Project description:Thalictrum is a phylogenetically and economically important genus in the family Ranunculaceae, but is also regarded as one of the most challengingly difficult in plants for resolving the taxonomical and phylogenetical relationships of constituent taxa within this genus. Here, we sequenced the complete plastid genomes of two Thalictrum species using Illumina sequencing technology via de novo assembly. The two Thalictrum plastomes exhibited circular and typical quadripartite structure that was rather conserved in overall structure and the synteny of gene order. By updating the previously reported plastome annotation of other nine Thalictrum species, we found that the expansion or contraction of the inverted repeat region affect the boundary of the single-copy regions in Thalictrum plastome. We identified eight highly variable noncoding regions-infA-rps8, ccsA-ndhD, trnSUGA-psbZ, trnHGUG-psbA, rpl16-rps3, ndhG-ndhI, ndhD-psaC, and ndhJ-ndhK-that can be further used for molecular identification, phylogenetic, and phylogeographic in different species. Selective pressure and codon usage bias of all the plastid coding genes were also analyzed for the 11 species. Phylogenetic relationships showed Thalictrum is monophyly and divided into two major clades based on 11 Thalictrum plastomes. The availability of these plastomes offers valuable genetic information for accurate identification of species and taxonomy, phylogenetic resolution, and evolutionary studies of Thalictrum, and should assist with exploration and utilization of Thalictrum plants.
Project description:Saxifraga giraldiana Engler is a common subalpine and alpine plant belonging to Saxifragaceae. However, the genetic diversity of this species has remained to be explored. In this study, we have assembled and characterized the complete chloroplast genome of S. giraldiana, filling this knowledge gap and uncovering its genetic composition. The chloroplast genome is 147,267 bp long and contains 131 genes, including 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Furthermore, we have performed a phylogenetic analysis of 19 representative species within Saxifraga. As a result, we have found that S. giraldiana, together with S. implicans and S. stellariifolia, forms a monophyletic group. These findings have implications for the conservation and utilization of S. giraldiana.
Project description:Thalictrum aquilegiifolium var. sibiricum, is an annual herb that grows on slopes or in mountain gullies in areas of damp forest. In this study, we report for the first time the complete plastome sequence of T. aquilegiifolium var. sibiricum. The plastome sequence is 156,244 bp in length and comprises a large single-copy region (85,447 bp), a small single-copy region (17,599 bp), and a pair of inverted repeat regions (26,480 bp). The genome encodes 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and four rRNAs, and has total GC content of 38.4%. Phylogenomic analysis based on the plastome sequences of 20 species in the family Ranunculaceae indicated that T. aquilegiifolium var. sibiricum is clustered with Thalictrum minus.
Project description:The complete plastome of Gymnotheca chinensis, an important medicinal herb, was firstly elucidated and analyzed in this study. The plastome is 161,621 bp in size, which comprises of one large single-copy (LSC) region and one small single-copy (SSC) region of 89,291 bp and 18,592 bp, respectively, separated by a pair of IR regions of 26,869 bp each. It encodes a total of 132 genes, including 87 protein-coding genes, 37 tRNA, and 8 rRNA. The phylogeny robustly supports that G. chinensis is sister to the clade including Piper kadsura, Piper cenocladum, Saruma henryi, Asarum sieboldii.
Project description:Polygonatum cirrhifolium (Wall.) Royle is a medicinal plant of commercial value. In the present study, we assembled the complete chloroplast genome of P. cirrhifolium. The total genome was a circular DNA molecule of 155,583 bp, which was made up of a large single copy region (84,412 bp), a small single copy region (18,427 bp), and a pair of inverted repeat regions (26,372 bp each). A total of 133 genes was annotated in the chloroplast genome, including 85 protein-coding genes, 40 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Overall, the chloroplast genome had a GC content of 37.66%. Phylogenetic analysis showed that P. cirrhifolium was closely related to P. kingianum.
Project description:The complete chloroplast genome (plastome) of Maclura tricuspidate Carriere, a thorny and deciduous tree, is determined. The plastome is 161,348 bp in length, consisting of a 89,364 bp large single-copy region, a 20,246 bp small single-copy region, and two 25,869 bp inverted repeat regions. The GC content of this plastome is 36.1%. A total of 112 unique genes are annotated for the plastome of M. tricuspidata, containing 78 protein coding genes (PCGs), 30 tRNAs, and four rRNAs. Phylogenetic analysis shows that M. tricuspidata is sister to the clade comprising Dorstenieae, Castilleae, and Ficeae.
Project description:Tanakaea radicans is classified in the monotypic genus Tanakaea in the Saxifragaceae. It is a small, evergreen plant with a disjunct distribution in Japan and China. Here, we report and characterize for the first time the complete plastid genome sequence of T. radicans. The chloroplast genome is 155,265 bp in length and contains a pair of inverted repeats (25,794 bp) separated by a large single copy (86,289 bp) and a small single copy (17,388 bp). A total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes, were annotated. Phylogenetic analysis showed that T. radicans was sister to Leptarrhena pyrolifolia within Huecheroids linage of Saxifragaceae.
Project description:Bactris gasipaes var. gasipaes (Arecaceae, Palmae) is an economically and socially important plant species for populations across tropical South and Central America. It has been domesticated from its wild variety, B. gasipaes var. chichagui, since pre-Columbian times. In this study, we sequenced the plastome of the cultivated variety, B. gasipaes Kunth var. gasipaes and compared it with the published plastome of the wild variety. The chloroplast sequence obtained was 156,580 bp. The cultivated chloroplast sequence was conserved compared to the wild type sequence with 99.8% of nucleotide identity. We did, however, identify multiple Single Nucleotide Variants (SNVs), insertions, microsatellites and a resolved region of missing nucleotides. A SNV in one of the core barcode markers (matK) was detected between the wild and cultivated accessions. Phylogenetic analysis was carried out across the Arecaceae family and compared to previous reports, resulting in an identical topology. This study is a step forward in understanding the genome evolution of this species.
Project description:Veronica undulata is a perennial herb, and the complete chloroplast genome (plastome) of V. undulata was determined in this study. The results showed that the plastome size of V. undulata was 151,178 bp, including a large single-copy region (68,533 bp), a small single-copy region (21,403 bp), and two inverted repeat regions (25,566 bp). The total GC content of the plastome was 38.1%. We annotated 115 unique genes in the plastome, including 81 protein-coding genes (PCGs), 30 tRNAs, and four rRNAs. Phylogenetic analysis showed that the species of V. undulata and Veronica clustered together.
Project description:Campsis radicans (L.) Bureau 1864, a species of Bignoniaceae, has a widespread paleotropical distribution and is utilized for horticultural and traditional Chinese medicinal purposes. Despite the plant's significance, its genetic diversity must be better understood. In this study, we have successfully assembled and characterized the complete plastome of C. radicans, marking a significant advancement toward comprehending its genetic composition. The plastome is 153,630 bp long and harbors 130 genes, including 86 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Our phylogenomic analysis of the representative species of Bignoniaceae indicated that C. radicans formed a monophyletic sister clade of Campsis with C. grandiflora. These findings are crucial for conserving and utilizing this important plant species. They also highlight the potential for future research into the evolution and preservation of C. radicans, which could be advantageous in pharmaceutical applications.