The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis.

BACKGROUND: The Coreopsideae tribe, a subset of the Asteraceae family, encompasses economically vital genera like Dahlia, Cosmos, and Bidens, which are widely employed in medicine, horticulture, ecology, and food applications. Nevertheless, the lack of reference genomes hinders evolutionary and biological investigations in this tribe. RESULTS: Here, we present 3 haplotype-resolved chromosome-level reference genomes of the tribe Coreopsideae, including 2 popular flowering plants (Dahlia pinnata and Cosmos bipinnatus) and 1 invasive weed plant (Bidens alba), with assembled genome sizes 3.93 G, 1.02 G, and 1.87 G, respectively. We found that Gypsy transposable elements contribute mostly to the larger genome size of D. pinnata, and multiple chromosome rearrangements have occurred in tribe Coreopsideae. Besides the shared whole-genome duplication (WGD-2) in the Heliantheae alliance, our analyses showed that D. pinnata and B. alba each underwent an independent recent WGD-3 event: in D. pinnata, it is more likely to be a self-WGD, while in B. alba, it is from the hybridization of 2 ancestor species. Further, we identified key genes in the inulin metabolic pathway and found that the pseudogenization of 1-FEH1 and 1-FEH2 genes in D. pinnata and the deletion of 3 key residues of 1-FFT proteins in C. bipinnatus and B. alba may probably explain why D. pinnata produces much more inulin than the other 2 plants. CONCLUSIONS: Collectively, the genomic resources for the Coreopsideae tribe will promote phylogenomics in Asteraceae plants, facilitate ornamental molecular breeding improvements and inulin production, and help prevent invasive weeds.

Analysis of the chloroplast genome and phylogenetic evolution of Bidens pilosa.

Chloroplast genomes for 3 Bidens plants endemic to China (Bidens bipinnata Linn., Bidens pilosa Linn., and Bidens alba var. radiata) have been sequenced, assembled and annotated in this study to distinguish their molecular characterization and phylogenetic relationships. The chloroplast genomes are in typical quadripartite structure with two inverted repeat regions separating a large single copy region and a small single copy region, and ranged from 151,599 to 154,478 bp in length. Similar number of SSRs and long repeats were found in Bidens, wherein mononucleotide repeats (A/T), forward and palindromic repeats were the most in abundance. Gene loss of clpP and psbD, IR expansion and contraction were detected in these Bidens plants. It seems that ndhE, ndhF, ndhG, and rpl32 from the Bidens plants were under positive selection while the majority of chloroplast genes were under purifying selection. Phylogenetic analysis revealed that 3 Bidens plants clustered together and further formed molophyletic clade with other Bidens species, indicating Bidens plants might be under radiation adaptive selection to the changing environment world-widely. Moreover, mutation hotspot analysis and in silico PCR analysis indicated that inter-genic regions of ndhD-ccsA, ndhI-ndhG, ndhF-rpl32, trnL_UAG-rpl32, ndhE-psaC, matK-rps16, rps2-atpI, cemA-petA, petN-psbM were candidate markers of molecular identification for Bidens plants. This study may provide useful information for genetic diversity analysis and molecular identification for Bidens species.

Elucidation of enzymes involved in the biosynthetic pathway of bioactive polyacetylenes in Bidens pilosa using integrated omics approaches.

Polyacetylene compounds from Bidens pilosa are known to have several pharmacological activities. In this study, we identified major genes encoding enzymes involved in the biosynthesis of polyacetylene in B. pilosa. Seven polyacetylene metabolites present in B. pilosa leaves were induced by methyl jasmonate (MeJA) treatment and physical wounding. Transcriptome analysis via high-throughput sequencing revealed 39 202 annotated gene fragment sequences. A DNA microarray established by the 39 202 annotated genes was used to profile gene expression in B. pilosa leaf and root tissues. As no polyacetylene compounds were found in roots, the gene expression pattern in root tissue was used as a negative control. By subtracting MeJA-induced genes in roots, we obtained 1216 genes in leaves showing an approximate three-fold increase in expression post-MeJA treatment. Nine genes encoding enzymes with desaturation function were selected for confirmation of expression by qRT-PCR. Among them, two genes, BPTC030748 and BPTC012564, were predicted to encode Δ12-oleate desaturase (OD) and Δ12-fatty acid acetylenase (FAA), respectively. In B. pilosa leaves, RNAi knock-down concomitantly decreased, while virus-mediated transient overexpression of either gene elevated polyacetylene content. In summary, we demonstrate that two important enzymes, Δ12-oleate desaturase and Δ12-fatty acid acetylenase, involved in desaturation of linear fatty acid precursors play a role in polyacetylene biosynthesis in an important medicinal plant, Bidens pilosa.

