Project description:We sequenced the complete chloroplast of Firmiana danxiaensis (Malvaceae), which is 161,253 bp in size and consists of a large single-copy region (LSC) of 90,142 bp and a short single copy region (SSC) of 20,067 bp. It was separated by two inverted repeats (IRs) regions of 25,522 bp for each. The GC content of the whole genome, LSC, SSC, and IRs region was 36.87%, 34.68%, 31.24%, and 42.97%, respectively. The overall base content was A (31.07%), T (32.05%), C (18.80%), and G (18.08%). The genome contained 127 genes, including 82 protein-coding sequences, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that F. danxiaensis is sister to F. simplex, and supported there was a close relationship among F. danxiaensis, F. simplex, and F. pulcherrima.
Project description:Pileadanxiaensis L.F.Fu, A.K.Monro & Y.G.Wei, a new species of Urticaceae from Danxia landform, Guangdong, China, is described and photographed. Phylogenetic analyses based on three DNA regions (ITS, trnL-F and rbcL) suggest that the new species belongs to P.sect.Pilea. Within the section, the new species is morphologically most similar to P.sinocrassifolia and P.peploides. Plastid genome and ribosomal DNA (rDNA) sequences of the new species are assembled and annotated. The plastid genome is 151,857 bp in length and comprises two inverted repeats (IRs) of 25,307 bp separated by a large single-copy of 82,836 bp and a small single-copy of 18,407 bp. A total of 113 functional genes are recovered, comprising 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. A global conservation assessment suggests that P.danxiaensis should be classified as of Least Concern (LC).
Project description:Mazusdanxiacola, a new species endemic to Danxia landform in east Jiangxi Province, eastern China, is described and illustrated. The systematic placement of this new species was confirmed by molecular phylogenetic analyses based on four plastid markers (matK, rbcL, rps16 and trnL-trnF) and nuclear ribosome ITS sequence, and its specific relationships within Mazus were discussed. Morphologically, the new species is clearly different from other Mazus species by having a series of uncommon traits, i.e., annual habit, without stolons and basal leaves, single, erect and unbranched stems, long petiolate leaves abaxially grayish green to silver gray, truncate to broadly cuneate leaf bases, racemes extremely elongated up to 35 cm long, white corolla, and palate densely covered by conspicuous clavate gland-like hairs. The new species is assigned to Critically Endangered (CR) according to the IUCN Red List Categories and Criteria.
Project description:A new species of the genus Camellia (Theaceae), Camelliazijinica, discovered in the Danxia landscape from Guangdong Province, China, is characterized and illustrated. Phylogenetic analysis based on chloroplast genomes suggested its affinity with C.drupifera, C.oleifera and C.fluviatilis, however, it morphologically differs from all of the latter by leaf shape and size. Phonologically, it most closely resembles C.microphylla, but can be distinguished from the latter by its young branchlets glabrous (vs. densely pubescent), fewer bracteoles and sepals, diverse leaf shape, midvein raised slightly with sparsely pubescent or glabrous (vs. prominently with densely pubescent) and leaf adaxially matt (vs. vernicose) when dried. By morphological and molecular analyses, Camelliazijinica represented a distinct new species of C.sect.Paracamellia.
Project description:Many Firmiana species are locally endemic, providing an interesting system for studying adaptation and speciation. Among these species, F. danxiaensis is a tree species endemic to Mount Danxia in Guangdong, China, which is an area known for presenting the Danxia landform. How F. danxiaensis could have adapted to the stressful environment of rocky cliffs covered with barren soils in the Danxia landform is still unknown. In this study, we performed de novo assembly of the transcriptome of F. danxiaensis, obtaining 47,221 unigenes with an N50 value of 987 bp. Homology analysis showed that 32,318 of the unigenes presented hits in the NCBI non-redundant database, and 31,857 exhibited significant matches with the protein database of Theobroma cacao. Gene Ontology (GO) annotation showed that hundreds of unigenes participated in responses to various stresses or nutritional starvation, which may help us to understand the adaptation of F. danxiaensis to Danxia landform. Additionally, we found 263 genes related to responses to Cd, partially explaining the high accumulation of Cd observed in Firmiana species. The EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed many genes playing roles in the biosynthesis of secondary metabolites and environmental adaptation, which may also contribute to the survivor and success of Firmiana species in extreme environments. Based on the obtained transcriptome, we further identified a Firmiana-specific whole-genome duplication event that occurred approximately 20 Mya, which may have provided raw materials for the diversification of Firmiana species.
Project description:Dunnia sinensis, a monotypic genus of the Rubiaceae, is an Endangered species endemic to China. Its complete chloroplast genome was determined to be 154,909 bp in length and the GC content was 37.80%. The sequence includes a large single-copy region of 84,894 bp, a small single-copy region of 16,973 bp, and the inverted region of 26,521 bp in length. It contains 130 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ML and BI analyses revealed D. sinensis was closely related to Galium mollugo and Leptodermis scabrida with strong bootstrap values belonging to the subfamily Rubioideae.
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:Foonchewia coriacea, a monotypic genus of the Rubiaceae, is endemic to China. Its complete chloroplast genome was determined to be 153,114 bp in length and the GC content was 37.90%. The sequence includes a large single-copy region of 83,978 bp, a small single-copy region of 18,290 bp, and the inverted region is 25,423 bp in length. It contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood (ML) and Bayesian inference (BI) analyses revealed F. coriacea was closely related to Dunnia sinensis with strong bootstrap values, belonging to the subfamily Rubioideae.
Project description:The complete chloroplast (cp) genome sequence of Clematis taeguensis Y.N.Lee (Ranunculaceae) was determined to be 159,534 bp in length, consisting of large (79,326 bp) and small (18,338 bp) single-copy regions and a pair of identical inverted repeats (30,935 bp). The genome contains 92 protein-coding genes, 32 tRNA genes, 8 rRNA genes, and 1 pseudogene (infA). Phylogenetic analysis of 19 taxa inferred from the chloroplast genome showed a relationship with C. taeguensis, which is also recognized as a species endemic to the Korean Peninsula. The complete cp genome sequence of C. taeguensis reported here provides important information for future phylogenetic and evolutionary studies in Ranunculaceae.
Project description:Heteroplexis incana (Asteraceae) is a rare species endemic to China. Here, we report and characterize the complete chloroplast genome sequence of H. incana based on Illumina paired-end sequencing data. The complete plastid genome was 152,605 bp in length, which contained two inverted repeats (IRs) of 24,954 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,427 bp and 18,270 bp, respectively. The cpDNA contains 132 genes, comprising 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 37.3%. The phylogenetic analysis of 17 selected chloroplast genomes demonstrated that Heteroplexis incana was closely related to Aster indicus.