Characterization of the complete plastid genome of Rauvolfia verticillata (Apocynaceae), with its phylogenetic analysis.
ABSTRACT: Rauvolfia verticillata is a medical plant (Apocynaceae) widely distributed from India to China, the Indo-China Peninsula, Indonesia, and the Philippines. The first complete plastid genome sequence of the species reported here was 155,856?bp in length, with the large single-copy (LSC) region of 86,085?bp, the small single-copy (SSC) region of 18,299?bp, and two inverted repeats (IRa and IRb) of 25,736?bp. The plastome contained 113 unique genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content was 37.92%. The result from phylogenetic analysis suggests that Rauvolfia is closely related to the genus Catharanthus.
Project description:A reassessment of collections of Marquesan Apocynaceae assigned to the genera Neisosperma Raf., Ochrosia Juss., and Rauvolfia L. revealed that two nomenclatural changes are necessary: 1) transfer of Neisosperma brownii Fosberg & Sachet to the genus Ochrosia, as Ochrosia brownii (Fosberg & Sachet) Lorence & Butaud, comb. nov., and 2) transfer of Ochrosia nukuhivensis Fosberg & Sachet to Rauvolfia as Rauvolfia nukuhivensis (Fosberg & Sachet) Lorence & Butaud, comb. nov. As a result, two species each of Ochrosia and Rauvolfia are recognized from the Marquesas Islands, all endemic. Recent field work has yielded important new data on their distribution, habitat, and conservation status. It is recommended that all four species should be added the IUCN Red List at the Critically Endangered (CR) category.
Project description:Abstract Tabernaemontana divaricate is a vulnerable species of Apocynaceae with significant medicinal values. In this study, the complete chloroplast (cp) genome of T. divaricate was determined through the Illumina NovaSeq platform. The circular molecular genome was157,954 bp in length with two inverted repeats (IRa and IRb) regions of 25,769 bp, a large single-copy (LSC) region of 88,246 bp, and a small single-copy (SSC) region of 18,170 bp. It contained 131 genes, including 86 protein-coding, 37 tRNA, and eight rRNA genes. Phylogenetic analysis showed that T. divaricata exhibited the closest relationship with Catharanthus roseus and Rauvolfia serpentina.
Project description:<i>Gigantochloa verticillata</i> is produced in Mengla and Jinghong, Yunnan Province, China, and cultivated in Hong Kong. Vietnam, Thailand, India, Indonesia, and Malaysia are distributed and cultivated. We determined the complete chloroplast genome sequence for <i>G. verticillata</i> using Illumina sequencing data. The complete chloroplast sequence is 139,489 bp, including large single-copy (LSC) region of 83,062 bp, small single-copy (SSC) region of 12,877 bp, and a pair of invert repeats (IR) regions of 21,775 bp. Plastid genome contain 132 genes, 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 23 chloroplast genomes indicates that <i>G. verticillata</i> is closely related to <i>Dendrocalamus latiflorus</i> in Bambusodae.
Project description:The complete chloroplast genome of <i>Cerber amanghas</i> L., a species of the tribe Plumerieae of the family Apocynaceae, is determined for the first time here. The chloroplast genome is 154,428 bp long, containing a large single-copy region (LSC) of 85,138 bp and a small single-copy region (SSC) of 17,390 bp, which are separated by a pair of 25,950 bp long inverted repeat regions (IRs). It encodes a total of 115 genes, including 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes.Phylogenetic analysis revealed that <i>C.manghas</i> is a member of the paraphyletic tribe Plumerieae of Apocynaceae and is closely related to <i>Thevetia peruviana.</i>
Project description:In this study, we determined the complete plastome sequence of <i>Carissa macrocarpa</i> (Eckl.) A. DC. (Apocynaceae) (NCBI acc. no. KX364402). The gene order and structure of the <i>C. macrocarpa</i> plastome are similar to those of a typical angiosperm. The complete plastome is 155,297?bp in length, and consists of a large single-copy region of 85,586?bp and a small single-copy region of 18,131?bp, which are separated by two inverted repeats of 25,792?bp. The plastome contains 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes and 4 are rRNA genes. Sixteen genes contained one intron and two genes have two introns. The average A-T content of the plastome is 62.0%. A total of 31 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that <i>C. macrocarpa</i> is a member of the paraphyletic subfamily Rauvolfioideae of Apocynaceae. The sister group relationship of <i>C. macrocarpa</i> to the Apocynoideae-Asclepiadoideae clade is supported by 100% bootstrap values.
Project description:The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 454 sequencing system and Sanger sequencing method to trace the evolutionary pattern in the tribe Parideae of the family Melanthiaceae (Liliales). The circular double-stranded cpDNA of P. verticillata (157,379 bp) consists of two inverted repeat regions each of 28,373 bp, a large single copy of 82,726 bp, and a small single copy of 17,907 bp. Gene content and order are generally similar to the previously reported cpDNA sequences within the order Liliales. However, we found that trnI_CAU was triplicated in P. verticillata. In addition, cemA is suspected to be a pseudogene due to the presence of internal stop codons created by poly(A) insertion and single small CA repeats. Such changes were not found in previously examined cpDNAs of the Melanthiaceae or other families of the Liliales, suggesting that such features are unique to the tribe Parideae of Melanthiaceae. The characteristics of P. verticillata cpDNA will provide useful information for uncovering the evolution within Paris and for further research of plastid genome evolution and phylogenetic studies in Liliales.
Project description:<i>Apocynum venetum</i> (<i>A. venetum</i>) has high medicinal value that belongs to the family Apocynaceae. Here, we reported the complete chloroplast (cp) genome of <i>A. venetum,</i> which was 150,858 bp in length. The cp genome was characterized by a typical quadripartite structure composed of a large single-copy region (LSC 81,919 bp) and a small single-copy region (SSC 17,257 bp) interspersed by a pair of 25,841 bp inverted repeat regions (IRs), and it contained 86 protein-coding genes, eight rRNAs, and 37 tRNAs. A maximum-likelihood (ML) phylogenetic tree indicated that <i>A. venetum</i> was closely related to <i>Trachelospermum jasminoides</i>.
Project description:Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284?bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae, and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome, and a nucleus copy was identified from two transcriptome data.
Project description:<i>Apocynum venetum</i> L. (Apocynaceae) or Luobuma is a widely known traditional medicine use to treat hypertension, relieve anxiety, soothe the nerves and promote diuresis. In this study, the complete chloroplast genome of this medicinal plant was determined through Illumina sequencing method. The <i>A. venetum</i> cp genome is 150,897 bp in length, containing a small single copy region (17,256 bp), a large single copy region (81,957 bp), and a pair of IR regions (25,842 bp). It encodes for a total of 131 genes, including 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis also reveals that <i>A. venetum</i> is relatively close to <i>Aganosma cymosa.</i>
Project description:<i>Pentasachme caudatum</i> Wallich ex Wight is considered as one of the Asian enigmatic genera classified in the Asclepiadoideae (Apocynaceae). To determine its evolutionary relationship in the family, we sequenced and characterized the complete chloroplast genome of <i>P. caudatum</i>. The plastid genome of <i>P. caudatum</i> is 158,487 bp in length, containing a large single-copy (90,380 bp), a small single-copy (18,585 bp), and a pair of inverted repeats (24,761 bp). It has 127 annotated genes, consisting of 83 protein-coding, eight rRNA and 36 tRNA genes. Phylogenetic analysis using 76 protein-coding regions of the plastid genomes of related taxa showed that <i>P. caudatum</i> was resolved in a fully supported clade with <i>Orthanthera albida</i>. The newly sequenced <i>P. caudatum</i> provides essential genetic information that is useful for future phylogenetic studies in the family Apocynaceae.