Insights into the Evolutionary History of the Hawaiian Bidens (Asteraceae) Adaptive Radiation Revealed Through Phylogenomics.

Hawaiian plant radiations often result in lineages with exceptionally high species richness and extreme morphological and ecological differentiation. However, they typically display low levels of genetic variation, hindering the use of classic DNA markers to resolve their evolutionary histories. Here we utilize a phylogenomic approach to generate the first generally well-resolved phylogenetic hypothesis for the evolution of the Hawaiian Bidens (Asteraceae) adaptive radiation, including refined initial colonization and divergence time estimates. We sequenced the chloroplast genome (plastome) and nuclear ribosomal complex for 18 of the 19 endemic species of Hawaiian Bidens and 4 outgroup species. Phylogenomic analyses based on the concatenated dataset (plastome and nuclear) resulted in identical Bayesian and Maximum Likelihood trees with high statistical support at most nodes. Estimates from dating analyses were similar across datasets, with the crown group emerging ~1.76-1.82 Mya. Biogeographic analyses based on the nuclear and concatenated datasets indicated that colonization within the Hawaiian Islands generally followed the progression rule with 67-80% of colonization events from older to younger islands, while only 53% of events followed the progression rule in the plastome analysis. We find strong evidence for nuclear-plastome conflict indicating a potentially important role for hybridization in the evolution of the group. However, incomplete lineage sorting cannot be ruled out due to the small number of independent loci analyzed. This study contributes new insights into species relationships and the biogeographic history of the explosive Hawaiian Bidens adaptive radiation.

Evaluation of Growth, Photosynthetic Pigments and Genotoxicity in the Wetland Macrophyte Bidens laevis Exposed to Tebuconazole.

The fungicide tebuconazole (TBZ) has been used to prevent terrestrial fungi in agroecosystems, but it can also induce negative effects to non-targeted aquatic organisms, such as plants. The aim of the present work was to evaluate the potential cyto- and genotoxicity of TBZ in the aquatic macrophyte Bidens laevis, exposed to a range of concentrations of 0.1-100 µg/L. Mitosis in root tips were analyzed showing decreased mitotic index and an increase of chromosomal aberrations at 10 and 100 µg/L. The regression of TBZ concentration vs. aneugenic aberrations was significant, indicating the mechanism of genotoxicity. The specific growth rate (Gr) for total length decreased in plants exposed to 0.1, 10 and 100 µg/L. Gr for root decreased in plants exposed at 0.1 and 10 µg/L, reaching a maximum percent inhibition root growth rate (Ir) of 68.8%. These results show that TBZ resulted cyto- and genotoxic to B. laevis at environmentally relevant levels.

[Biomorphological Features and Microevolution of the Invasive Species Bidens L. in European Russia].

Species of the genus Bidens that have invaded natural communities in Europe were observed. Fourteen species have been introduced in European botanical gardens since the 18th century, but only two of them have become invasive in Russia-Bidensfrondosa and B. connata. B.frondosa demonstrates microevolutional ability in the second distribution range. Nevertheless, it has a low ability of hybridization. B. frondosa has higher competitiveness compared with that of B. connata.

Genetic and biochemical biomarkers in the macrophyte Bidens laevis L. exposed to a commercial formulation of endosulfan.

Previous studies in the wetland macrophyte Bidens laevis L have demonstrated that the insecticide endosulfan induces a high frequency of somatic chromosome aberrations in anaphase-telophase (CAAT) but no DNA changes as determined by the single cell gel electrophoresis (Comet) assay. Thus, cytogenetic biomarkers appear to be more sensitive to the toxic effects of the insecticide than the DNA molecule in the studied species. For this reason, the goals of this study were to use cytogenetic biomarkers--CAAT and abnormal metaphase--and defense biomarkers such as the activity of the antioxidant enzymes--guaiacol peroxidases (POD), glutathione reductase, and microsomal and cytosolic (m- and c-) glutathione-S-transferase (GST)--to evaluate in B. laevis effects caused by a commercial formulation of endosulfan. The frequency of CAAT was increased at 5, 10, 50, and 100 µg/L endosulfan with respect to the negative controls by 3.1, 2.5, 2.5, and 3.2-fold, respectively while the frequency of abnormal metaphases was also increased at the same concentrations by 3.5, 2.8, 3.2, and 11.3-fold, respectively. In addition to these aneugenic effects, other abnormalities such as C-mitosis and chromosome clumping were observed at 10 µg/L endosulfan. On the other hand, POD induction at 0.02, 0.5, 5, and 10 µg/L and m-GST inhibition at 0.5, 10, and 50 µg/L in plants exposed during 24 h to endosulfan were observed but all of these responses were highly variable. In conclusion, only cytogenetic biomarkers like CAAT in B. laevis can serve potentially as early warning systems to detect environmentally relevant concentrations of endosulfan in aquatic ecosystems.

