The complete chloroplast genome sequence of Viburnum erosum (Adoxaceae).
ABSTRACT: Viburnum erosum is a deciduous shrub distributed in eastern Asia. As part of the systematic study to understand the phylogenetic relationship of V. erosum, we present the complete chloroplast genome of V. erosum. Its length is 158,624?bp and it has four subregions: 87,060?bp of large single-copy and 18,530?bp of small single-copy regions separated by a pair of inverted repeat regions of 26,517?bp each, including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic analyses show that V. erosum is sister to Viburnum japonicum, supporting morphological affinity of the two species.
Project description:The wax-leafed <i>Viburnum japonicum</i> (Adoxaceae) is an evergreen shrub distributed in Japan, Korea, and Taiwan. We sequenced its complete chloroplast (cp) genome to examine its phylogenetic relationship within Dipsacales. This genome is 158,614?bp long and features a large single-copy region (87,059?bp) and a small single-copy region (18,523?bp), separated by two inverted-repeat regions (26,516?bp each). It contains 128 genes, including 84 coding genes, eight rRNAs, and 36 tRNAs. The overall GC content is 38.1%. Our phylogenetic tree showed that <i>V</i>. <i>japonicum</i> is closely related to <i>V</i>. <i>utile</i> and is clustered together with four species in the family Adoxaceae.
Project description:We presented the second complete chloroplast genome of the plant. The length of chloroplast genome is 158,587?bp, consisting of four subregions: 87,050?bp of LSC and 18,503?bp of SSC regions separated by a pair of 26,517?bp IR regions. It includes 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). A low-level of molecular variation within <i>Viburnum erosum</i> was found with 16 SNPs and 49 indels. The phylogenetic tree shows that the two accessions of <i>V. erosum</i> are clustered with <i>Viburnum japonicum</i> with no resolution between the species, suggesting that chloroplast genome in these species evolve slowly.
Project description:The whole chloroplast (cp) genome sequence of <i>Viburnum schensianum</i> has been characterized from Illumina pair-end sequencing. The complete cp genome was 158,408?bp in length, containing a large single copy region (LSC) of 86,998?bp and a small single copy region (SSC) of 18,386?bp, which were separated by a pair of inverted repeat (IR) regions of 26,512?bp. The genome contained 130 genes, including 84 protein-coding genes, 37 tRNA genes, eight ribosomal RNA genes (four rRNA species), and a pseudogene. Most genes occur as a single copy, whereas 16 gene species are duplicated. Phylogenetic analysis revealed that <i>V. schensianum</i> is closely related to the species of <i>V. utile.</i>
Project description:Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.
Project description:PREMISE OF THE STUDY:Microsatellite loci were isolated from four species of Viburnum (Adoxaceae) to study population structure and assess species boundaries among morphologically similar South American Viburnum species of the Oreinotinus clade. METHODS AND RESULTS:Using a microsatellite-enriched library and mining next-generation sequence data, 16 microsatellites were developed. Each locus was tested on two populations of V. triphyllum and one population of V. pichinchense. For nuclear loci, one to 13 alleles were recovered, expected heterozygosity ranged from 0 to 0.8975, Simpson diversity index ranged from 0.0167 to 1.000, and Shannon diversity index ranged from 0 to 2.3670 in a given population. For the mitochondrial locus, three to six alleles were recovered and unbiased haploid diversity values ranged from 0.756 to 0.853 in a given population. CONCLUSIONS:The 16 microsatellite loci developed for the Oreinotinus clade (Viburnum, Adoxaceae) will inform investigations of population structure and species boundaries within this group.
Project description:Comparative wood anatomy of Viburnum was carried out to understand the differences in wood features amongst the species which might be useful for taxonomic discrimination in the genus. Altogether, nine taxa belonging to five clades were investigated using a sliding microtome and light microscopy. The growth rings are well represented and earlywood and latewood are distinguishable in cross-section. Some of the important wood features include angular, oval and rounded vessels with scalariform perforation plates, opposite to scalariform inter-vessel pitting, rounded pits with slit-like apertures, thick-walled xylem tracheids with simple, rounded bordered pits, diffuse axial parenchyma, uni- and multiseriate rays, 2-4 cells wide. In general, there is a remarkable uniformity in the qualitative wood features in Viburnum species, although quantitative measurement showed some disparities. The most significant quantitative wood variables which might be useful for taxonomic groupings of the species comprise a frequency of vessels and rays, the diameter of the vessels and tracheids in the radial and tangential planes and height and width of rays in the tangential plane.
