Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete plastome genome of Pergularia tomentosa L. (Asclepiadoideae, Apocynaceae).

ABSTRACT: Pergularia tomentosa is a medicinal plant mainly found in Saudi Arabia, northern and southern Africa. In this study, we present the sequence of the complete chloroplast (cp) genome of P. tomentosa in order to evaluate the evolutionary relationship in the subfamily Asclepiadoideae. The cp is 164,213 bp in lengh with 37.3% GC content, inverted repeat (IR) regions of 21,411 bp each, a large single-copy (LSC) region of 80,102 bp, and a small single-copy (SSC) region of 17,022 bp. It constitutes of 89 protien-coding genes, 44 tRNA genes, and 8 rRNA genes. The phylogenetic relationship showed close relationship between P. tomentosa and other Asclepiadeae members with Marsedineae subtribe. The study will help for future research on evolutionary studies of Apoceanaceae.

SUBMITTER: Abba A

PROVIDER: S-EPMC7748634 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete sequence of Cynanchum rostellatum (Apocynaceae: Asclepiadoideae) chloroplast genome and its phylogenetic analysis.

Project description:Cynanchum rostellatum (Turcz.) Liede and Khanum 2016 is a perennial herbaceous twining vine that is widely distributed in Japan, South Korea, the United States of America, and China. In this study, the complete chloroplast (cp) genome of C. rostellatum was sequenced using the Illumina platform and assembled for the first time. This plastome has a circular structure with a length of 160,641 bp. The GC content of the plastome was 37.82%. The cp genome contained 113 unique genes, including 79 protein-coding, 30 transfer RNA, and four ribosomal RNA genes. Phylogenetic analysis based on the complete cp genome sequences of the Asclepiadoideae subfamily showed that C. rostellatum was closely related to C. bungei in the genus Cynanchum. These results provide useful information for both phylogenetic research and the utilization of C. rostellatum.

| S-EPMC9341368 | biostudies-literature

Complete chloroplast genome of Vincetoxicum hainanense (Apocynaceae: Asclepiadoideae), an endangered liana endemic to China.

Project description:Vincetoxicum hainanense is an endangered liana species endemic to China. Habitat destruction coupled with difficulties in natural pollination has reduced its population size over time. As present studies have focussed more on breeding programmes instead of molecular aspects, here we reported on the complete chloroplast (cp) genome sequence of V. hainanense. The cp genome is 161,280 bp in size and includes two inverted repeat (IR) regions of 24,884 bp each, which is separated by a large-single copy (LSC) region of 92,084 bp and a small-single copy (SSC) region of 19,428 bp. A total of 131 genes were predicted, including 37 tRNA, 8 rRNA, and 86 protein-coding genes. Phylogenetic analysis showed that V. hainanense is clustered with other Apocynaceae species and sister to Biondia chinensis.

| S-EPMC7707277 | biostudies-literature

Characterization of the complete chloroplast genome of Biondia chinensis (Apocynaceae: Asclepiadoideae: Asclepiadeae), a rare and threatened liana endemic to China.

Project description:The complete chloroplast genome of Biondia chinensis, a rare liana of the Asclepiadoideae endemic to China, was determined in this study. It is classified as Vulnerable species because of the sharp decline in its population size due to the habitat destruction. The whole chloroplast genome was 160,308 bp long, comprising of a large single copy (LSC) region of 91,335 bp and a small single copy (SSC) region of 19,185 bp, which were separated by a pair of 24,894 bp long inverted repeat (IR) regions. It encoded a total of 131 genes, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Most of the gene species appeared as a single copy, while 22 gene species appeared in double copies. The overall A + T content was 62.2%, while the corresponding values of the LSC, SSC, and IR regions were 63.9, 68.1, and 56.7%, respectively. Phylogenetic analysis suggested that, among all the species which have been analyzed B. chinensis was relatively close to Vincetoxicum rossisum.

| S-EPMC7799909 | biostudies-literature

The complete plastome sequence of Carissa macrocarpa (Eckl.) A. DC. (Apocynaceae).

Project description:In this study, we determined the complete plastome sequence of Carissa macrocarpa (Eckl.) A. DC. (Apocynaceae) (NCBI acc. no. KX364402). The gene order and structure of the C. macrocarpa 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 C. macrocarpa is a member of the paraphyletic subfamily Rauvolfioideae of Apocynaceae. The sister group relationship of C. macrocarpa to the Apocynoideae-Asclepiadoideae clade is supported by 100% bootstrap values.

| S-EPMC7800814 | biostudies-literature

Complete plastome sequence of Hoya carnosa (L. f.) R. Br. (Apocynaceae).