Invasive congeners are unlikely to hybridize with native Hawaiian Bidens (Asteraceae).

PREMISE OF THE STUDY: Invasive plant species threaten native plants in multiple ways, one of which is genetic assimilation through hybridization. However, information regarding hybridization between related alien and native plant species is generally lacking. In Hawaii, the invasive Central American species Bidens pilosa and Bidens alba have colonized natural areas and often grow alongside the native Hawaiian Bidens species, a clade representing an adaptive radiation of 27 endemic taxa, many of which are threatened or endangered. • METHODS: To assess the risk of hybridization between introduced and native Hawaiian Bidens (which will readily hybridize with one another), we undertook crosses in cultivation between the invasive species and nine native Bidens taxa. • KEY RESULTS: The majority of the crosses formed no viable seed. Although seed did mature in several of the crosses, morphological screening of the resulting seedlings indicated that they were the result of self-pollination. • CONCLUSIONS: This result suggests that B. alba and B. pilosa are incapable of hybridizing with these Hawaiian Bidens taxa. Further, we found that B. alba in Hawaii was self-compatible, despite self-incompatibility throughout its native range, and that the tetraploid species B. alba and the hexaploid species B. pilosa were cross-compatible, although pollen fertility was low.

Bidens identification using the noncoding regions of chloroplast genome and nuclear ribosomal DNA.

Bidens pilosa L. is a plant producing barbed fruits which, due to its method of seed dispersal, is commonly found during forensic investigations. In Taiwan there are three varieties of the species, radiata, minor and pilosa. Fragments of these three varieties are difficult to differentiate by traditional morphological characteristics and until now little is known of their genetic composition. To discover genetic polymorphisms among these varieties, five loci within the nuclear and chloroplast genomes were screened. A total of 161 specimens were used in this study comprising different geographical populations. Seven samples of Bidens biternata were included as an out-group control. DNA fragments of all samples at the trnL intron and trnL-trnF IGS loci of the chloroplast genome, internal transcribed spacer (ITS1 and ITS2) and the 5.8S of nuclear ribosomal DNA (nrDNA) were amplified and sequenced. There were 3, 4, 20, 12 and 9 sequence types at these five loci, respectively. The sequence types for any locus of trnL intron, ITS1, ITS2 and 5.8S were found to be useful markers to identify Bidens biternata and B. pilosa. The resulting 84 haplotypes at the 5 loci could differentiate the var. radiata from the varieties of B. pilosa with only the exception of 1 type. The genetic polymorphisms can be used when comparing botanical remains to identify the variety of B. pilosa present at a crime scene.

Genotoxicity evaluation of the insecticide endosulfan in the wetland macrophyte Bidens laevis L.

The frequency of micronuclei (MN) and chromosome aberrations in anaphase-telophase (CAAT) was determined in root tips of the wetland macrophyte Bidens laevis exposed to environmentally relevant concentrations of endosulfan (0.01, 0.02, 0.5 and 5microg/L) for 48h. MN frequency varied from 0 in negative controls and plants exposed to 0.01microg/L endosulfan to 0-3 in plants exposed to 5microg/L. Moreover, a significant concentration-dependent increase of CAAT was observed. The higher proportion of laggards and vagrand chromosomes observed at 5microg/L would indicate that endosulfan interacts with the spindle interrupting normal chromosome migration. Endosulfan resulted genotoxic to B. laevis, a species of potential value for bioassays and in situ monitoring of environmental contamination by pesticides.

Low allozymic variation in the Bidens pilosa L. complex (Asteraceae).

Bidens alba, B. subalternans, and B. pilosa form a complex group based on their morphological similarities. Bidens pilosa L. and B. subalternans DC. are herbs with a wide distribution in agricultural and disturbed areas. Bidens alba (L.) DC. varies in size from herb to subshrub and has a coastal distribution. Enzyme electrophoresis was used to evaluate genetic diversity in 12 populations of Bidens. All but three loci (Lap-1, Est, and Got) were monomorphic. Est-1 and Got were polymorphic only in B. alba. Lap-1 was polymorphic only in B. pilosa and B. subalternans. The estimates of genetic variability were low for all three taxa and all of the populations studied. Genetic diversity varied from 0.01 to 0.03. Mean genetic identities were high among populations of each species (0.99 for B. alba and 1.00 for B. pilosa and B. subalternans) and among the three species (1.00). Bidens pilosa and B. subalternans could be considered a single species if the taxonomy of the group were based solely on isozyme data.