Project description:<h4>Background</h4>The chloroplast genes matK and rbcL have been proposed as a "core" DNA barcode for identifying plant species. Published estimates of successful species identification using these loci (70-80%) may be inflated because they may have involved comparisons among distantly related species within target genera. To assess the ability of the proposed two-locus barcode to discriminate closely related species, we carried out a hierarchically structured set of comparisons within Viburnum, a clade of woody angiosperms containing ca. 170 species (some 70 of which are currently used in horticulture). For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS).<h4>Results</h4>At most, rbcL + matK could discriminate 53% of all Viburnum species, with only 18% of the comparisons having genetic distances >1%. When comparisons were progressively restricted to species within major Viburnum subclades, there was a significant decrease in both the discriminatory power and the genetic distances. trnH-psbA and nrITS show much higher levels of variation and potential discriminatory power, and their use in plant barcoding should be reconsidered. As barcoding has often been used to discriminate species within local areas, we also compared Viburnum species within two regions, Japan and Mexico and Central America. Greater success in discriminating among the Japanese species reflects the deeper evolutionary history of Viburnum in that area, as compared to the recent radiation of a single clade into the mountains of Latin America.<h4>Conclusions</h4>We found very low levels of discrimination among closely related species of Viburnum, and low levels of variation in the proposed barcoding loci may limit success within other clades of long-lived woody plants. Inclusion of the supplementary barcodes trnH-psbA and nrITS increased discrimination rates but were often more effective alone rather than in combination with rbcL + matK. We surmise that the efficacy of barcoding in plants has often been overestimated because of the lack of comparisons among closely related species. Phylogenetic information must be incorporated to properly evaluate relatedness in assessing the utility of barcoding loci.
Project description:<i>Diospyros</i> is the largest genus (about 485 species) in Ebenaceae. It is a deciduous or evergreen tree or shrub. It grows in pantropical and extending into temperate regions. Here, we report and characterize the complete plastid genome sequences of <i>D. maclurei</i> Merr. and <i>D. hainanensis</i> Merr. in an effort to provide genomic resources useful for promoting their systematics research and potential economic development. The complete plastome of <i>D. maclurei</i> is 157,946?bp in length, including two Inverted Repeat (IR) regions of 26,081?bp, a Large Single-Copy (LSC) region of 87,387?bp, and a Small Single-Copy (SSC) region of 18,397?bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of <i>D. maclurei</i> is 62.60%. The complete plastome of <i>D. hainanensis</i> is 157,999?bp in length, including two Inverted Repeat (IR) regions of 26,077?bp, a Large Single-Copy (LSC) region of 87,523?bp, and a Small Single-Copy (SSC) region of 18,322?bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of <i>D. hainanensis</i> is 62.60%. The complete plastome sequences of <i>D. Maclurei</i> and <i>D. hainanensis</i> will provide a useful resource for the conservation genetics of the two species as well as for the phylogenetic studies of <i>Diospyros.</i>
Project description:Angiosperms with simple vessel perforations have evolved many times independently of species having scalariform perforations, but detailed studies to understand why these transitions in wood evolution have happened are lacking. We focus on the striking difference in wood anatomy between two closely related genera of Adoxaceae, Viburnum and Sambucus, and link the anatomical divergence with climatic and physiological insights.After performing wood anatomical observations, we used a molecular phylogenetic framework to estimate divergence times for 127 Adoxaceae species. The conditions under which the genera diversified were estimated using ancestral area reconstruction and optimization of ancestral climates, and xylem-specific conductivity measurements were performed.Viburnum, characterized by scalariform vessel perforations (ancestral), diversified earlier than Sambucus, having simple perforations (derived). Ancestral climate reconstruction analyses point to cold temperate preference for Viburnum and warm temperate for Sambucus This is reflected in the xylem-specific conductivity rates of the co-occurring species investigated, showing that Viburnum lantana has rates much lower than Sambucus nigra CONCLUSIONS: The lack of selective pressure for high conductive efficiency during early diversification of Viburnum and the potentially adaptive value of scalariform perforations in frost-prone cold temperate climates have led to retention of the ancestral vessel perforation type, while higher temperatures during early diversification of Sambucus have triggered the evolution of simple vessel perforations, allowing more efficient long-distance water transport.
Project description:PREMISE:A key question in plant dispersal via animal vectors is where and why fruit colors vary between species and how color relates to other fruit traits. To better understand the factors shaping the evolution of fruit color diversity, we tested for the existence of syndromes of traits (color, morphology, and nutrition) in the fruits of Viburnum. We placed these results in a larger phylogenetic context and reconstructed ancestral states to assess how Viburnum fruit traits have evolved across the clade. RESULTS:We find that blue Viburnum fruits are not very juicy, and have high lipid content and large, round endocarps surrounded by a small quantity of pulp. Red fruits display the opposite suite of traits: they are very juicy with low lipid content and smaller, flatter endocarps. The ancestral Viburnum fruit may have gone through a sequence of color changes before maturation (green to yellow to red to black), though our reconstructions are equivocal. In one major clade of Viburnum (Nectarotinus), fruits mature synchronously with reduced intermediate color stages. Most transitions between fruit colors occurred in this synchronously fruiting clade. CONCLUSIONS:It is widely accepted that fruit trait diversity has primarily been driven by the differing perceptual abilities of bird versus mammal frugivores. Yet within a clade of largely bird-dispersed fruits, we find clear correlations between color, morphology, and nutrition. These correlations are likely driven by a shift from sequential to synchronous development, followed by diversification in color, nutrition, and morphology. A deeper understanding of fruit evolution within clades will elucidate the degree to which such syndromes structure extant fruit diversity.