Characterization of the complete chloroplast genome of Viburnum schensianum (Adoxaceae).
ABSTRACT: The whole chloroplast (cp) genome sequence of Viburnum schensianum 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 V. schensianum is closely related to the species of V. utile.
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:<i>Viburnum erosum</i> is a deciduous shrub distributed in eastern Asia. As part of the systematic study to understand the phylogenetic relationship of <i>V</i>. <i>erosum</i>, we present the complete chloroplast genome of <i>V</i>. <i>erosum</i>. 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 <i>V. erosum</i> is sister to <i>Viburnum japonicum</i>, supporting morphological affinity of the two species.
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: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:The whole chloroplast (cp) genome sequence of <i>Musella lasiocarpa</i> has been characterized from Illumina pair-end sequencing. The complete cp genome was 169,178?bp in length, containing a large single copy (LSC) region of 87,884?bp and a small single copy (SSC) region of 11,144?bp, which were separated by a pair of 35,075?bp inverted repeat (IR) regions. The genome contained 138 genes, including 88 protein-coding genes (87 PCG species), 37 tRNA genes (30 tRNA species), and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 23 gene species occur in double copies. The overall AT content of <i>M. lasiocarpa</i> cp genome is 63.3%, while the corresponding values of the LSC, SSC, and IR regions are 64.9, 69.2, and 60.3%, respectively. The cp genome sequence is similar to that of the genus Musa.
Project description:The whole chloroplast (cp) genome sequence of <i>Actinidia melanandra</i> has been characterized from Illumina pair-end sequencing. The complete cp genome was 156,124?bp in length, containing a large single-copy region (LSC) of 88,006?bp and a small single-copy region (SSC) of 20,332?bp, which were separated by a pair of inverted repeat (IR) regions of 23,893?bp. The genome contained 131 genes, including 84 protein-coding genes, 39 tRNA genes, and 8 ribosomal RNA genes (4 rRNA species). Most genes occur as a single copy, while 17 gene species are duplicated. Phylogenetic analysis revealed that <i>A. melanandra</i> is closely related to the species of <i>A. deliciosa</i> and <i>A. chinensis.</i>
Project description:The complete chloroplast (cp) genome sequence of <i>Actinidia eriantha</i> was sequenced and assembled using Illumina paired-end data. The cp genome from <i>A. eriantha</i> is 156,964?bp in length, composed of a pair of 23,892?bp inverted repeat regions (IR) separated by a large single copy region (LSC) of 88,639?bp and a small single copy region (SSC) of 20,541?bp. The cp genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four ribosomal RNA genes. The phylogenetic position of <i>A. eriantha</i> based the cp genome data was sister to the group <i>A. rufa</i>, <i>A. deliciosa</i>, and <i>A. chinensis</i>.
Project description:In this study, the complete chloroplast (cp) genome of <i>Melampyrum roseum</i> was determined through Illumina sequencing method. The complete cp genome of <i>M. roseum</i> was 143,896?bp in length and contained a pair of IR regions (25,210?bp) separated by a small single-copy region (10,292?bp) and a large single-copy region (83,184?bp). The cp genome of <i>M. roseum</i> encoded 117 genes including 78 protein-coding genes, 31 tRNA genes, and 8 rRNA genes. The overall GC content of <i>M. roseum</i> cp genome is 38.1%. By phylogenetic analysis using maximum-likelihood (ML) method, <i>M. roseum</i> was placed in Rhinantheae clade as expected.