Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Wei XF

PROVIDER: S-EPMC7748618 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Wei Xue-Fen XF Zeng Si-Jin SJ Zhang Guo-Qiang GQ Tang Guang-Da GD Huang Jiu-Xiang JX

Mitochondrial DNA. Part B, Resources 20200117 1

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 dup ...[more]

PMID: 33366630

Similar Datasets

Complete plastome sequence of Hoya pottsii Traill and Hoya liangii Tsiang (Apocynaceae).

Project description:Hoya is the largest genus (about 350-450 species) within Apocynaceae. It is a subshrub or liana, epiphytic or epilithic. Most species grow in tropical and subtropical South and Southeast Asia. Here we report and characterize the complete plastid genome sequence of Hoya pottsii Traill and Hoya liangii Tsiang in an effort to provide genomic resources useful for promoting its systematics research. The complete plastome of H. pottsii is 161,565 bp in length, including two Inverted Repeat (IR) regions of 24,657 bp, a Large Single-Copy (LSC) region of 92,532 bp, and a Small Single-Copy (SSC) region of 19,719 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. pottsii is 62.40%. The complete plastome of H. liangii is 162,989 bp in length, including two IR regions of 24,841 bp, a LSC region of 93,292 bp, and a SSC region of 20,015 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. pottsii is 62.30%. The complete plastome sequence of H. pottsii and H. liangii will provide a useful resource for the conservation genetics of the two species as well as for the phylogenetic studies of Hoya.

| S-EPMC7800117 | biostudies-literature

Plastome evolution and organisation in the Hoya group (Apocynaceae).

Project description:The genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus.

| S-EPMC8282776 | 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

Hoya carnosa

Project description:Hoya carnosa Genome sequencing

| PRJNA1274607 | ENA

Hoya carnosa

Project description:Hoya carnosa overview

| PRJNA1275528 | ENA

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

Project description: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.

| S-EPMC7748634 | 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

Near-complete reference genome assembly of Hoya carnosa

Project description:reference genome of Hoya carnosa

| PRJEB90480 | ENA

A new species of Hoya R.Br. (Apocynaceae, Asclepiadoideae) from the Philippines

Project description:Abstract Hoyamedusa M.D.De Leon, Cabactulan, Cuerdo & Rodda, sp. nov. (Apocynaceae, Asclepiadoideae) is described from the Philippines. Even though numerous taxa with a shrubby habit from this area are known, it can be immediately separated because of its urceolate corolla and prominent elongated corona lobes. No other species in the genus possesses such a combination of characters.

| S-EPMC10209511 | 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