Project description:BACKGROUND: Transcriptome sequencing analysis is a powerful tool in molecular genetics and evolutionary biology. Here we report the results of de novo 454 sequencing, characterization, and comparison of inflorescence transcriptomes of two closely related dogwood species, Cornus canadensis and C. florida (Cornaceae). Our goals were to build a preliminary source of genome sequence data, and to identify genes potentially expressed differentially between the inflorescence transcriptomes for these important horticultural species. RESULTS: The sequencing of cDNAs from inflorescence buds of C. canadensis (cc) and C. florida (cf), and normalized cDNAs from leaves of C. canadensis resulted in 251799 (ccBud), 96245 (ccLeaf) and 114648 (cfBud) raw reads, respectively. The de novo assembly of the high quality (HQ) reads resulted in 36088, 17802 and 21210 unigenes for ccBud, ccLeaf and cfBud. A reference transcriptome for C. canadensis was built by assembling HQ reads of ccBud and ccLeaf, containing 40884 unigenes. Reference mapping and comparative analyses found 10926 sequences were putatively specific to ccBud, and 6979 putatively specific to cfBud. Putative differentially expressed genes between ccBud and cfBud that are related to flower development and/or stress response were identified among 7718 shared sequences by ccBud and cfBud. Bi-directional BLAST found 87 (41.83% of 208) of Arabidopsis genes related to inflorescence development had putative orthologs in the dogwood transcriptomes. Comparisons of the shared sequences by ccBud and cfBud yielded 65931 high quality SNPs between two species. The twenty unigenes with the most SNPs are listed as potential genetic markers for evolutionary studies. CONCLUSIONS: The data provide an important, although preliminary, information platform for functional genomics and evolutionary developmental biology in Cornus. The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and/or disease resistance in dogwoods for future analyses. Results of the study also provide markers useful for dogwood phylogenomic studies.
Project description:Big-bracted dogwoods (Cornus sp.) are well-known plants in North America and eastern Asia where they occur as wild, generally spring-flowering understory trees. They are also popular ornamental landscape plants, and many economically important cultivars are propagated and sold across North America, Europe, and Asia. Starting in the late 1960s, Elwin Orton of Rutgers University in New Jersey (USA) utilized three geographically disjunct species of dogwoods, Cornusflorida (eastern North America), Cornusnuttallii (western North America), and Cornuskousa (East Asia), in an extensive interspecific hybridization program. He was successful in developing the first-ever interspecific F1 hybrids of these species, several of which have become staple items in the ornamental nursery trade due to their enhanced ornamental qualities and resistance to diseases. The original F1 plants are still alive at Rutgers University. While they have been available for decades in horticultural commerce, the interspecific hybrid crosses were never formally described and their scientific hybrid names were never published. For the Cornuskousa × Cornusflorida hybrids, the name Cornus 'rutgersensis' has been used on occasion in the horticultural trade, but without proper citation and description. Here, it is formally named Cornus×rutgersensis Mattera, T. Molnar, & Struwe, hybr. nov. For the Cornuskousa × Cornusnuttallii hybrids, no previous name has been used, and it is hereby named Cornus×elwinortonii Mattera, T. Molnar, & Struwe, hybr. nov. The need for providing scientific names for commonly used horticultural hybrids is discussed. Holotype material for both hybrid names was collected from the original F1 hybrids for full documentation, typification, and description. The comparative intermediate development of leaves, inflorescence structures, and fruit types of the hybrids and their parents is discussed and illustrated. Etymology, phenology, and cultivation aspects of these hybrids and their cultivars including backcrosses to Cornuskousa are also presented.
Project description:Chloroplast DNA is a part of plant non-nuclear genome, and is of particular interest for lineage studies. Moreover, the non-coding regions of cpDNA display higher mutation rates than the conserved coding cpDNA, which has been employed for phylogenetic and population research. We analyzed the cpDNA of 332 gDNA samples from collections of Cornus florida and C. kousa (commercial cultivars, breeding selections, and wild kousa accessions from Asia), using the chlorotyping system developed on North America-native, wild accessions of C. florida. Our results indicated significant differences in chlorotype frequencies between the two species. Cornus florida samples were represented by all major chlorotypes previously described, whereas all C. kousa samples analyzed had only one of the chlorotype patterns shown by C. florida. The chlorotyping analytic panel was then expanded by sequencing the targeted three non-coding cpDNA regions. Results indicated a major difference in the maternally-inherited cpDNA between the two closely related Big-Bracted Cornus species. Chlorotype diversity and differences in the proportion of informative sites in the cpDNA regions of focus emphasized the importance of proper loci choice for cpDNA-based comparative studies between the closely related dogwood species. Phylogenetic analyses of the retrieved sequences for the other species of Cornus provided information on the relative utility of the cpDNA regions studied and helped delineate the groups (Big-Bracted, Cornelian Cherries, Blue/White-Fruited) within the genus. Genealogical relationships based on the cpDNA sequences and the inferred chlorotype networks indicated the need for continued analyses across further non-coding cpDNA regions to improve the phylogenetic resolution of dogwoods.
Project description:The fruits of some Cornus species (dogwoods) are used in traditional medicine and considered potential anti-diabetic and hypolipemic agents. The aim of the study was to determine the ability of extracts from Cornus alba (CA), Cornus florida (CF), and Cornus sanguinea (CS) to inhibit digestive enzymes namely ?-amylase, pancreatic lipase, and ?-glucosidase, as well as isolation of compounds from plant material with the strongest effect. In addition, the phytochemical profile and antioxidant activity of extracts from three dogwoods were compared with HPLC-DAD-MS/MS and DPPH scavenging assay, respectively. Among the aqueous-ethanolic extracts, the activity of ?-amylase was the most strongly inhibited by the fruit extract of CA (IC50 = 115.20 ± 14.31 ?g/mL) and the activity of ?-glucosidase by the fruit of CF (IC50 = 38.87 ± 2.65 ?g/mL). Some constituents of CA fruit extract, such as coumaroylquinic acid, kaempferol, and hydroxytyrosol derivatives, were isolated. Among the three species of dogwood studied, the greatest biological potential was demonstrated by CA extracts, which are sources of phenolic acids and flavonoid compounds. In contrast, iridoid compounds or flavonoid glycosides found in fruits of CF or CS extracts do not play a significant role in inhibiting digestive enzymes but exert antioxidant activity.
Project description:Cornus officinalis, an important traditional medicinal plant, is used as major constituents of tonics, analgesics, and diuretics. While several studies have focused on its characteristic bioactive compounds, little is known on their biosynthesis. In this study, we performed LC-QTOF-MS-based metabolome and RNA-seq-based transcriptome profiling for seven tissues of C. officinalis. Untargeted metabolome analysis assigned chemical identities to 1,215 metabolites and showed tissue-specific accumulation for specialized metabolites with medicinal properties. De novo transcriptome assembly established for C. officinalis showed 96% of transcriptome completeness. Co-expression analysis identified candidate genes involved in the biosynthesis of iridoids, triterpenoids, and gallotannins, the major group of bioactive metabolites identified in C. officinalis. Integrative omics analysis identified 45 cytochrome P450s genes correlated with iridoids accumulation in C. officinalis. Network-based integration of genes assigned to iridoids biosynthesis pathways with these candidate CYPs further identified seven promising CYPs associated with iridoids' metabolism. This study provides a valuable resource for further investigation of specialized metabolites' biosynthesis in C. officinalis.
Project description:The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants.