Project description:Ranunculus yunnanensis Franch is endemic in Yunnan and Sichuan Provinces, southwestern China. Here, we report the complete chloroplast (cp) genome of R. yunnanensis. The chloroplast genome is 156,050 bp in length, with 111 encoded genes, including 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. Maximum-likelihood phylogenetic reconstruction using the existing data of Ranunculus shows that R. yunnanensis is revealed at the basal position of the marsh buttercup clade. This result has improved a better understanding of the internal relationship of the Ranunculus.
Project description:Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed among Ranunculus species. The chloroplast genome was assembled from Illumina HiSeq 2500 sequencing raw data. The genome was 156,329 bp and had a typical quadripartite structure comprising a small single-copy region, a large single-copy region, and two inverted repeats. Fifty-three simple sequence repeats were identified in the four quadrant structural regions. The region between the ndhC and trnV-UAC genes could be useful as a genetic marker to distinguish between R. sceleratus populations from Republic of Korea and China. The Ranunculus species formed a single lineage. To differentiate between Ranunculus species, we identified 16 hotspot regions and confirmed their potential using specific barcodes based on phylogenetic tree and BLAST-based analyses. The ndhE, ndhF, rpl23, atpF, rps4, and rpoA genes had a high posterior probability of codon sites in positive selection, while the amino acid site varied between Ranunculus species and other genera. Comparison of the Ranunculus genomes provides useful information regarding species identification and evolution that could guide future phylogenetic analyses.
Project description:Ranunculus pekinensis (L. Liou) Luferov 1997, a perennial aquatic herb, is endemic to Beijing, China and has high water quality requirements. Because its habitat is under great threat and its population is declining, it is now listed as a national protected plant in China. To provide genomic resources for future research of this endangered species, the complete chloroplast genome sequence of R. pekinensis was assembled and annotated for the first time. The complete chloroplast genome sequence was 156,139 bp in length, containing a large single copy region (LSC) of 85,430 bp and a small single copy region (SSC) of 19,970 bp, which were separated by a pair of 25,367 bp inverted repeat regions (IRs). The complete chloroplast sequence contained 112 unique genes, including 30 tRNA, 4 rRNA, and 78 protein-coding genes. The overall guanine-cytosine (GC) content of the chloroplast genome was 37.8%, and the GC contents of the LSC, SSC, and IR regions were 36.0%, 31.3%, and 43.5%, respectively. Phylogenetic analysis with the reported chloroplast sequences showed that R. pekinensis was closely related to R. bungei Steud. 1841, both of which belonged to Ranunculus Sect. Batrachium DC. 1817. These data will provide essential resources regarding the evolution and conservation of R. pekinensis.
Project description:The complete chloroplast genome sequence of Caltha palustris, a species of the Ranunculaceae family, was characterized from the de novo assembly of HiSeq (Illumina Co.) paired-end sequencing data. The chloroplast genome of C. palustris was 155,292 bp in length, with a large single-copy (LSC) region of 84,120 bp, a small single-copy (SSC) region of 18,342 bp, and a pair of identical inverted repeat regions (IRs) of 26,415 bp. The genome contained a total of 114 genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The phylogenetic analysis of C. palustris with 14 related species revealed the closest taxonomical relationship with Hydrastis canadensis in the Ranunculaceae family.
Project description:Beesia deltophylla is an endemic and rare species only distributed in Xizang, China. The chloroplast genome of B. deltophylla is 157,397 bp in length, with 112 encoded genes including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic reconstruction has confirmed the placement of B. deltophylla as sister to B. calthifolia. These two species formed a clade closely to a Japan endemic species Anemonopsis macrophylla.
Project description:The perennial herbal medicine species Aconitum tschangbaischanense, is endemic to Changhai Mountain, Jilin province. In this study, we attempted to uncover the complete chloroplast (cp) genome of A. tschangbaischanense based on sequencing data using the Illumina sequencing technology. As per the results: (1) the length of its complete cp genome is 155,881 bp with a typical tetrad structure; (2) the structure of its cp genome contains large single-copy and small single-copy (LSC and SSC) regions of 86,351 and 16,9444 bp, respectively, isolated by two inverted repeat regions (IRs) of 26,293 bp; (3) we annotated a total 131 genes, consisting of 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. According to the maximum-likelihood phylogenetic tree based on complete cp genomes, A. tschangbaischanense, showed close association with A. carmichaelii, which belongs to clade I. Finally, this study provides the characteristics of the cp genome of A. tschangbaischanense, and its phylogenetic position.
Project description:The complete chloroplast genome sequence of Anemone reflexa exhibited a typical quadripartite structure with two inverted repeats (IRa and IRb) of 31,260 bp, a large single-copy region (LSC) of 80,767 bp, and a small single-copy region (SSC) of 17,623 bp. The chloroplast genome encoded a set of 133 genes, comprised of 89 protein coding genes, 36 tRNA genes and 8 rRNA genes. Phylogenetic analysis suggested that A. reflexa was closely related to A. raddeana. The complete chloroplast genome sequence of A. reflexa will provide valuable genetic resources for molecular identification and phylogenetic analysis of Anemone.
Project description:Eranthis stellate belong to Ranunculaceae, which is interest in phylogenetic research because it has often been considered one of the most basal eudicots families. However, there are few chloroplastg enome data of Ranunculaceae available. Here, to provide available genomic data for the phylogenetic of Ranunculaceae, we determined the complete chloroplast genome of E. stellate. The complete chloroplast sequence is 158,817 bp, including a large single-copy (LSC) region of 87,137 bp, a small single-copy (SSC) region of 16,834 bp, a pair of invert repeats (IR) regions of 27,424 bp. Plastid genome contain129 genes, 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 14 chloroplast genomes indicates that E. stellata is sister to Aconitum austrokoreense clade in Ranunculaceae.
Project description:Ranunculus japonicus is an important medicinal herb widely used in East Asia. In this study, we report the first complete chloroplast genome sequence of Ranunculus japonicus using next-generation sequencing technology. The chloroplast genome size of R. japonicus was 156,981 bp. A total of 129 genes were included, consisting 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Thirteen protein-coding genes had intron (ycf3 gene, rps12 gene, rps12 gene, clpP gene contained two introns). A further phylogenomic analysis of Ranunculaceae, including 10 taxa, was conducted for assessing the placement of R. japonicus. It will provide valuable genetic information for this medicinally important species.