the genome size difference observed between the two species. Further, we demonstrate that microsynteny inferred from end-sequence data can be applied to the rapid identification and cloning of genomic regions of interest from nonmodel species. These results suggest that among diploid relatives of Arabidopsis, small- to medium-scale shotgun sequencing approaches can provide rapid and cost-effective benefits to evolutionary and/or functional comparative genomic frameworks.

A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers

A coalescent-based method was used to investigate the origins of the allotetraploid Arabidopsis suecica, using 52 nuclear microsatellite loci typed in eight individuals of A. suecica and 14 individuals of its maternal parent Arabidopsis thaliana, and four short fragments of genomic DNA sequenced in a sample of four individuals of A. suecica and in both its parental species A. thaliana and Arabidopsis arenosa. All loci were variable in A. thaliana but only 24 of the 52 microsatellite loci and none of the four sequence fragments were variable in A. suecica. We explore a number of possible evolutionary scenarios for A. suecica and conclude that it is likely that A. suecica has a recent, unique origin between 12,000 and 300,000 years ago. The time estimates depend strongly on what is assumed about population growth and rates of mutation. When combined with what is known about the history of glaciations, our results suggest that A. suecica originated south of its present distribution in Sweden and Finland and then migrated north, perhaps in the wake of the retreating ice.

Sequence divergence at the putative flowering time locus COL1 in Brassicaceae

An insertion/deletion polymorphism (Ind2) in the Brassica nigra CONSTANS LIKE 1 (Bni COL1) gene was previously found to be associated with variation in flowering time. In the present study we examine the inter-specific divergence of COL1 in the family Brassicaceae. Analysis of codon substitution models did not reveal evidence of positive Darwinian selection, but comparisons of the COL1 gene in different species revealed a surprising number of indels. A total of 24 indels were found in the 650 bp of the middle variable region of the gene. This high number of indels could reflect a lack of constraint on length of this region of the protein, or the effect of positive selection. The number of indels was close to that expected in non-coding DNA, but the indels were longer in COL1 than those observed in non-coding regions. Reconstruction of indel evolution indicated that most indels resulted from deletions rather than insertions. The Ind2 indel that has shown association with flowering time in Brassica nigra exhibited a remarkable distribution in the Brassicaceae family, indicating that the polymorphism may have persisted more than ten million years. Considering presumed historic populations sizes of Brassicaceae species, such a long persistence time seems unlikely for a neutral polymorphism.

Comparative analysis of rDNA distribution in chromosomes of various species of Brassicaceae

BACKGROUND AND AIMS

The Brassicaceae family encompasses numerous species of great agronomic importance, belonging to such genera, as Brassica, Raphanus, Sinapis and Armoracia. Many of them are characterized by extensive intraspecific diversity of phenotypes. The present study focuses on the polymorphism of number, appearance and chromosomal localization of ribosomal DNA (rDNA) sites and, when possible, in relation to polyploidy, in 42 accessions of Brassica species and ten accessions of Diplotaxis, Eruca, Raphanus and Sinapis species.

METHODS

Chromosomal localization of ribosomal DNA was carried out using dual colour fluorescence in situ hybridization (FISH) with 5S rDNA and 25S rDNA sequences as probes on enzymatically digested root-tip meristematic cells.

KEY RESULTS

Loci for 5S and 18S-5.8S-25S rDNA were determined for the first time in six taxa, and previously unreported rDNA constellations were described in an additional 12 accessions. FISH revealed frequent polymorphism in number, appearance and chromosomal localization of both 5S and 25S rDNA sites. This phenomenon was most commonly observed in the A genome of Brassica, where it involves exclusively pericentromeric sites of 5S and 25S rRNA genes. The intraspecific polymorphism was between subspecies/varieties or within a variety or cultivar (i.e. interindividual).

CONCLUSIONS

The number of rDNA sites can differ up to 5-fold in species with the same chromosome number. In addition to the eight previously reported chromosomal types with ribosomal genes, three new variant types are described. The extent of polymorphism is genome dependent. Comparing the A, B and C genomes revealed the highest rDNA polymorphism in the A genome. The loci carrying presumably inactive ribosomal RNA genes are particularly prone to polymorphism. It can also be concluded that there is no obvious polyploidization-related tendency to reduce the number of ribosomal DNA loci in the allotetraploid species, when compared with their putative diploid progenitors. The observed differences are rather caused by the prevailing polymorphism within the diploids and allotetraploids. This would make it difficult to predict expected numbers of rDNA loci in natural polyploids.

Phylogeny of tribe Brassiceae (Brassicaceae) based on chloroplast restriction site polymorphisms and nuclear ribosomal internal transcribed spacer and chloroplast trnL intron sequences

Using sequence data from the ITS region (internal transcribed spacers ITS-1 and ITS-2 of nuclear DNA and the 5.8 rRNA gene), chloroplast DNA (cpDNA) sequence data from the trnL intron, and cpDNA restriction site polymorphism data, we examined the evolutionary relationships of the tribe Brassiceae (Brassicaceae). A group of approximately 50 genera, it is distinguished by the presence of conduplicate cotyledons and (or) heteroarthrocarpic fruit. cpDNA restriction site data and ITS, trnL, and combined ITS/trnL sequence data were obtained for 22, 104, 94, and 87 taxa in the tribe, respectively. Results from maximum parsimony analyses of the cpDNA and ITS and ITS/trnL sequence data showed a monophyletic origin for the tribe, with the inclusion of controversial members Calepina, Conringia, and Orychophragmus. ITS- and ITS/trnL-based clades corresponded to taxonomic subtribes: Vellinae, Zillinae, and Savignyinae; but as with previous cpDNA studies, there was little support for subtribes Brassicinae, Raphaninae, and Moricandiinae. Although there was no support for the Rapa/Oleracea or Nigra cpDNA lineages, many cpDNA subclades within each of them were evident in the ITS- and ITS/trnL-based phylogeny. The trnL sequence data provided little or no resolution of tribal or subtribal limits. The ITS data indicated polyphyletic origins for Brassica, Diplotaxis, and Erucastrum.Key words: Brassiceae, Calepina, Conringia, Orychophragmus, ITS, trnL, cpDNA restriction site polymorphisms.

The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects

Arabidopsis is a model system not only for studying numerous aspects of plant biology, but also for understanding mechanisms of the rapid evolutionary process associated with genome duplication and polyploidization. Although in animals interspecific hybrids are often sterile and aneuploids are related to disease syndromes, both Arabidopsis autopolyploids and allopolyploids occur in nature and can be readily formed in the laboratory, providing an attractive system for comparing changes in gene expression and genome structure among relatively 'young' and 'established' or 'ancient' polyploids. Powerful reverse and forward genetics in Arabidopsis offer an exceptional means by which regulatory mechanisms of gene and genome duplication may be revealed. Moreover, the Arabidopsis genome is completely sequenced; both coding and non-coding sequences are available. We have developed spotted oligo-gene and chromosome microarrays using the complete Arabidopsis genome sequence. The oligo-gene microarray consists of ~26 000 70-mer oligonucleotides that are designed from all annotated genes in Arabidopsis, and the chromosome microarray contains 1 kb genomic tiling fragments amplified from a chromosomal region or the complete sequence of chromosome 4. We have demonstrated the utility of microarrays for genome-wide analysis of changes in gene expression, genome organization and chromatin structure in Arabidopsis polyploids and related species.

Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: a case study from Naucleeae (Rubiaceae)

The internal transcribed spacer (ITS) of nuclear ribosomal DNA has been widely used by systematists for reconstructing phylogenies of closely related taxa. Although the occurrence of ITS putative pseudogenes is well documented for many groups of animals and plants, the potential utility of these pseudogenes in phylogenetic analyses has often been underestimated or even ignored in part because of deletions that make unambiguous alignment difficult. In addition, long branches often can lead to spurious relationships, particularly in parsimony analyses. We have discovered unusually high levels of ITS polymorphism (up to 30%, 40%, and 14%, respectively) in three tropical tree species of the coffee family (Rubiaceae), Adinauclea fagifolia, Haldina cordifolia, and Mitragyna rubrostipulata. Both secondary structure stability and patterns of nucleotide substitutions in a highly conserved region (5.8S gene) were used for distinguishing presumed functional sequences from putative pseudogenes. The combination of both criteria was the most powerful approach. The sequences from A. fagifolia appear to be a mix of functional genes and highly distinct putative pseudogenes, whereas those from H. cordifolia and M. rubrostipulata were identified as putative pseudogenes. We explored the potential utility of the identified putative pseudogenes in the phylogenetic analyses of Naucleeae sensu lato. Both Bayesian and parsimony trees identified the same monophyletic groups and indicated that the polymorphisms do not transcend species boundaries, implying that they do not predate the divergence of these three species. The resulting trees are similar to those produced by previous analyses of chloroplast genes. In contrast to results of previous studies therefore, divergent putative pseudogenes can be useful for phylogenetic analyses, especially when no sequences of their functional counterparts are available. Our studies clearly show that ITS polymorphism may not necessarily mislead phylogenetic inference. Despite using many different PCR conditions (different primers, higher denaturing temperatures, and absence or presence of DMSO and BSA-TMACl), we recovered only a few functional ITS copies from A. fagifolia and none from H. cordifolia and M. rubrostipulata, which suggests that PCR selection is occurring and/or the presumed functional alleles are located at minor loci (with few ribosomal DNA copies).

Diversity of the Hyaloperonospora parasitica complex from core brassicaceous hosts based on ITS rDNA sequences

Sequence analysis of the ITS region of rDNA was used to investigate the level of genetic diversity occurring within Hyaloperonospora parasiticia, and to show the relationship between phylogenies of these fungi and their hosts (Brassicaceae). Maximum parsimony and neighbour-joining analyses were performed using sequences from 32 isolates of Hyaloperonospora and Perofascia, which infect core brassicaceous hosts. For comparison, five isolates of Peronospora were also studied. The constructed phylogenetic trees showed trichotomy, showing that Hyaloperonospora, Perofascia, and Peronospora have different evolutionary histories. Although isolates from Peronospora and Perofascia clearly formed respective clades, the Hyaloperonospora group allowed separation of the isolates into four distinct clades, which shared significantly low sequence similarities. We suggest that H. parasitica infecting brassicaceous hosts should be divided into a number of distinct species. The comparison of the phylogeny of H. parasitica and that of the Brassicaceae suggests that this fungus is closely related with tribes Arabidae and Brassiceae within this host family, illustrating the potential of downy mildews for co-evolution with their hosts.

Ribosomal ITS sequences and plant phylogenetic inference

One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. The prominence of this source of nuclear DNA sequence data is underscored by a survey of phylogenetic publications involving comparisons at the genus level or below, which reveals that of 244 papers published over the last five years, 66% included ITS sequence data. Perhaps even more striking is the fact that 34% of all published phylogenetic hypothesis have been based exclusively on ITS sequences. Notwithstanding the many important contributions of ITS sequence data to phylogenetic understanding and knowledge of genome relationships, a number of molecular genetic processes impact ITS sequences in ways that may mislead phylogenetic inference. These molecular genetic processes are reviewed here, drawing attention to both underlying mechanism and phylogenetic implications. Among the most prevalent complications for phylogenetic inference is the existence in many plant genomes of extensive sequence variation, arising from ancient or recent array duplication events, genomic harboring of pseudogenes in various states of decay, and/or incomplete intra- or inter-array homogenization. These phenomena separately and collectively create a network of paralogous sequence relationships potentially confounding accurate phylogenetic reconstruction. Homoplasy is shown to be higher in ITS than in other DNA sequence data sets, most likely because of orthology/paralogy conflation, compensatory base changes, problems in alignment due to indel accumulation, sequencing errors, or some combination of these phenomena. Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis. It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.

Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing

In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3-kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae species, several other motifs, but not the LFY and WUS binding sites identified previously, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for the activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection but also demonstrate that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.

A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA

There are two evolutionary lineages in the genus Brassica: the rapa/oleracea lineage and the nigra lineage. Using nuclear DNA sequences such as the intergenic spacer between 5S rRNA genes and the internal transcribed spacer between 18S and 25S rRNA genes, we and others had previously demonstrated that Raphanus sativus is closely related to the nigra lineage. In the present study, we sequenced the chloroplast noncoding region between trnT and trnF and that between trnD and trnT in seven species and showed that R. sativus is more closely related to the rapa/oleracea lineage than to the nigra lineage. The conflicting results from nuclear DNA and chloroplast DNA support the hypothesis that Raphanus was derived from a hybridization between the rapa/oleracea and the nigra lineages. We estimated the date of this hybridization event to be 60% of the divergence time between the two Brassica lineages. In addition, the pattern and rate of nucleotide substitution were studied. There were more transversions than transitions in these noncoding regions, which have a high AT content. Furthermore, the proportion of transversions among the substitutions at a site increases with increasing A + T content of its two adjacent nucleotides. An influence of immediate 5(') pyrimidine on substitution pattern is also observed when both adjacent bases in the two DNA strands are A or T. The rate of nucleotide substitution in the trnL group I intron is only about one third of the rate in the nearby intergenic spacers in the trnT-trnF fragment. The rate of nucleotide substitution in the rapa/oleracea lineage is at least 1.5 times that in the nigra lineage.

Evolution of Caulanthus amplexicaulis var. barbarae (Brassicaceae), a rare serpentine endemic plant: a molecular phylogenetic perspective

Intra- and interspecific phylogenetic relationships of the rare serpentine endemic taxon Caulanthus amplexicaulus var. barbarae and related taxa in the "Streptanthoid Complex" of genera (Streptanthus, Caulanthus, Guillenia) were examined using nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL intron sequences. Phylogenetic hypotheses generated from 81 variable ITS nucleotide sites and six variable trnL nucleotide sites indicate that Streptanthus and Caulanthus are nonmonophyletic groups. Caulanthus amplexicaulis var. barbarae and its more widespread nonserpentine sister taxon Caulanthus amplexicaulis var. amplexicaulis formed a distinct monophyletic group. Among the taxa in our study, C. amplexicaulis was most closely related to Streptanthus tortuosus. The ITS sequences supported monophyly of subgenus Euclesia, which includes the bulk of the serpentine endemics in the Streptanthoid Complex. The serpentine taxa were nonmonophyletic, occurring in at least three distinct clades, suggesting that tolerance to serpentine may be gained or lost through relatively few genetic changes. Intraspecific ITS1 and ITS2 sequence divergence within C. amplexicaulis (1.3-1.8%) was higher than in comparable species (0.0-0.3%); implications of this genetic differentiation for the conservation status of C. amplexicaulis var. barbarae are discussed. Evidence is presented that supports a "biotype depletion" model for the origin of this rare endemic taxon.

Identification and characterization of a polymorphic receptor kinase gene linked to the self-incompatibility locus of Arabidopsis lyrata

We study the segregation of variants of a putative self-incompatibility gene in Arabidopsis lyrata. This gene encodes a sequence that is homologous to the protein encoded by the SRK gene involved in self-incompatibility in Brassica species. We show by diallel pollinations of plants in several full-sib families that seven different sequences of the gene in A. lyrata are linked to different S-alleles, and segregation analysis in further sibships shows that four other sequences behave as allelic to these. The family data on incompatibility provide evidence for dominance classes among the S-alleles, as expected for a sporophytic SI system. We observe no division into pollen-dominant and pollen-recessive classes of alleles as has been found in Brassica, but our alleles fall into at least three dominance classes in both pollen and stigma expression. The diversity among sequences of the A. lyrata putative S-alleles is greater than among the published Brassica SRK sequences, and, unlike Brassica, the alleles do not cluster into groups with similar dominance.