Project description:Hoya is a remarkable genus with high horticultural ornamental value. In this study, we report and characterize the complete plastid genome sequence of Hoya carnosa. The complete chloroplast genome was 176,340 bp in length, which includes a pair of inverted repeat regions (IRs) of 41,381 bp separated by a large single copy region (LSC) 91,281 bp and a small single copy region (SSC) 2,297 bp. Interestingly, IRs expanded into SSC, with the result that most of the genes in SSC were duplicated. This chloroplast genome contained 110 genes, including 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The complete plastome sequence of H. carnosa will provide some useful information for future phylogenetic study of Hoya and its horticultural application.

| S-EPMC7748618 | biostudies-literature

Two new species of Hoya R.Br. (Apocynaceae, Asclepiadoideae) from Borneo.

Project description:Two new Hoya R.Br. species from Borneo are described and illustrated. The first, Hoyaruthiae Rodda was collected in Sabah on Bukit Baturong, a limestone outcrop. It is one of the few species in the genus to have clear exudate. It is compared with the morphologically related Hoyauncinata Teijsm. and Binn. The other, Hoyabakoensis Rodda, was collected in the kerangas forests of Bako National Park. It belongs to HoyasectionAcanthostemma (Bl.) Kloppenb., a section with numerous members in the Philippines but under-represented in Borneo.

| S-EPMC4547025 | biostudies-literature

The complete plastome of Cynanchum rostellatum (Apocynaceae), an indigenous plant in Korea.

Project description:The climbing plant Cynanchum rostellatum (Turcz.) Liede & Khanum is widely distributed throughout Korea and Northeast Asia as a member of the Apocynaceae family. Although this plant has a high value in medicinal and industrial purposes, genetic research on this plant is insufficient. This study announces the complete plastid genome (plastome) sequence of C. rostellatum with 663× mean coverage, which was assembled using 763 Mbp short-read data generated by the Illumina HiSeq X platform. The C. rostellatum plastome was 158,018 bp in length and displayed the typical quadripartite structure composed of the large single-copy (LSC) region (89,058 bp), the small single-copy (SSC) region (18,718 bp), and a pair of inverted repeat (IR) regions (25,116 bp). A total of 129 genes have been annotated, including 84 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis indicated the genus Cynanchum including 12 Cynanchum plastome sequences, was monophyletic and was located within the sub-family Asclepiadoideae. Two C. rostellatum plastomes, including the plastome assembled in this study, formed a subclade and were sister to the C. thesioides plastome, whereas the other C. rostellatum, which was previously reported one, was located within the clade of C. wilfordii and C. bungei.

| S-EPMC9744207 | biostudies-literature

Complete plastome of the medicinally important plant, Alstonia scholaris (Apocynaceae).

Project description:Alstonia scholaris is an evergreen tropical tree with significant medicinal values. To better understand its genetic and genomic profiles, we sequenced and assembled the completed plastome of A. scholaris. The plastome is 154,699 bp in length, consisting of a large (LSC, 85,364 bp) and a small single-copy region (SSC, 18,027 bp), which are separated by a pair of inverted repeat regions (IRs, 25,654 bp). It possesses 116 unique genes (82 protein-coding genes, 30 tRNAs, and 4 rRNAs). Phylogenetic analysis suggests that A. scholaris is sister to the clade including remaining Apocynaceae species.

| S-EPMC7706523 | biostudies-literature

Heterostemma cucphuongense (Apocynaceae, Asclepiadoideae), a new species from Vietnam.

Project description:Heterostemma cucphuongense (Apocynaceae, Asclepiadoideae), a new species from Vietnam is described, illustrated and compared with the similar species Heterostemma succosum Kerr. Heterostemma cucphuongense differs from H. succosum by the morphology of the rachis of the inflorescence, the margins of the corolla lobes and the colour of the adaxial surface of the corolla.

| S-EPMC7266833 | biostudies-literature

Pitfall Flower Development and Organ Identity of Ceropegia sandersonii (Apocynaceae-Asclepiadoideae).

Project description:Deceptive Ceropegia pitfall flowers are an outstanding example of synorganized morphological complexity. Floral organs functionally synergise to trap fly-pollinators inside the fused corolla. Successful pollination requires precise positioning of flies headfirst into cavities at the gynostegium. These cavities are formed by the corona, a specialized organ of corolline and/or staminal origin. The interplay of floral organs to achieve pollination is well studied but their evolutionary origin is still unclear. We aimed to obtain more insight in the homology of the corona and therefore investigated floral anatomy, ontogeny, vascularization, and differential MADS-box gene expression in Ceropegia sandersonii using X-ray microtomography, Light and Scanning Electronic Microscopy, and RT-PCR. During 10 defined developmental phases, the corona appears in phase 7 at the base of the stamens and was not found to be vascularized. A floral reference transcriptome was generated and 14 MADS-box gene homologs, representing all major MADS-box gene classes, were identified. B- and C-class gene expression was found in mature coronas. Our results indicate staminal origin of the corona, and we propose a first ABCDE-model for floral organ identity in Ceropegia to lay the foundation for a better understanding of the molecular background of pitfall flower evolution in Apocynaceae.

| S-EPMC7764971 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data